Datasets:

---

kejian

/

SciRIFF-4096-0214-v2

like 0

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Acetaminophen and ibuprofen are generally safe for reducing fever in young children.\n\nResearch Abstract:\nIbuprofen is an over-the-counter medication that is used widely for the treatment of pain and fever during COVID-19 pandemic.\nA concern was raised regarding the safety of ibuprofen use because of its role in increasing ACE2 levels within the Renin-Angiotensin-Aldosterone system.\nACE2 is the coreceptor for the entry of SARS-CoV-2 into cells, and so, a potential increased risk of contracting COVID-19 disease and/or worsening of COVID-19 infection was feared with ibuprofen use.\nHowever, available data from limited studies show administration of recombinant ACE2 improves lung damage caused by respiratory viruses, suggesting ibuprofen use may be beneficial in COVID-19 disease.\nAt this time, there is no supporting evidence to discourage the use of ibuprofen.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Ibuprofen is an over-the-counter medication that is used widely for the treatment of pain and fever during COVID-19 pandemic.\", \"However, available data from limited studies show administration of recombinant ACE2 improves lung damage caused by respiratory viruses, suggesting ibuprofen use may be beneficial in COVID-19 disease.\", \"At this time, there is no supporting evidence to discourage the use of ibuprofen.\"]}", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\na 55-year - old male underwent implantation of a secondary prevention dual chamber boston scientific incepta implantable cardioverter - defibrillator ( icd ) .\na dual coil df-4 lead ( endotak reliance llhh 64 cm ) was positioned at the right ventricular apex ( rva ) with normal intracardiac electrograms ( egm ) .\nparameters were satisfactory ( r - wave sensing of 7.9 mv , impedance of 960 , threshold of 0.6 v @ 0.5 ms , and a high voltage impedance of 39 ) and defibrillation threshold testing ( dft ) was acceptable .\nsubsequent to defibrillation testing , unusual low amplitude and medium frequency signals were observed on the ventricular egm ( fig . 1 ) and detected on the marker channel during pacing threshold testing ( fig . \nfluoroscopic review of set - screw positioning was unremarkable and manipulation of the device did not influence the signals .\nno further intervention was performed at that stage and pacing threshold testing the next day demonstrated no over sensing recurrence and he proceeded to have an event free six - week follow - up .\na 42-year - old female underwent implantation of a secondary prevention dual chamber medtronic maximo ii df-4 icd with a dual coil ( sprint quattro secure 6947 m 64 cm ) ventricular lead at the rva .\nafter multiple attempts at positioning the lead , the best r - wave sensing obtained was only 6.8 mv , while other pacing parameters were satisfactory ( v - lead impedance of 684 , v - lead threshold of 0.5 v @ 0.5 ms , high threshold impedance of 42 and a dft test of < 25 j ) .\nshe represented one day after with lead integrity alerts due to high ventricular impedance ( > 3000 ) .\nchest x - ray demonstrated the pin beyond the set - screw ( fig . 4 ) . during pocket revision , whilst the lead was still connected , only tapping the header reproduced similar noise , while traction of the lead and movement of the generator were unremarkable .\na moderate hematoma was evacuated and lead testing unconnected to the header was also unexceptional .\ninterrogation after the header was cleaned and reconnected showed normalized function with no further over - sensing .\nin this report , we present two unusual cases of intermittent ventricular over - sensing in the new df-4 connector system . in both cases , causes of inappropriate sensing of physiologic signals such as myopotentials , t waves , p waves , r - wave double counting , after potentials , and far - field physiologic signals were not present .\nthese include electromagnetic interference from an external source , lead / connector problems ( loose set screw , adapter , or header ) , and lead failure ( insulation defect or conductor coil fracture ) .\nboth of our cases share several similar characteristics : ( 1 ) the over - sensing occurred acutely post implantation ( within 24 h ) ; ( 2 ) the over - sensing was intermittent and did not have a constant relationship to the cardiac cycle ; ( 3 ) although the over - sensing could be reproduced with specific maneuvers ( during pacing in case 1 , and only with tapping of the header in case 2 ) , manipulation of the leads and generator did not recreate the over - sensing ; ( 4 ) the over - sensing had resolved spontaneously ( as in the first case ) or on reconnection without replacing the lead or the device ( as in the second case ) ; ( 5 ) peri - procedural lead function was normal ; ( 6 ) there was no evidence radiographically to suggest incomplete lead advancement ; and ( 7 ) no sources of electromagnetic interference , including electro - cautery were present .\nthese features seem to make an obvious lead - connector problem or lead failure unlikely .\ncase 1 likely relates to the improper venting of the grommet seal plug ( and similar issues have been previously reported with is-1 systems ) .\nthe seal plug is a polymer plug with a narrow slit through which the set - screw torque wrench is inserted through to the grommet .\nit is designed to allow access of the wrench to the set - screw and maintain electrical isolation afterwards by preventing body fluids from entering the header ports once the wrench is removed . at wrench\ninsertion , care should be exercised to locate the pre - slit depression of the seal plug and carefully guide the wrench through the slit to the set - screw cavity beneath prior to insertion of the lead into the port .\nthis will open up the seal plug , relieving any potential pressure build - up within the lead port by providing a pathway to release trapped fluid or air during lead insertion . if this is not performed adequately , or if damage occurs during wrench insertion or faulty from manufacturing , the trapped air ( an electrical insulator ) is able to intermittently escape the header , altering the baseline contact between the normally separated extracellular fluid and the conductive elements of the connector causing transient alterations in the voltage input to the sense amplifier and resulting in make - break potentials .\nonce the air has fully escaped , there is equilibration of charge and the over - sensing ceases , . in our case\n, it is likely that the wrench was not adequately engaged prior to lead insertion into the header considering that gross review of the seal plugs revealed no clear abnormality , and that the signals resolved spontaneously without the need for generator replacement .\nthe resulting signals , however , had occurred post dft testing only , and over - sensed during ventricular threshold testing . during defibrillation testing chest wall movement or transient pressurization from the shock or both , could also have encouraged air - bubble release .\ncuriously , the over - sensing had only occurred during instances when the signals were located just after the post - pacing blanking period .\nafter a paced ventricular event , all icds have the ability to adjust sensitivity dynamically , beginning from the end of the blanking period , with the threshold starting at a more sensitive setting .\nour second case , however , raises some novel risks that may need to be considered with this new generation lead - connector system .\nthis technology encompasses a combined single port cavity with four contacts of which both high- and low - voltage applications can be placed within the same cavity which result in compromised space for insulation and sealing .\nfurthermore , contact pressure of the seals and the pins has to be limited to allow for easy insertion and retraction of the lead connector .\nthis was achieved by alterations in the design with integration of the sealed rings within the header itself ( instead of being mounted on the lead ) as well as the development of a unique torque wrench activated levering of the spring loaded pin contacts .\nconsequently , df-4 lead plugs have to go through four seals with three intermediate spring contacts while its predecessor , the is-1 lead connectors , have only one seal on the lead and no spring contacts .\nthis raises potential issues with sealing failures , which may cause sensing problems or short circuits . in case 2 , we hypothesize that blood from the hematoma may have entered the header via a\n grommet punch - out post wrench removal ( which has been previously reported in medtronic df-1 header connections ) or forced into the header through imperfections of the more complex - designed sealed rings .\nthe silicone rubber used for seal plugs has a shape memory . however , during the re - bonding process after wrench removal , they may require a short time to reseal .\nuntil the seal fully closes , it is possible that the header may be infiltrated by body fluid .\nthis could have been further compounded by issues with trapped air that were mentioned earlier in the manuscript .\nthe extracellular fluid in the header from case 2 could then have contributed to minute misalignment of the newly developed spring contacts with the lead , causing the observed increase in impedance and the intermittent non - physiological ventricular over - sensing .\nthis hypothesis was supported by the resolution of the noise when the system was cleaned and simply reconnected without changing the device , as well as by the lack of any macroscopic appearance of lead - connecter or set - screw issues . to the best of our knowledge ,\ncases of non - physiological ventricular over - sensing have rarely been reported involving the new df-4 system .\nthe advantages of this standard over its predecessor mainly relate to procedural ease and patient comfort by reducing the risk of lead - to - port mismatch , reduced risk of lead - to - can abrasion ( because of fewer connectors ) , a reduced size of device header and subsequently a much less bulky pocket .\nhowever , these design changes may have several potential risks as we have highlighted as well as some logistical drawbacks .\nthe compact system is also likely to be less flexible like in instances where there may be a need for the addition of pace / sense leads ( in cases of sensing problems ) or additional shock leads ( e.g. subcutaneous arrays ) .\ncurrently , a single post - market study has demonstrated that the df-4 lead has performed well at a 36-month follow - up period in 1701 cases with complication rates reported to be at a low 0.015 per patient - year of follow - up with no adverse set - screw events .\nhowever , it is important to note that there have been two previous adverse event reports found in the manufacturer and user facility device experience ( maude ) database run by the fda .\nthey both relate to noise and inappropriate therapy , and were put down to lead - connection issues but with no conclusive evidence of set - screw problems .\nthe df-4 connector system is becoming industry standard but our current cases underscore that potential problems regarding lead header attachment , that were seen with the older connector systems , continue to remain an identifiable cause for over - sensing .\nfurthermore , they highlight certain concerns over novel lead - connector problems that need to be adequately tackled to reduce improper delivery of device therapies and increased patient morbidity . unanticipated problems with df-4 icd leads are likely to accumulate . in a comprehensive review on this topic in europace in april 2012 , sticherling and burri express concern that the complex design of the header / lead interface could lead to sensing or electrical isolation problems .\ncorrect torque wrench technique continues to be an important aspect in device implantation , but it is clear that further research and development is required to address any other potential newer causes of non - physiological over - sensing whose magnitude of risk may not yet be fully evident at the present time .", "role": "user" }, { "content": "the df-4 is a new defibrillator lead technology . \n we present two cases of non - physiological transient ventricular over - sensing in patients who underwent implantation of an icd for secondary prevention . \n case 1 had ventricular over - sensing during pacing threshold evaluation post defibrillation testing while case 2 had the lead integrity alert triggered immediately post discharge with transient over - sensing . \n no lead - connector issues were found . \n case 1 was likely due to improper venting of the header and trapped air . \n case 2 was hypothesized to be due to intermittent header pin non - contact secondary to blood in the header . \n these cases reveal that df-4 leads are subject to both reported and potentially novel causes of transient acute ventricular over - sensing .", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nPerson re-identification (ReID) aims to match people across multiple non-overlapping video cameras deployed at different locations. To address this challenging problem, many metric learning approaches have been proposed, among which triplet loss is one of the state-of-the-arts. In this work, we explore the margin between positive and negative pairs of triplets and prove that large margin is beneficial. In particular, we propose a novel multi-stage training strategy which learns incremental triplet margin and improves triplet loss effectively. Multiple levels of feature maps are exploited to make the learned features more discriminative. Besides, we introduce global hard identity searching method to sample hard identities when generating a training batch. Extensive experiments on Market-1501, CUHK03, and DukeMTMCreID show that our approach yields a performance boost and outperforms most existing state-of-the-art methods.\n\nCited Works Summary:\n[1]: In the past few years, the field of computer vision has gone through a revolution fueled mainly by the advent of large datasets and the adoption of deep convolutional neural networks for end-to-end learning. The person re-identification subfield is no exception to this. Unfortunately, a prevailing belief in the community seems to be that the triplet loss is inferior to using surrogate losses (classification, verification) followed by a separate metric learning step. We show that, for models trained from scratch as well as pretrained ones, using a variant of the triplet loss to perform end-to-end deep metric learning outperforms most other published methods by a large margin.\n\n[2]: Despite significant recent advances in the field of face recognition [10, 14, 15, 17], implementing face verification and recognition efficiently at scale presents serious challenges to current approaches. In this paper we present a system, called FaceNet, that directly learns a mapping from face images to a compact Euclidean space where distances directly correspond to a measure of face similarity. Once this space has been produced, tasks such as face recognition, verification and clustering can be easily implemented using standard techniques with FaceNet embeddings as feature vectors.\n\n[3]: \n\n[4]: The accuracy of k-nearest neighbor (kNN) classification depends significantly on the metric used to compute distances between different examples. In this paper, we show how to learn a Mahalanobis distance metric for kNN classification from labeled examples. The Mahalanobis metric can equivalently be viewed as a global linear transformation of the input space that precedes kNN classification using Euclidean distances. In our approach, the metric is trained with the goal that the k-nearest neighbors always belong to the same class while examples from different classes are separated by a large margin. As in support vector machines (SVMs), the margin criterion leads to a convex optimization based on the hinge loss. Unlike learning in SVMs, however, our approach requires no modification or extension for problems in multiway (as opposed to binary) classification. In our framework, the Mahalanobis distance metric is obtained as the solution to a semidefinite program. On several data sets of varying size and difficulty, we find that metrics trained in this way lead to significant improvements in kNN classification. Sometimes these results can be further improved by clustering the training examples and learning an individual metric within each cluster. We show how to learn and combine these local metrics in a globally integrated manner.", "role": "user" }, { "content": "Strictly speaking, triplet loss was first introduced by [4] . They trained the metric with the goal that the k-nearest neighbors belong to the same class and examples of different classes can be dissociated by a large margin. Based on this work, [2] improved the loss to learn a unified embedding for face recognition. They pushed forward the concept of triplet and minimized the distance between an anchor and a positive while maximized the distance between the anchor and a negative. [3] improved the triplet loss function by restricting positive pairs within a small distance. And this improved loss was used to train a multi-channel parts-based convolutional neural network model. Recently, [1] summarized the works of ReID using triplet loss, and proposed some training strategies to improve the performance of triplet loss. While our work is also based on triplet loss, we investigate the influence of the margin, which has received little attention so far.", "role": "assistant" } ]

[ { "content": "Analyze the provided text to identify gene-related entities. \n\nFormat your findings as a JSON object: {\"Gene\": [\"ExampleGene\", ...]}. Use the entity type as the key, and list the entities under it. If no entities are found, use an empty list.\n\nFocus solely on the JSON output.\n\nText:\n\nMale 11β-HSD1 Knockout Mice Fed Trans-Fats and Fructose Are Not Protected From Metabolic Syndrome or Nonalcoholic Fatty Liver Disease. Nonalcoholic fatty liver disease (NAFLD) defines a spectrum of conditions from simple steatosis to nonalcoholic steatohepatitis (NASH) and cirrhosis and is regarded as the hepatic manifestation of the metabolic syndrome. Glucocorticoids can promote steatosis by stimulating lipolysis within adipose tissue, free fatty acid delivery to liver and hepatic de novo lipogenesis. Glucocorticoids can be reactivated in liver through 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme activity. Inhibition of 11β-HSD1 has been suggested as a potential treatment for NAFLD. To test this, male mice with global (11β-HSD1 knockout [KO]) and liver-specific (LKO) 11β-HSD1 loss of function were fed the American Lifestyle Induced Obesity Syndrome (ALIOS) diet, known to recapitulate the spectrum of NAFLD, and metabolic and liver phenotypes assessed. Body weight, muscle and adipose tissue masses, and parameters of glucose homeostasis showed that 11β-HSD1KO and LKO mice were not protected from systemic metabolic disease. Evaluation of hepatic histology, triglyceride content, and blinded NAFLD activity score assessment indicated that levels of steatosis were similar between 11β-HSD1KO, LKO, and control mice. Unexpectedly, histological analysis revealed significantly increased levels of immune foci present in livers of 11β-HSD1KO but not LKO or control mice, suggestive of a transition to NASH. This was endorsed by elevated hepatic expression of key immune cell and inflammatory markers. These data indicate that 11β-HSD1-deficient mice are not protected from metabolic disease or hepatosteatosis in the face of a NAFLD-inducing diet. However, global deficiency of 11β-HSD1 did increase markers of hepatic inflammation and suggests a critical role for 11β-HSD1 in restraining the transition to NASH.", "role": "user" }, { "content": "{\"Gene\": [\"11\\u03b2-HSD1\", \"11\\u03b2-hydroxysteroid dehydrogenase type 1\"]}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Methodological Review: A review of causal inference for biomedical informatics \nChapter Title: Causal explanation \n1. Abstract of Cited Paper (BIB001): The literature on causal discovery has focused on interventions that involve randomly assigning values to a single variable. But such a randomized intervention is not the only possibility, nor is it always optimal. In some cases it is impossible or it would be unethical to perform such an intervention. We provide an account of ‘hard’ and ‘soft’ interventions and discuss what they can contribute to causal discovery. We also describe how the choice of the optimal intervention(s) depends heavily on the particular experimental setup and the assumptions that can be made. \n2. Abstract of Cited Paper (BIB002): Thank you very much for reading making things happen a theory of causal explanation. Maybe you have knowledge that, people have search hundreds times for their chosen novels like this making things happen a theory of causal explanation, but end up in infectious downloads. Rather than reading a good book with a cup of tea in the afternoon, instead they juggled with some malicious bugs inside their desktop computer.\n\nReview Chapter:", "role": "user" }, { "content": "Giving the reasons why an event occurred by citing the causal relationships related to the situation (e.g. it is known that a patient smoked and then developed lung cancer. The relationship between smoking and lung cancer explains why he developed lung cancer) or providing information about an event (e.g. If the relationship between smoking and lung cancer is known, then a particular patient's lung cancer can be explained by providing information on his smoking). This can also be called causal reasoning Causal inference The process of finding causal relationships. Here we mean the process of doing this in an automated way from data. This is sometimes referred to as causal discovery Confounding In this context, confounding is when variables may seem causally related, but the relationship is fully explained by another factor such as a common cause Necessary cause If a cause is necessary, the effect cannot occur without it Prediction The process of using a causal model of a system to find the probability of future events and, ideally, what will result from an intervention on the system. This is sometimes referred to as causal inference or causal reasoning Sufficient cause A sufficient cause is one such that whenever it is true, it brings about the effect regime change, such as a diabetic whose glucose is under control most of the time, but who has periods of hypoglycemia. During these times there may be different sets of causal relationships governing their health. While methods that incorporate time windows can account for this type of behavior to some extent, it will be important to take this into account in a more explicit way in order to allow both accurate prediction as well as better inference (such as based on a time series that has been segmented into periods of relative stationarity). We have endeavored to cover the primary methods for causal inference, but it is not possible to discuss all approaches in depth. We now highlight some key omissions and areas for further reading. First, we focused on the inference of causal relationships from data, and did not discuss the creation of causal models, which may be done using background knowledge or a combination of prior knowledge to create the structure of the model and then inference of the probabilities or numerical relationships in the structure from data. One of the key approaches in this area is structural equation modeling (SEM) , which relates to the path analysis approach of Wright . Secondly, in many cases we want to understand what will happen if we change something in a system -intervening by forcing a variable to take a certain value, and it is also possible to understand causality in terms of such interventions (where causes are roughly ways of manipulating effects) BIB003 BIB002 . One approach to quantifying the effect of interventions is the Rubin causal model (RCM), or potential outcomes approach BIB001 .", "role": "assistant" } ]

[ { "content": "Consider the following research inquiry and associated key terms. Review the dataset summaries provided and determine which datasets are suitable for addressing the research question. Base your decision on your understanding of machine learning datasets.\nProvide your answer as a JSON list. For example, for the inquiry \"Semi supervised image classification\", a possible response could be: [\"CIFAR-10\", \"CIFAR-100\"]. Ensure the response contains only the dataset names in JSON format.\n\nResearch Inquiry: A novel image captioning model which combines human gaze information with a soft attention mechanism.\n\nKey Terms: image captioning images text paragraph-level\n\nDataset Summaries:\nnocaps: The nocaps benchmark consists of 166,100 human-generated captions describing 15,100 images from the OpenImages validation and test sets.\nCOCO: The MS COCO (Microsoft Common Objects in Context) dataset is a large-scale object detection, segmentation, key-point detection, and captioning dataset. The dataset consists of 328K images.\nSALICON: The SALIency in CONtext (SALICON) dataset contains 10,000 training images, 5,000 validation images and 5,000 test images for saliency prediction. This dataset has been created by annotating saliency in images from MS COCO.\nActivityNet Captions: The ActivityNet Captions dataset is built on ActivityNet v1.3 which includes 20k YouTube untrimmed videos with 100k caption annotations. The videos are 120 seconds long on average.\nVQA-HAT: VQA-HAT (Human ATtention) is a dataset to evaluate the informative regions of an image depending on the question being asked about it. The dataset consists of human visual attention maps over the images in the original VQA dataset.\n\nDataset Options: A: nocaps B: COCO C: SALICON D: ActivityNet Captions E: VQA-HAT", "role": "user" }, { "content": "[\"COCO\", \"SALICON\"]", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Blocking and Filtering Techniques for Entity Resolution: A Survey \nChapter Title: ML-based Methods. \n1. Abstract of Cited Paper (BIB001): Record linkage is the process of matching records across data sets that refer to the same entity. One issue within record linkage is determining which record pairs to consider, since a detailed comparison between all of the records is impractical. Blocking addresses this issue by generating candidate matches as a preprocessing step for record linkage. For example, in a person matching problem, blocking might return all people with the same last name as candidate matches. Two main problems in blocking are the selection of attributes for generating the candidate matches and deciding which methods to use to compare the selected attributes. These attribute and method choices constitute a blocking scheme. Previous approaches to record linkage address the blocking issue in a largely ad-hoc fashion. This paper presents a machine learning approach to automatically learn effective blocking schemes. We validate our approach with experiments that show our learned blocking schemes outperform the ad-hoc blocking schemes of non-experts and perform comparably to those manually built by a domain expert. \n2. Abstract of Cited Paper (BIB002): In data integration tasks, records from a single dataset or from different sources must often be compared to identify records that represent the same real world entity. The cost of this search process for finding duplicate records grows quadratically as the number of records available in the data sources increases and, for this reason, direct approaches, such as comparing all record pairs, must be avoided. In this context, blocking methods are used to create groups of records that are likely to correspond to the same real world entity, so that the deduplication can be applied to these blocs only. In the recent literature, machine learning processes are used to find the best blocking function, based on a combination of low cost rules, which define how to perform the record blocking. In this paper we present a new blocking method based on machine learning. Different from other methods, our method is based on genetic programming, allowing for the use of more flexible rules and a larger number of such rules for defining blocking functions, leading to a more effective process for the identification of duplicate records. Experimental results with real and synthetic data show that our method achieves over 95\\% of correctness when generating block of potential duplicate. \n3. Abstract of Cited Paper (BIB003): Record linkage is the process of matching records between two (or multiple) data sets that represent the same real-world entity. An exhaustive record linkage process involves computing the similarities between all pairs of records, which can be very expensive for large data sets. Blocking techniques alleviate this problem by dividing the records into blocks and only comparing records within the same block. To be adaptive from domain to domain, one category of blocking technique formalizes 'construction of blocking scheme' as a machine learning problem. In the process of learning the best blocking scheme, previous learning-based techniques utilize only a set of labeled data. However, since the set of labeled data is usually not large enough to well characterize the unseen (unlabeled) data, the resultant blocking scheme may poorly perform on the unseen data by generating too many candidate matches. To address that, in this paper, we propose to utilize unlabeled data (in addition to labeled data) for learning blocking schemes. Our experimental results show that using unlabeled data in learning can remarkably reduce the number of candidate matches while keeping the same level of coverage for true matches. \n4. Abstract of Cited Paper (BIB004): De-duplication - identification of distinct records referring to the same real-world entity - is a well-known challenge in data integration. Since very large datasets prohibit the comparison of every pair of records, blocking has been identified as a technique of dividing the dataset for pairwise comparisons, thereby trading off recall of identified duplicates for efficiency. Traditional de-duplication tasks, while challenging, typically involved a fixed schema such as Census data or medical records. However, with the presence of large, diverse sets of structured data on the web and the need to organize it effectively on content portals, de-duplication systems need to scale in a new dimension to handle a large number of schemas, tasks and data sets, while handling ever larger problem sizes. In addition, when working in a map-reduce framework it is important that canopy formation be implemented as a hash function, making the canopy design problem more challenging. We present CBLOCK, a system that addresses these challenges. CBLOCK learns hash functions automatically from attribute domains and a labeled dataset consisting of duplicates. Subsequently, CBLOCK expresses blocking functions using a hierarchical tree structure composed of atomic hash functions. The application may guide the automated blocking process based on architectural constraints, such as by specifying a maximum size of each block (based on memory requirements), impose disjointness of blocks (in a grid environment), or specify a particular objective function trading off recall for efficiency. As a post-processing step to automatically generated blocks, CBLOCK rolls-up smaller blocks to increase recall. We present experimental results on two large-scale de-duplication datasets from a commercial search engine - consisting of over 140K movies and 40K restaurants respectively - and demonstrate the utility of CBLOCK. \n5. Abstract of Cited Paper (BIB005): A pair wise comparison of data objects is a requisite step in many data mining applications, but has quadratic complexity. In applications such as record linkage, blocking methods may be applied to reduce the cost. That is, the data is first partitioned into a set of blocks, and pair wise comparisons computed for pairs within each block. To date, blocking methods have required the blocking scheme be given, or the provision of training data enabling supervised learning algorithms to determine a blocking scheme. In either case, a domain expert is required. This paper develops an unsupervised method for learning a blocking scheme for tabular data sets. The method is divided into two phases. First, a weakly labeled training set is generated automatically in time linear in the number of records of the entire dataset. The second phase casts blocking key discovery as a Fisher feature selection problem. The approach is compared to a state-of-the-art supervised blocking key discovery algorithm on three real-world databases and achieves favorable results.\n\nReview Chapter:", "role": "user" }, { "content": "We distinguish these methods into supervised and unsupervised ones. The former rely on a labelled dataset that includes pairs of matching and non-matching entities, called positive and negative instances, respectively. This dataset is used to learn blocking predicates, i.e., combinations of an attribute name and a transformation function (e.g., {title, First3Characters}). Entities sharing the same output for a particular blocking predicate are considered candidate matches (i.e., hash-based functionality). Disjunctions of conjunctions of predicates, called supervised blocking schemes, are learned by optimizing an objective function. To tackle the lack or scarcity of labelled datasets, unsupervised methods have been proposed, as well. Supervised Methods. One of the first methods of this kind is ApproxRBSetCover BIB001 , which learns disjunctive supervised blocking schemes by solving a standard weighted set cover problem. The cover is iteratively constructed by adding in each turn the blocking predicate that maximizes the ratio of the previously uncovered positive pairs over the covered negative pairs. Note that this is a \"soft cover\", since some positive instances may remain uncovered. ApproxDNF BIB001 alters ApproxRBSetCover so that it learns supervised blocking schemes in Disjunctive Normal Form (DNF). Instead of individual predicates, each turn greedily learns a conjunction of up to k predicates that maximizes the ratio of positive and negative covered instances. A similar approach is Blocking Scheme Learner (BSL) BIB002 . Based on an adaptation of the Sequential Covering Algorithm, it learns supervised blocking schemes that maximize RR, while maintaining PC above a predetermined threshold. Its output is a disjunction of conjunctions of blocking predicates. BSL is typically faster than ApproxRBSetCover and ApproxDNF, as it exclusively considers positive instances, thus requiring a smaller training set. BSL is improved by Conjunction Learner BIB004 , which minimizes the candidate matches not only in the labelled, but also in the unlabelled data, while maintaining high PC. The effect of the unlabelled data is determined through a weight, whose maximum value (1) indicates that they are equally important as the labelled ones, while its minimum value (0) disregards unlabelled data completely, falling back to BSL. This semi-supervised approach requires every supervised blocking scheme to be applied to the large set of unlabelled data, which is impractical. For high scalability, a random sample of the unlabelled data is used in practice. On another line of research, Blocking based on Genetic Programming (BGP) BIB003 employs a tree representation of supervised blocking schemes, where every leaf node corresponds to a blocking predicate. In every turn, a set of genetic programming operators, such as copy, mutation and crossover, are applied to the initial, random set of supervised blocking schemes. A fitness function is then used to infer their performance from the harmonic mean of PC and RR. The best schemes identified through this search process are returned as output. Yet, a major disadvantage of BGP is the large number of internal parameters (e.g., probability of mutation), which are hard to fine-tune. Another approach using a tree representation is CBLOCK BIB005 . In this case, every edge is annotated with a hash (i.e., transformation) function and every node n i comprises the set of entities that result after applying all hash functions from the root to n i . CBLOCK is the only proactive MLbased method, restricting the maximum size of its blocks. Every node that exceeds this limit is split into smaller, disjoint blocks through a greedy algorithm that picks the best hash function based on the resulting PC. To minimize the human effort, a drill down approach is proposed for bootstrapping. CBLOCK is also the only ML-based method suitable for the MapReduce framework. Every entity runs through the learned tree and is directed to the machine corresponding to its leaf node. Finally, DNF Learner integrates the learning of supervised blocking schemes with entity matching to address the scarcity of labelled instances. A matching algorithm is applied to a sample of entity pairs to automatically create a labelled dataset. Then, the learning of supervised blocking schemes is cast as a DNF learning problem. To scale it to the exponential search space of possible schemes, their complexity is restricted to manageable levels (e.g., they comprise at most k predicates). Unsupervised Methods. FisherDisjunctive BIB006 is an unsupervised algorithm that uses a weak training set generated by leveraging the TF-IDF similarity of two entities. Pairs with very low (high) values are considered as negative (positive) instances. A boolean feature vector is then associated with every labelled instance. The discovery of DNF supervised blocking schemes is then cast as a Fisher feature selection problem.", "role": "assistant" } ]

[ { "content": "Analyze the provided text excerpt from a scientific document. Identify and extract distinct entities based on predefined categories.\n\nDeliver the results as a JSON structure where each key represents an entity category, and the associated value is a list of identified entities. If no entities are found for a category, return an empty list.\n\nText Excerpt:\n\nComparative analysis identifies conserved tumor necrosis factor receptor-associated factor 3 binding sites in the human and simian Epstein-Barr virus oncogene LMP1. Nonhuman primates are naturally infected with a B-lymphotropic herpesvirus closely related to Epstein-Barr virus (EBV). These simian EBV share considerable genetic, biologic, and epidemiologic features with human EBV, including virus-induced tumorigenesis. However, latent, transformation-associated viral genes demonstrate marked sequence divergence among species despite the conserved functions. We have cloned the latent membrane protein 1 (LMP1) homologs from the simian EBV naturally infecting baboons (cercopithicine herpesvirus 12, herpesvirus papio) and rhesus monkeys (cercopithicine herpesvirus 15) for a comparative study with the human EBV oncogene. The transmembrane domains are well conserved, but there is striking sequence divergence of the carboxy-terminal cytoplasmic domain essential for B-cell immortalization and interaction with the tumor necrosis factor receptor signaling pathway. Nevertheless, the simian EBV LMP1s retain most functions in common with EBV LMP1, including the ability to induce NF- (kappa) B activity in human cells, to bind the tumor necrosis factor-associated factor 3 (TRAF3) in vitro, and to induce expression of tumor necrosis factor-responsive genes, such as ICAM1, in human B lymphocytes. Multiple TRAF3 binding sites containing a PXQXT / S core sequence can be identified in the simian EBV LMP1s by an in vitro binding assay. A PXQXT / S-containing sequence is also present in the cytoplasmic domain of the Hodgkin 's disease marker, CD30, and binds TRAF3 in vitro. The last 13 amino acids containing a PXQXT / S sequence are highly conserved in human and simian EBV LMP1 but do not bind TRAF3, suggesting a distinct role for this conserved region of LMP1. The conserved TRAF3 binding sites in LMP1 and the CD30 Hodgkin 's disease marker provides further evidence that a TRAF3-mediated signal transduction pathway may be important in malignant transformation.", "role": "user" }, { "content": "{\"CellLine\": [], \"CellType\": [\"B - cell\", \"human cells\", \"human B lymphocytes\"], \"DNA\": [\"tumor necrosis factor receptor - associated factor 3 binding sites\", \"TRAF3 binding sites\", \"oncogene LMP1\", \"human and simian Epstein - Barr virus oncogene LMP1\", \"PXQXT / S core sequence\", \"LMP1\", \"ICAM1\", \"PXQXT / S sequence\", \"PXQXT / S - containing sequence\", \"tumor necrosis factor - responsive genes\"], \"Protein\": [\"tumor necrosis factor - associated factor 3\", \"cytoplasmic domain\", \"TRAF3\", \"tumor necrosis factor receptor\", \"LMP1s\", \"CD30 Hodgkin \\u0027s disease marker\", \"tumor necrosis factor receptor - associated factor 3\", \"NF - (kappa) B\", \"LMP1\", \"latent membrane protein 1 (LMP1) homologs\", \"carboxy - terminal cytoplasmic domain\", \"simian EBV LMP1s\", \"CD30\", \"latent membrane protein 1\", \"last 13 amino acids\"], \"RNA\": []}", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nThis paper considers the problem of estimating a power-law degree distribution of an undirected network. Although power-law degree distributions are ubiquitous in nature, the widely used parametric methods for estimating them (e.g. linear regression on double-logarithmic axes, maximum likelihood estimation with uniformly sampled nodes) suffer from the large variance introduced by the lack of data-points from the tail portion of the power-law degree distribution. As a solution, we present a novel maximum likelihood estimation approach that exploits the to sample more efficiently from the tail of the degree distribution. We analytically show that the proposed method results in a smaller bias, variance and a Cram e r-Rao lower bound compared to the maximum-likelihood estimate obtained with uniformly sampled nodes (which is the commonly used method in literature). Detailed simulation results are presented to illustrate the performance of the proposed method under different conditions and how it compares with alternative methods.\n\nCited Works Summary:\n[1]: Distributions following a power-law are an ubiquitous phenomenon. Methods for determining the exponent of a power-law tail by graphical means are often used in practice but are intrinsically unreliable. Maximum likelihood estimators for the exponent are a mathematically sound alternative to graphical methods.\n\n[2]: Power-law distributions occur in many situations of scientific interest and have significant consequences for our understanding of natural and man-made phenomena. Unfortunately, the detection and characterization of power laws is complicated by the large fluctuations that occur in the tail of the distribution—the part of the distribution representing large but rare events—and by the difficulty of identifying the range over which power-law behavior holds. Commonly used methods for analyzing power-law data, such as least-squares fitting, can produce substantially inaccurate estimates of parameters for power-law distributions, and even in cases where such methods return accurate answers they are still unsatisfactory because they give no indication of whether the data obey a power law at all. Here we present a principled statistical framework for discerning and quantifying power-law behavior in empirical data. Our approach combines maximum-likelihood fitting methods with goodness-of-fit tests based on the Kolmogorov-Smirnov (KS) statistic and likelihood ratios. We evaluate the effectiveness of the approach with tests on synthetic data and give critical comparisons to previous approaches. We also apply the proposed methods to twenty-four real-world data sets from a range of different disciplines, each of which has been conjectured to follow a power-law distribution. In some cases we find these conjectures to be consistent with the data, while in others the power law is ruled out.\n\n[3]: This short communication uses a simple experiment to show that fitting to a power law distribution by using graphical methods based on linear fit on the log-log scale is biased and inaccurate. It shows that using maximum likelihood estimation (MLE) is far more robust. Finally, it presents a new table for performing the Kolmogorov-Smirnov test for goodness-of-fit tailored to power-law distributions in which the power-law exponent is estimated using MLE. The techniques presented here will advance the application of complex network theory by allowing reliable estimation of power-law models from data and further allowing quantitative assessment of goodness-of-fit of proposed power-law models to empirical data.\n\n[4]: Many complex networks in natural and social phenomena have often been characterized by heavy-tailed degree distributions. However, due to rapidly growing size of network data and concerns on privacy issues about using these data, it becomes more difficult to analyze complete data sets. Thus, it is crucial to devise effective and efficient estimation methods for heavy tails of degree distributions in large-scale networks only using local information of a small fraction of sampled nodes. Here we propose a tail-scope method based on local observational bias of the friendship paradox. We show that the tail-scope method outperforms the uniform node sampling for estimating heavy tails of degree distributions, while the opposite tendency is observed in the range of small degrees. In order to take advantages of both sampling methods, we devise the hybrid method that successfully recovers the whole range of degree distributions. Our tail-scope method shows how structural heterogeneities of large-scale complex networks can be used to effectively reveal the network structure only with limited local information.", "role": "user" }, { "content": "It has been shown in the literature that maximum likelihood methods are more suitable for estimating power-law degree distributions of the form in Eq. compared to alternative methods [3] [1] [2] . Further, exploiting the friendship paradox (Theorem ) has shown to be effective in empirical estimation of heavy-tailed degree distributions by including more high degree nodes into the sample [4] . Motivated by these findings, this paper combines maximum likelihood estimation with friendship paradox based sampling in a principled manner to obtain an asymptotically unbiased, strongly consistent and statistically efficient estimate that outperforms the state of the art.", "role": "assistant" } ]

[ { "content": "Analyze the following excerpt from a biomedical text. Identify the relevant information needed to respond to the inquiry. Provide only the necessary details in your answer.\n\nContext: The newly recognized disease, hantavirus cardiopulmonary syndrome, HCPS (or hantavirus pulmonary syndrome), was linked to infection by the newly-discovered Sin Nombre virus (SNV), and the rodent Peromyscus maniculatus (deer mouse) was identified as the reservoir [13] . However, hantavirus infections have a much longer history. A review of ancient Chinese writings, dating back to approximately 960 AD, revealed descriptions closely resembling hemorrhagic fever with renal syndrome (HFRS), the syndrome caused by Old World hantaviruses [14] . During the twentieth century, cases of acute febrile disease with renal compromise were described from several Eurasian countries and Japan, often in association with military engagements [15] . HFRS as a distinct syndrome, however, was first brought to the attention of western medicine in association with an outbreak that occurred among United Nations troops during the Korean conflict between 1951 and 1954, where more than 3,200 soldiers were afflicted [16] . It took more than two decades until the etiologic agent, Hantaan virus (HTNV), was isolated from the striped field mouse Apodemus agrarius, detected in part by the binding of antibodies from patient serum samples to the lung tissues of healthy, wild-caught field mice [17, 18] . The virus was later found to represent the type species of a new genus Hantavirus of the family Bunyaviridae, although it was later apparent that the first hantavirus to be isolated was the shrew-borne Thottapalayam virus [19] . The categorization of hantaviruses as belonging to the family Bunyaviridae is due in part to the consistent presence of three RNA genomes that are circularized in vivo as a result of the presence of terminal complementary nucleotides that help fold the genome into a -hairpin‖ morphology, first described for the Uukuniemi phlebovirus [19, 20] . Table 1 is a list of the predominant, serologically distinct pathogenic hantaviruses. Many other named genotypes are described, but such other pathogenic forms are generally closely related to Andes or, in some cases, Sin Nombre virus. During virus maturation, the precursor form GPC is processed using a membrane -bound protease into Gn and Gc, a cleavage that occurs, and appears to be signaled, after the conserved peptide signal WAASA at the C-terminal of Gn [24] . Although the two proteins can be expressed independently through transfection, they can be retained in the wrong cellular compartment (ER or aggresome); they thus must be co-expressed to allow them stability so that the two can be assembled correctly in the Golgi [25, [27] [28] [29] . A number of activities and properties have been identified for the hantavirus envelope glycoproteins, including some features that are suspected to be involved in the pathogenicity of the disease-causing serotypes, a possibility that has engendered experimental attention. The glycoproteins are the known or presumed ligands for at least two distinct cellular receptors, the 3 integrin chain and decay accelerating factor, or DAF [30, 31] ; with gC1qR/p32 also identified as another potential entry receptor [32] . Comparisons with the tick-borne encephalitis virus E protein, led Tischler et al. to consider the Gc glycoprotein as a potential class II fusion protein, perhaps imparting fusion activity to the virion, and this hypothesis has gained support in other studies [33, 34] . Additional activities have been identified with, or claimed to be related to, Gn. For many of these studies, an underlying premise has held that there are differences between the glycoproteins of -pathogenic‖ hantaviruses relative to viruses in the genus that are dubbed to be -non-pathogenic‖. While it is true that it has not yet been possible to link Prospect Hill virus (PHV) to human disease, the absence of evidence for its pathogenicity should perhaps not be equated with the evidence of its absence. One might only consider that the level of disease (e.g., lethargy, fever, proteinuria, and azotemia) associated with infection of nonhuman primates by PHV is not significantly different from that recorded for nonhuman primate models using the known-pathogen Puumala virus (PUUV) [35, 36] . For the purpose of this discussion we will presume that apathogenic hantaviruses are indeed apathogenic. While some studies have suggested that Gn glycoproteins are directed more rapidly into the ubiquitin-proteosome pathway than are apathogenic forms, others have interpreted differences in the handling of Gn glycoproteins across hantavirus species by the ubiquitin-proteosomal system as independent of pathogenicity [37] [38] [39] . Some investigators have directed their efforts toward identifying a differential capacity, either kinetic or in absolute magnitude, in the ability of pathogenic and apathogenic hantaviruses to elicit an interferon response in cells. One premise that emerges is that apathogenic forms would tend to induce an earlier innate response that would render it more likely that the virus would be quickly cleared or rendered less competent in its replication so as to blunt any pathological response in the host [40] [41] [42] . The anti-hantavirus innate response can in some cases be attributed to viral interaction as a ligand of TLR-3, but not in others, and in endothelial cells, it appears not to require more than the viral particle itself, even when introduced in replication-incompetent form [43, 44] . Proteins and mRNAs prominently induced by hantaviruses include MxA and IFIT-1 (ISG-56) and others including some with known or suspected anti-viral activity. Those hantaviruses, often highly pathogenic strains, that fail to induce a potent antiviral response, are suspected or presumed to have a (more) potent interferon-pathway antagonism mechanism relative to other viruses, a mechanism that acts positively to prevent an effective innate response from forming, at least early in infection [42, 45] . Yet some instances are reported wherein highly pathogenic hantaviruses, such as SNV, are also able to induce expression of interferon-stimulated gene mRNAs, even very early in infection, with ISG proteins, as expected, taking longer to appear in the cell [44] . Anti-interferon activities have also been attributed to the NSs protein that may be elaborated in cells infected by serotypes that encode this protein [46] . Other investigators have examined the activities of hantavirus glycoproteins and other proteins that might themselves directly affect some aspects of the pathogenic progression associated with hantavirus infection of humans, such as vascular permeability changes. While early attempts to directly cause increases in permeability of endothelial monolayers with viral particles or viral infection were largely disappointing, hantaviruses have been identified as adversely affecting endothelial migration over substrata and in potentiating VEG-F-induced endothelial permeability [47, 48] . The shorter (50-kD) nucleocapsid or N protein is a structural component of the viral nucleocapsid, along with the genomic viral RNA segments. As an RNA-binding protein that engages the hairpin termini of the genomic segments with high affinity [49, 50] , it limits the access of the RNA to host nucleases and helps to render viral replication a closed process within the cytoplasm. It also acts as a peripheral membrane protein, as does the L protein [51] , an activity that could play a role in its presumed, but not yet demonstrated function as matrix [52] . Until recently, it had not been appreciated that N has a wide variety of other activities, some of which can be linked, not only to fundamental requirements of replication, but also to the interference with an array of the intracellular processes of the normal cell. Thus, an interaction between the amino terminus of the hantavirus N protein and the cellular protein Daxx has been proposed, with the suggestion of potential pro-apoptotic consequences [51] . N is also reported to interact with actin microfilaments, and the SUMO-1 protein [53, 54] . Using reporter-gene based assays, Connie Schmaljohn and her colleagues have reported that Hantaan virus' nucleocapsid protein has an inhibitory role in inflammatory responses mediated by NF kappa B (NF-B). The effects on NF-B expression appeared to be confined to prevention of its nuclear translocation after its attempted activation with lipopolysaccharide, LPS [55] . In the cytoplasm of infected cells, N protein can be found in cellular P bodies where it sequesters and protects 5' caps. It may locate the caps through its interaction with DCP1, a key constituent of P bodies. During hantavirus infection, the viral RNAs become concentrated in P bodies, through their interaction with N and DCP1. The N protein demonstrates preferential protection of mRNAs engineered to prematurely terminate their encoded protein in comparison to native mRNAs [56] . N protein has been increasingly linked to viral replication and translation, sometimes in previously unanticipated ways. It is among a growing family of diverse viral proteins that can serve as a nonspecific -RNA chaperone‖, an activity that should facilitate the L polymerase's access to vRNA for transcription and replication, in that it can transiently dissociate misfolded RNA structures [57] . Some of N protein's effects on translation might not immediately be recognized to be adaptive in nature. It can replace the entire EIF4F translational initiation complex, simultaneously presenting the ribosome with a replacement for the cap-binding activity of eIF 4E, binding to the 43S pre-initiation complex as does eIF 4G, while replacing the helicase activity of eIF 4A, which is presumed to be needed to dissociate higher-order RNA structure [56, 58] . These three factors normally work together to achieve translational initiation. In P bodies, N protein's ability to bind at high affinity to capped native cellular oligoribonucleotides, along with its activity in protecting capped RNAs from degradation likely facilitates the access of capped oligonucleotides for use in transcriptional initiation by L polymerase (-cap snatching‖). Trafficking of N for viral assembly: Classically, N protein in infected cells appears to be clustered or particulate in nature, with a heavy concentration at a single perinuclear location, widely considered to be the Golgi [27] . The N proteins of hantaviruses are found in association with particulate fractions, and confocal microscopy and biochemical-inhibitor studies have shown that N tracks along microtubules but not with actin filaments [52] . The ultimate destination for N, for its assembly into viral particles is the Golgi, and it traffics there via the endoplasmic reticulum-Golgi intermediate complex (ERGIC), also known as vesicular-tubular cluster [52] . A dominant negative inhibitor, dynamitin, associated with dynein-mediated transport, reduced N's accumulation in the Golgi. Later studies suggested that the specific dependence on microtubular transport is specific to Old World hantaviruses such as HTNV, but that the New World hantavirus ANDV is instead associated with actin filaments [59] . However, recent data indicates that microtubular transport is indeed utilized for the New World hantavirus SNV [60] . Hantavirus diseases of man have long been suspected of having an immunopathogenic basis in part because of their relatively long incubation period of 2-3 weeks and the observed temporal association between immunologic derangements and the first appearance of signs and symptoms of hantavirus illness. HFRS and HCPS share many clinical features, leading many investigators to consider them to be, in essence, different manifestations of a similar pathogenic process, differing mainly in the primary target organs of disease expression ( Table 2 ). The pathogenesis of hantavirus infections is the topic of a continuously-updated review in the series UpToDate [61] . By the time symptoms appear in HCPS, both strong antiviral responses, and, for the more virulent viral genotypes, viral RNA can be detected in blood plasma or nucleated blood cells respectively [63, 64] . At least three studies have correlated plasma viral RNA with disease severity for HCPS and HFRS, suggesting that the replication of the virus plays an ongoing and real-time role in viral pathogenesis [65] [66] [67] . Several hallmark pathologic changes have been identified that occur in both HFRS and HCPS. A critical feature of both is a transient (~ 1-5 days) capillary leak involving the kidney and retroperitoneal space in HFRS and the lungs in HCPS. The resulting leakage is exudative in character, with chemical composition high in protein and resembling plasma. The continued experience indicating the strong tissue tropism for endothelial cells, specifically, is among the several factors that make β3 integrin an especially attractive candidate as an important in vivo receptor for hantaviruses. It is likely that hantaviruses arrive at their target tissues through uptake by regional lymph nodes, perhaps with or within an escorting lung histiocyte. The virus seeds local endothelium, where the first few infected cells give rise, ultimately, to a primary viremia, a process that appears to take a long time for hantavirus infections [62, 63] . By the time that secondary viremia emerges, the agents of the more severe forms of HFRS and HCPS have begun to achieve sufficient mass as to induce, through PAMP-PRR interactions and other means, the expression of proinflammatory cytokines [64] . For HCPS, that expression favors the pulmonary bed and lymphoid organs, yet, for unknown reasons, spares the retroperitoneum and, in general, the kidney. In HFRS the situation is reversed, and yet it is often not appreciated that the expected preferential tissue tropism of HFRS-associated viruses and their HCPS-associated counterparts for the renal and pulmonary beds, respectively, is not as one would predict through the manifestations of the two diseases. Local elaboration of inflammatory and chemotactic mediators is considered to be a requirement for the development of systemic disease symptoms, with those abnormalities sometimes culminating in shock and death. Yet it is not hypoxemia, due to the prominent pulmonary edema, that leads to death in most fatal cases of HCPS, but rather intoxication of the heart by as-yet-undefined mediators that leads to the low cardiac output state and the associated shock syndrome [64, 65] . It is tempting to speculate that mediators produced in the lung in connection with the inflammatory infiltrate can percolate through the coronary circulation with minimal dilution in HCPS, a disadvantageous consequence of the close anatomic juxtaposition of the two organs. Thus, at least three classes of potential mechanisms, some overlapping and all certainly nonexclusive of the others, could be presumed to underlie the pathogenesis of HCPS. These include:\n\n(1) Innate immune mechanisms.\n\nInquiry: What was identified as the reservoir of SNV?", "role": "user" }, { "content": "the rodent Peromyscus maniculatus (deer mouse)", "role": "assistant" } ]

[ { "content": "Review the provided collection of medical RCT summaries. Your objective is to distill the essential insights into a brief conclusion. Focus solely on the synthesis of findings without additional commentary. The RCT summaries are as follows:\n\n\n\nReport Title 1:\nImproved outcomes from the administration of progesterone for patients with acute severe traumatic brain injury: a randomized controlled trial.\nReport Abstract 1:\nSevere traumatic brain injury (TBI) has been increasing with greater incidence of injuries from traffic or sporting accidents. Although there are a number of animal models of TBI using progesterone for head injury, the effects of progesterone on neurologic outcome of acute TBI patients remain unclear. The aim of the present clinical study was to assess the longer-term efficacy of progesterone on the improvement in neurologic outcome of patients with acute severe TBI.\n A total of 159 patients who arrived within 8 hours of injury with a Glasgow Coma Score </= 8 were enrolled in the study. A prospective, randomized, placebo-controlled trial of progesterone was conducted in the Neurotrauma Center of our teaching hospital. The patients were randomized to receive either progesterone or placebo. The primary endpoint was the Glasgow Outcome Scale score 3 months after brain injury. Secondary efficacy endpoints included the modified Functional Independence Measure score and mortality. In a follow-up protocol at 6 months, the Glasgow Outcome Scale and the modified Functional Independence Measure scores were again determined.\n Of the 159 patients randomized, 82 received progesterone and 77 received placebo. The demographic characteristics, the mechanism of injury, and the time of treatment were compared for the two groups. After 3 months and 6 months of treatment, the dichotomized Glasgow Outcome Scale score analysis exhibited more favorable outcomes among the patients who were given progesterone compared with the control individuals (P = 0.034 and P = 0.048, respectively). The modified Functional Independence Measure scores in the progesterone group were higher than those in the placebo group at both 3-month and 6-month follow-up (P < 0.05 and P < 0.01). The mortality rate of the progesterone group was significantly lower than that of the placebo group at 6-month follow-up (P < 0.05). The mean intracranial pressure values 72 hours and 7 days after injury were lower in the progesterone group than in the placebo group, but there was no statistical significance between the two groups (P > 0.05). Instances of complications and adverse events associated with the administration of progesterone were not found.\n Our data suggest that acute severe TBI patients with administration of progesterone hold improved neurologic outcomes for up to 6 months. These results provide information important for further large and multicenter clinical trials on progesterone as a promising neuroprotective drug.\n ACTRN12607000545460.\n\n\nReport Title 2:\nProTECT: a randomized clinical trial of progesterone for acute traumatic brain injury.\nReport Abstract 2:\nLaboratory evidence indicates that progesterone has potent neuroprotective effects. We conducted a pilot clinical trial to assess the safety and potential benefit of administering progesterone to patients with acute traumatic brain injury.\n This phase II, randomized, double-blind, placebo-controlled trial was conducted at an urban Level I trauma center. One hundred adult trauma patients who arrived within 11 hours of injury with a postresuscitation Glasgow Coma Scale score of 4 to 12 were enrolled with proxy consent. Subjects were randomized on a 4:1 basis to receive either intravenous progesterone or placebo. Blinded observers assessed patients daily for the occurrence of adverse events and signs of recovery. Neurologic outcome was assessed 30 days postinjury. The primary safety measures were differences in adverse event rates and 30-day mortality. The primary measure of benefit was the dichotomized Glasgow Outcome Scale-Extended 30 days postinjury.\n Seventy-seven patients received progesterone; 23 received placebo. The groups had similar demographic and clinical characteristics. Laboratory and physiologic characteristics were similar at enrollment and throughout treatment. No serious adverse events were attributed to progesterone. Adverse and serious adverse event rates were similar in both groups, except that patients randomized to progesterone had a lower 30-day mortality rate than controls (rate ratio 0.43; 95% confidence interval 0.18 to 0.99). Thirty days postinjury, the majority of severe traumatic brain injury survivors in both groups had relatively poor Glasgow Outcome Scale-Extended and Disability Rating Scale scores. However, moderate traumatic brain injury survivors who received progesterone were more likely to have a moderate to good outcome than those randomized to placebo.\n In this small study, progesterone caused no discernible harm and showed possible signs of benefit.\n\n\nReport Title 3:\n[Clinical study on the therapeutic effects and mechanism of progesterone in the treatment for acute severe head injury].\nReport Abstract 3:\nTo evaluate the therapeutic effects of Progesterone (PG) on the patients with acute severe traumatic brain injury, and investigate it's neuroprotective mechanisms.\n Fifth-six patients with acute severe traumatic head injury were divided randomly into two groups: 26 cases were treated with PG and 30 cases were control. Neurological outcome of the patients were assessed using Glasgow Coma Scale (GCS), Glasgow Outcome Scale (GOS), verbal and motor functions scale and Karnofsky Performance Scale (KPS). The serum concentrations of PG, TNF-alpha and 15-F(2t)-isoprostane were measured at day 1, 5 and 10 after trauma.\n In the two groups, There were no significant difference in the mortality, GCS of acute healing phase, GOS and verbal and motor functions at 10th days after treatment (P>0.05); After follow-up for 3 months, GOS, verbal functions and KPSin the PG treatment group were better than those in the control group (P<0.05); In addition, there was no difference of motor functions in the two groups (P>0.05). At 5th day after trauma, serum 15-F(2t)-isoprostane and TNF-alpha levels increased in the control group, but decreased at 10th day after trauma. Compared with the control group serum PG levels increased, serum 15-F(2t)-isoprostane and TNF-alpha levels reduced significantly in the PG treatment group at 5th and 10th day after injury (P<0.05).\n It indicated that successive early application of PG will benefit the patients with acute severe head injury by improving the recovery and reducing the disability, which may be related to its alleviating inflammatory and lipid peroxidation response.", "role": "user" }, { "content": "Current clinical evidence from three small RCTs indicates progesterone may improve the neurologic outcome of patients suffering TBI. This evidence is still insufficient and further multicentre randomised controlled trials are required.", "role": "assistant" } ]

[ { "content": "Transform the following sections from a biomedical study into a simple summary for the general public. Focus on making the information accessible and easy to understand.\n\nResearch Heading: Transcriptional Repression of Hox Genes by C. elegans HP1/HPL and H1/HIS-24\nContent:\nAbstract:\nElucidation of the biological role of linker histone( H1) and heterochromatin protein 1( HP1) in mammals has been difficult owing to the existence of a least 11 distinct H1 and three HP1 subtypes in mice. Caenorhabditis elegans possesses two HP1 homologues( HPL-1 and HPL-2) and eight H1 variants. Remarkably, one of eight H1 variants, HIS-24, is important for C. elegans development. Therefore we decided to analyse in parallel the transcriptional profiles of HIS-24, HPL-1/-2 deficient animals, and their phenotype, since hpl-1, hpl-2, and his-24 deficient nematodes are viable. Global transcriptional analysis of the double and triple mutants revealed that HPL proteins and HIS-24 play gene-specific roles, rather than a general repressive function. We showed that HIS-24 acts synergistically with HPL to allow normal reproduction, somatic gonad development, and vulval cell fate decision. Furthermore, the hpl-2; his-24 double mutant animals displayed abnormal development of the male tail and ectopic expression of C. elegans HOM-C/Hox genes( egl-5 and mab-5), which are involved in the developmental patterning of male mating structures. We found that HPL-2 and the methylated form of HIS-24 specifically interact with the histone H3 K27 region in the trimethylated state, and HIS-24 associates with the egl-5 and mab-5 genes. Our results establish the interplay between HPL-1/-2 and HIS-24 proteins in the regulation of positional identity in C. elegans males.\nIntroduction:\nLinker histone H1 and heterochromatin protein HP1 are involved in numerous processes ranging from stabilizing heterochromatin condensation to the regulation of gene expression[1]–[5]. As has been reported, a methylation mark on vertebrate histone H1 is specifically recognized by the chromodomain of HP1. However, the exact biological role of HP1 binding to linker histone has not been determined[6]. The functions of HP1 and H1 proteins are mainly dependent on the cell type in which particular variants are expressed. Although the number of H1( 11) and HP1 variants( 3) presents difficulties in studying the effect of H1 and HP1 depletion in mice, some data has emerged[3],[7]–[10]. For example, loss of HP1β results in defective development of neuromuscular junctions and the cerebral cortex[10], whereas depletion of three of eleven H1 genes causes lethality connected with a very broad range of defects in mice[11]–[12]. In ES cells, the lack of three somatic H1 variants leads to changes in nucleosome spacing and local chromatin compaction, and this is correlated with decreased levels of H3K27 trimethylation[11]. Additionally, H1 is necessary to establish and maintain the DNA methylation pattern in a subset of genes including the reproductive homeobox( Rhox) gene cluster[13]. C. elegans possesses eight linker histone variants and two HP1 homologues, HPL-1 and HPL-2[14]–[16]. Mutation of hpl-2 results in defective vulval and germline development at elevated temperatures[15]–[17]. hpl-1, in contrast to hpl-2, does not have visible effects on C. elegans development at different temperatures, however, hpl-1 acts redundantly with hpl-2 to control larval development, somatic gonad development and vulval cell fate determination[17]. Our previous study revealed that HPL-1 recognizes the linker histone variant HIS-24 when it is mono-methylated at lysine 14( HIS-24K14me1), similar to the situation in vertebrates[16]. Additionally, we showed that HIS-24 interacts with H3K27me3[18]. The H3K27me3 modification correlates with a repressive chromatin state that inhibits expression of many developmentally regulated genes. This is consistent with studies of Hox loci demonstrating that enrichment of H3K27me3 recruits the binding of Polycomb group proteins( PcG)[19]. The Hox genes encode conserved homeodomain-containing transcription factors that control the positional identities of cells along the anterior–posterior axis[20]–[21]. The expression pattern of Hox genes appears to be regulated by two evolutionarily conserved PcG complexes, the ESC/E( Z) complex and the PRC1 complex. Both have been identified in flies and mammals and are linked to modulation of repressive chromatin structures[21]. The C. elegans Hox cluster consisting of lin-39, ceh-13, mab-5 and egl-5( orthologs of Drosophila Scr, labial, ftz and Abd-B, respectively) is quite degenerated in comparison to Hox clusters in other species[22] but, as in mammals, is also globally repressed by Polycomb group( PcG) proteins[20],[23]. Mutations in mes-2 and mes-6, which encode the C. elegans ESC/E( Z) complex, result in ectopic expression of Hox genes[23]. A similar phenotype has also been observed in the absence of sop-2 or sor-1 genes. SOP-2 and SOR-1 form another C. elegans PcG-like complex which shares many structural and functional properties with the Drosophila PRC1, and is involved in the global repression of Hox gene expression. Loss of sop-2 and sor-1 results in gross homeotic transformations[24]–[25]. To elucidate the function of H1 and HP1 related proteins in C. elegans, we decided to generate double and triple mutants, since hpl-1, hpl-2 and his-24 deficient nematodes are viable, and since HIS-24K14me1 is recognized by HPL-1[16]–[17],[26]. We performed global transcriptional analyses of single, double and triple mutant animals, and we found that HPL-1/-2 and HIS-24 regulate a relatively small number of genes. We provide evidence that the methylated form of HIS-24( HIS-24K14me1) and HPL-2 are involved in the regulation of mab-5 and egl-5 expression by binding to H3K27me3, although HIS-24K14me1 does not interact with HPL-2[16]. Furthermore, we observed that HIS-24 and HPL-2 act in parallel pathway as MES( PcG) proteins, and loss of their activity causes defects of male tail structures. Overall, our data suggest a common and dual role for C. elegans H1 and HP1, functioning both as chromatin architectural proteins and at the same time as modifiers of a small subset of genes. Furthermore, we provide the first direct evidence for redundant functions of H1 and HP1 in metazoan development.\nDiscussion:\nOur microarray analyses support a role of H1 and HP1 in specific gene regulation, rather than a general repressive function[34]–[36]. Despite global changes in chromatin compaction and synergism of HIS-24 and HPL in aspects of many developmental processes we observed very few and slight changes in gene expression profile of mutants when compared with wild type animals. We detected a set of shared up- and down-regulated genes by HIS-24 and HPL suggesting that redundant roles for HIS-24 and HPL also exist. The relatively small number of regulated genes in observed triple mutant animals may indicate that HPL proteins and HIS-24 serve to fine-tune the regulation of key genes during development or differentiation. This model can be explained by the fact that the sequential arrangement of the linker histone HIS-24 and HPL-2 on the chromatin fibre might influence higher-order chromatin structure and effect nucleosome positioning, and stability[36]. It is possible that the different HPL subtypes and HIS-24 confer subtle differences in the properties of the chromatin fiber which allow for quantitative modulation of gene expression[34],[35]. Although the changes in gene transcription are subtle, we think that even 1. 5-fold differences in expression can contribute to the marked phenotypic consequences we observed. We demonstrated that HIS-24K14me1, together with HPL-2, has a causal role in transcriptional silencing of egl-5 and mab-5. We propose that HPL-2 and HIS-24K14me1 may serve as essential protein components in establishing and/or maintaining the repressive chromatin state at the selected Hox genes through their interactions with H3K27me3. While we did not observe any phenotypic effects on male tail development either in hpl-2; hpl-1 nor in hpl-1 his-24 background, we speculate that HPL-2 acts redundantly with HIS-24K14me1 to regulate the positional identity in the C. elegans males. Loss of the two heterochromatin components, HIS-24K14me1 and HPL-2, causes significant changes in chromatin structure affecting Hox gene expression in C. elegans. However, since no interaction of HPL-2 and HIS-24K14me1 was observed in immunoprecipitation experiments, it is possible that HPL-2 together with HIS-24K14me1 might be a part of the same protein group involved in the regulation of Hox gene expression. The high degree of redundancy between his-24 and hpl-2 in Hox gene regulation might indicate that these two proteins are the only readers acting in parallel to perform the same role in translating the effects of histone H3K27 trimethylation. However, since we have failed so far to detect HPL-2 at the Hox gene region using direct ChIP approach, it is possible that the mechanisms by which HPL-2 regulates mab-5 and egl-5 might be indirect, involve intermediate factors( RNAi machinery, transcription factors) and depend on an architectural level in the cellular context. In mammals, H1 regulates Hox gene activation by promoting DNA demethylation[13]. Although C. elegans does not possess methylated DNA, we speculate that H1 can still influence Hox gene regulation and, together with HPL-2, regulate Hox gene expression as a part of the PcG silencing complex. The interaction of HPL-2 and HIS-24K14me1 with H3K27me3 can regulate the Hox gene in parallel pathway as MES-2 or MES-3, and can be directed to specific parts of the genome. Notably C. elegans HP1/HPL-2 does not follow the H3K9me2/me3 code[37]–[41] but it is sufficient to recognize, and to bind H3K27me2/me3. Remarkably, HIS-24 is required for optimal HPL-2 binding to H3K27me3 in vivo. Interestingly, some PcG proteins containing a chromodomain similar to that found in C. elegans HPL-2 and mammalian HP1s have been shown to bind H3K27me3[30],[42]. Overall, these and our previous results implicate that HPL and HIS-24 share some common functions even though there are differences among these proteins[16]–[17],[26]. We conclude that a combination of the H3K27me3 methylation mark, HPL-2 and HIS-24K14me1 could be a major factor in the establishment of stable patterns of selected homeotic gene expression.", "role": "user" }, { "content": "Linker histone ( H1 ) and heterochromatin protein 1 ( HP1 ) play central roles in the formation of higher-order chromatin structure and gene expression . Recent studies have shown a physical interaction between H1 and HP1; however , the biological role of histone H1 and HP1 is not well understood . Additionally , the function of HP1 and H1 isoform interactions in any organism has not been addressed , mostly due to the lack of knockout alleles . Here , we investigate the role of HP1 and H1 in development using the nematode C . elegans as a model system . We focus on the underlying molecular mechanisms of gene co-regulation by H1 and HP1 . We show that the loss of both HP1 and H1 alters the expression of a small subset of genes . C . elegans HP1 and H1 have an overlapping function in the same or parallel pathways where they regulate a shared target , the Hox genes .", "role": "assistant" } ]

[ { "content": "You will be presented with the full text of a scientific research paper. Write an abstract summarizing the key points. Your response should contain only the abstract without any other text.\n\nArticle text:\nthe thomas fermi ( tf ) equation has proved useful for the treatment of many physical phenomena that include atoms@xcite , molecules@xcite , atoms in strong magnetic fields@xcite , crystals@xcite and dense plasmas@xcite among others .\nfor that reason there has been great interest in the accurate solution of that equation , and , in particular , in the accurate calculation of the slope at origin@xcite . besides\n, the mathematical aspects of the tf equation have been studied in detail@xcite .\nsome time ago liao@xcite proposed the application of a technique called homotopy analysis method ( ham ) to the solution of the tf equation and stated that `` it is the first time such an elegant and explicit analytic solution of the thomas fermi equation is given '' .\nthis claim is surprising because at first sight earlier analytical approaches are apparently simpler and seem to have produced much more accurate results@xcite .\nrecently , khan and xu@xcite improved liao s ham by the addition of adjustable parameters that improve the convergence of the perturbation series .\nthe purpose of this paper is to compare the improved ham with a straightforward analytical procedure based on pad approximants@xcite supplemented with a method developed some time ago@xcite . in section [ sec : ham ]\nwe outline the main ideas of the ham , in section [ sec : hpm ] apply the hankel pad method ( hpm ) to the tf equation , and in section [ sec : conclusions ] we compare the ham with the hpm and with other approaches .\nin order to facilitate later discussion we outline the main ideas behind the application of the ham to the tf equation .\nthe tf equation @xmath0 is an example of two point nonlinear boundary value problem . when solving this ordinary differential equation one faces problem of the accurate calculation of the slope at origin @xmath1 that is consistent with the physical boundary conditions indicated in equation ( [ eq : tf ] ) . in what follows\nwe choose the notation of khan and xu@xcite whose approach is more general than the one proposed earlier by liao@xcite .\nthey define the new solution @xmath2 , where @xmath3 and rewrite the tf equation as @xmath4 where @xmath5 is the inverse of the slope at origin ( @xmath6 ) and @xmath7 is an adjustable parameter .\nkhan and xu@xcite state that the solution to eq .\n( [ eq : tf2 ] ) can be written in the form @xmath8 that reduces to liao s expansion@xcite when @xmath9 . in principle\nthere is no reason to assume that the series ( [ eq : g_series ] ) converges and no proof is given in that sense@xcite . besides , the partial sums of the series ( [ eq : g_series ] ) will not give the correct asymptotic behaviour at infinity@xcite as other expansions do@xcite .\nliao@xcite and kahn and xu@xcite do not use the ansatz ( [ eq : g_series ] ) directly to solve the problem but resort to perturbation theory .\nfor example ,\nkahn and xu@xcite base their approach on the modified equation @xmath10 = q\\hbar \\mathcal{n}% \\left [ \\phi ( \\xi ; q),\\gamma ( q)\\right ] \\label{eq : ham}\\ ] ] where @xmath11 and @xmath12 are linear and nonlinear operators , respectively , @xmath13 is a perturbation parameter and @xmath14 is another adjustable parameter . besides , @xmath15 is a conveniently chosen initial function and @xmath16 becomes the solution to equation ( [ eq : tf2 ] ) when @xmath17@xcite .\nboth @xmath16 and @xmath18 are expanded in a taylor series about @xmath19 as in standard perturbation theory , and @xmath20 is another adjustable parameter@xcite .\nthe authors state that ham is a very flexible approach that enables one to choose the linear operator and the initial solution freely@xcite and also to introduce several adjustable parameters@xcite .\nhowever , one is surprised that with so many adjustable parameters the results are far from impressive , even at remarkable great perturbation orders@xcite .\nfor example the @xmath21 $ ] pad approximant of the ham series yields @xmath22 with three exact digits@xcite , while the @xmath23 $ ] pad approximant of the @xmath24 expansion@xcite provides slightly better results@xcite . a more convenient expansion of the solution of the tf equation leads to many more accurate digits@xcite with less terms .\nin what follows we outline a simple , straightforward analytical method for the accurate calculation of @xmath1 . in order to facilitate the application of the hpm we define the variables @xmath25 and @xmath26 ,\nso that the tf equation becomes @xmath27 -f(t)f^{\\prime } ( t)-2t^{2}f(t)^{3}=0 \\label{eq : tf3}\\ ] ] we expand the solution @xmath28 to this differential equation in a taylor series about @xmath29 : @xmath30 where the coefficients @xmath31 depend on @xmath32 . on substitution of the series ( [ eq : f_series ] ) into equation ( [ eq : tf3 ] ) we easily calculate as many coefficients @xmath31 as desired ; for example , the first of them are @xmath33 the hpm is based on the transformation of the power series ( [ eq : f_series ] ) into a rational function or pad approximant @xmath34(t)=\\frac{\\sum_{j=0}^{m}a_{j}t^{j}}{\\sum_{j=0}^{n}b_{j}t^{j } } \\label{eq:[m / n]}\\ ] ] one would expect that @xmath35 in order to have the correct limit at infinity ; however , in order to obtain an accurate value of @xmath36 it is more convenient to choose @xmath37 , @xmath38 as in previous applications of the approach to the schrdinger equation ( in this case it was called riccati pad method ( rpm))@xcite .\nthe rational function ( [ eq:[m / n ] ] ) has @xmath39 coefficients that we may choose so that @xmath40,t)=\\mathcal{o}(t^{2n+d+1})$ ] and the coefficient @xmath41 remains undetermined .\nif we require that @xmath40,t)=\\mathcal{o}% ( t^{2n+d+2})$ ] we have another equation from which we obtain @xmath36 . however , it is convenient to proceed in a different ( and entirely equivalent ) way and require that @xmath34(t)-\\sum_{j=0}^{2n+d+1}f_{j}t^{j}=\\mathcal{o}(t^{2n+d+2 } ) \\label{eq:[m / n]2}\\ ] ] in order to satisfy this condition it is necessary that the hankel determinant vanishes @xmath42 where @xmath43 is the dimension of the hankel matrix .\neach hankel determinant is a polynomial function of @xmath36 and we expect that there is a sequence of roots @xmath44}$ ] , @xmath45 that converges towards the actual value of @xmath46 for a given value of @xmath47 .\nwe compare sequences with different values of @xmath47 for inner consistency ( all of them should give the same limit ) .\nnotice that a somewhat similar idea was also proposed by tu@xcite , although he did not develop it consistently .\npresent approach is simple and straightforward : we just obtain the taylor coefficients @xmath31 from the differential equation ( [ eq : tf3 ] ) in terms of @xmath36 , derive the hankel determinant , and calculate its roots . since @xmath48 is the first nonzero coefficient that depends on @xmath36 we choose hankel sequences with @xmath49 .\nthe hankel determinant @xmath50 exhibits many roots and their number increases with @xmath51 .\nif we compare the roots of @xmath50 with those of @xmath52 we easily identify the sequence @xmath44}$ ] that converges towards the actual value of @xmath36 .\n[ fig : logconv ] shows @xmath53}-2f_{2}^{[d-1,d]}\\right| $ ] for @xmath54 that provides a reasonable indication of the convergence of the sequence of roots .\nwe clearly appreciate the great convergence rate of the sequences with @xmath55 and @xmath56 . for example , for @xmath55 and @xmath57 it is approximately given by @xmath58}-2f_{2}^{[d-1,3]}\\right|=14.2\\times 10^ { -0.705d}$ ] . from the sequences for @xmath57 we estimate @xmath59 which we believe is accurate to the last digit .\nwe are not aware of a result of such accuracy in the literature with which we can compare our estimate .\nit is certainly far more accurate than the result obtained by kobayashi et al@xcite by numerical integration that is commonly chosen as a benchmark@xcite .\npresent rational approximation to the tf function is completely different from previous application of the pad approximants , where the slope at origin was determined by the asymptotic behaviour of at infinity@xcite .\nour approach applies to @xmath60 and the slope at origin is determined by a local condition at that point ( [ eq:[m / n]2 ] ) which results in the hankel determinant ( [ eq : hankel ] ) . in this sense\nour approach is similar to ( although more systematic and consistent than ) tu s one@xcite as mentioned above .\nonce we have the slope at origin we easily obtain an analytical expression for @xmath61 in terms of the rational approximation ( [ eq:[m / n ] ] ) to @xmath28 . in order to have the correct behaviour at infinity we choose @xmath62@xcite .\ntable [ tab : u(x ) ] shows values of @xmath61 and its first derivative for @xmath63 ( the approximation is obviously much better for @xmath64 ) given by the approximant @xmath65 $ ] .\nour results are in remarkably agreement with the numerical calculation of kobayashi et al@xcite and are by far much more accurate than those provided by the ham@xcite .\nnotice that we are comparing a @xmath65 $ ] pad approximant on the straightforward series expansion ( [ eq : f_series ] ) with @xmath66 $ ] and @xmath67 $ ] approximants on an elaborated perturbation series@xcite .\nany accurate analytical expression of the solution @xmath61 to the tf equation requires an accurate value of the unknown slope at origin @xmath1 , and the hpm provides it in a simple and straightforward way . in this sense\nthe hpm appears to be preferable to other accurate approaches@xcite and is far superior to the ham@xcite .\nnotice for example that our estimate @xmath68}=-1.588 $ ] , based on a rational approximation @xmath69 $ ] , is better than the result provided by a @xmath21 $ ] pad approximant on the improved ham perturbation series@xcite . besides , by comparing table 2 of khan and xu@xcite with our fig .\n[ fig : logconv ] one realizes the different convergence rate of both approaches .\none should also take into account that the hpm does not have any adjustable parameter for tuning up its convergence properties , while , on the other hand , the `` flexible '' ham with some such parameters plus a pad summation results in a much smaller convergence rate@xcite . we also constructed a pad approximant\n@xmath65 $ ] from the series ( [ eq : f_series ] ) and obtained the tf function and its derivative with an accuracy that outperforms the @xmath66 $ ] and @xmath21 $ ] pad approximants on the ham perturbation series@xcite .\nit is clear that the hpm is by far simpler , more straightforward , and much more accurate than the ham .\nin addition to the physical utility of the hpm we think that its mathematical features are most interesting .\nalthough we can not provide a rigorous proof of the existence of a convergent sequence of roots for each nonlinear problem , or that the sequences will converge towards the correct physical value of the unknown , a great number of successful applications to the schrdinger equation@xcite suggest that the hpm is worth further investigation .\nnotice that we obtain a global property of the tf equation @xmath1 from a local approach : the series expansion about the origin ( [ eq : f_series ] ) .\nthe fact that our original rational approximation ( [ eq:[m / n ] ] ) does not have the correct behaviour at infinity is not at all a problem because we may resort to a more conventient expansion@xcite once we have an accurate value of the unknown slope at origin .\nd .. 2d .. 12d .. 12 & & + 1 & 0.424008 & 0.273989 + 5 & 0.078808 & 0.023560 + 10 & 0.024315 & 0.0046028 + 20 & 0.005786 & 0.00064727 + 30 & 0.002257 & 0.00018069 + 40 & 0.001114 & 0.00006969 + 50 & 0.000633 & 0.00003251 + 60 & 0.000394 & 0.0000172 + 70 & 0.0002626&0.000009964 + 80 & 0.0001838 & 0.000006172 + 90 & 0.0001338 & 0.000004029 + 100&0.0001005 & 0.000002743 + 1000&0.000000137&0.00000000040 +", "role": "user" }, { "content": "we discuss a recently proposed analytic solution to the thomas fermi ( tf ) equation and show that earlier approaches provide more accurate results . \n in particular , we show that a simple and straightforward rational approximation to the tf equation yields the slope at origin with unprecedented accuracy , as well as remarkable values of the tf function and its first derivative for other coordinate values .", "role": "assistant" } ]

[ { "content": "Review the following segment from a research document in AI. Answer the subsequent query based solely on the provided information. Limit your response to the answer itself.\n\nResearch Segment: Following YOLO9000 our system predicts bounding boxes using dimension clusters as anchor boxes [15]. The network predicts 4 coordinates for each bounding box, t_{x}, t_{y}, t_{w}, t_{h}. If the cell is offset from the top left corner of the image by (c_{x},c_{y}) and the bounding box prior has width and height p_{w}, p_{h}, then the predictions correspond to:\n\nInquiry: How the YOLOv3 algorithm calculates the coordinates of the predicted box from anchor box and output coordinates?", "role": "user" }, { "content": "The question is partially answered as \"If the cell is offset from the top left corner of the image by (c_{x},c_{y}) and the bounding box prior has width and height p_{w}, p_{h}, then the predictions correspond to:\", but is completely answered in the continuation of the paper (in the expression).", "role": "assistant" } ]

[ { "content": "Analyze the following text to identify specific entities. Focus on the categories provided: [\"Chemical\", \"Protein\"].\n\nDeliver your findings as a JSON structure: {\"Chemical\": [\"ExampleChemical\", ...], \"Protein\": [\"ExampleProtein\", ...]}. Each key represents an entity type, and the associated list contains the entities found. \n\nEnsure the response is strictly the JSON format without any extra text.\n\nSource:\n\nPeroxynitrite mediates testosterone-induced vasodilation of microvascular resistance vessels.\nOur knowledge of how androgens influence the cardiovascular system is far from complete, and this lack of understanding is especially true of how androgens affect resistance vessels. Our aim was to identify the signaling mechanisms stimulated by testosterone (TES) in microvascular arteries and to understand how these mechanisms mediate TES-induced vasodilation. Mesenteric microvessels were isolated from male Sprague-Dawley rats. Tension studies demonstrated a rapid, concentration-dependent, vasodilatory response to TES that did not involve protein synthesis or aromatization to 17β-estradiol. Dichlorofluorescein fluorescence and nitrotyrosine immunoblot experiments indicated that TES stimulated peroxynitrite formation in microvessels, and functional studies demonstrated that TES-induced vasodilation was inhibited by scavenging peroxynitrite. As predicted, TES enhanced the production of both peroxynitrite precursors (i.e., superoxide and nitic oxide), and xanthine oxidase was identified as the likely source of TES-stimulated superoxide production. Functional and biochemical studies indicated that TES signaling involved activity of the phosphoinositide 3 (PI3) kinase-protein kinase B (Akt) cascade initiated by activation of the androgen receptor and culminated in enhanced production of cGMP and microvascular vasodilation. These findings, derived from a variety of analytical and functional approaches, provide evidence for a novel nongenomic signaling mechanism for androgen action in the microvasculature: TES-stimulated vasodilation mediated primarily by peroxynitrite formed from xanthine oxidase-generated superoxide and NO. This response was associated with activation of the PI3 kinase-Akt signaling cascade initiated by activation of the androgen receptor. We propose this mechanism could account for TES-stimulated cGMP production in microvessels and, ultimately, vasodilation.", "role": "user" }, { "content": "{\"Chemical\": [\"TES\", \"Peroxynitrite\", \"peroxynitrite\", \"cGMP\", \"xanthine\", \"phosphoinositide\", \"17\\u03b2-estradiol\", \"androgen\", \"testosterone\", \"nitic oxide\", \"superoxide\", \"androgens\", \"Dichlorofluorescein\", \"NO\", \"nitrotyrosine\"], \"Protein\": [\"Akt\", \"phosphoinositide 3 (PI3) kinase\", \"xanthine oxidase\", \"androgen receptor\", \"protein kinase B\", \"PI3 kinase\"]}", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nThe third model, which assumes unrelatedness, accounts for the possibility “that the blunted VS response as observed in individuals with ADHD is related to additional disease-related factors and not trait impulsivity per se” (20).", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\na single - page questionnaire ( technical appendix ) was sent to the lead cf physician in all uk pediatric and adult cf centers identified by the principal uk cf charity , the cystic fibrosis trust , in 2009 .\nresults were tabulated and basic statistical analysis performed by using microsoft excel 2007 ( microsoft , redmond , wa , usa ) . because m. chelonae and m. abscessus have common phenotypic characteristics and not all samples were fully sequenced by a reference laboratory , we combined these for reporting as mabsc .\ntwenty - three adult and 29 pediatric uk cf centers , with 8,513 cf patients , were sent questionnaires .\nresponses were received from 19 ( 83% ) and 24 ( 83% ) of these centers respectively , comprising 7,122 patients ( 3,805 adults , 3,317 children ) , or 84% of the uk cf population . as expected , the prevalence of any ntm isolate was higher in the adult ( 5.0% ) than in the pediatric ( 3.3% ) population ( table ) .\nfifteen adult and 17 pediatric centers cultured samples for ntm yearly ; most remaining centers tested for ntm only if there was a specific clinical indication\n. the ntm pathogens most frequently cultured were the rapidly growing mabsc ( 62% of adults , 68% of children who were ntm - positive ) , followed by mac ( 28% of adults , 27% of children ) .\nother species ( m. gordonae , kansasii , xenopi , fortuitum , simiae , malmoense , mucogenicum , perigrinum ) together made up 8% of the total .\nwide geographic variation was noted , increasing from northwest to southeast , manifesting lowest prevalence in northern ireland ( 1.9% ) and highest in south east england ( 7.5% ) ( figure ) .\nregional variation in percentage of cystic fibrosis patients in whom nontuberculous mycobacteria were isolated , united kingdom , 2009 .\nnineteen of 23 adult and 24 of 29 pediatric cf centers , accounting for 7,122 of 8,513 ( 84% ) cf patients , participated in the survey .\nmost centers required clear clinical or radiologic deterioration in addition to positive cultures , but a significantly higher proportion of adult centers ( 42% ) than pediatric centers ( 21% ) were prepared to commence treatment on the basis of repeated culture or smear positivity alone . despite this , similar proportions of ntm - positive adults and children had received specific treatment for ntm in the 2 years preceding the survey : 44% of adults and 47% of children with any ntm isolate were treated , and 62% of adults and 70% of children in whom > 2 isolates were found were treated .\nsix adults and 2 children who had cf had been refused a lung transplant on the basis of persistent ntm infection .\nour results differ from a 2003 multicenter us survey ( 9 ) in 2 crucial ways .\nfirst , the overall prevalence of ntm of 4.2% during the study period in the united kingdom was much lower than the 13% reported for the study done in the united states .\nthis could be caused in part by lower sampling frequency , occurring annually in most uk clinics , compared with 3 times annually as reported in the us study .\nthe proportion of patients having > 2 positive cultures was similar : 3.9% for the us study and 3.0% for our study .\nfurthermore , the denominator used for prevalence estimation may have been overestimated in this study : it may have included some patients missed for annual culture ; and particularly for pediatric clinics , the denominator would include non sputum producers ( cough swabs are normally not cultured for ntm ) .\nthe questionnaire we used did not specify which source documents respondents used ; therefore , recall bias may be an issue .\nhowever , all uk centers extract and report ntm data to a national database annually .\nthe second striking difference between this study and the us study was that rapid - growing mycobacteria ( especially mabsc ) predominated in this survey while mac predominated in the us study .\nour results are more in keeping with subsequent european and middle east prevalence studies ( 7,10,12 ) . rapid - growing mycobacteria such as mabsc\nare now recognized to be of greater clinical importance in cf than mac ( 1 ) , and a recent us single - center survey ( 13 ) has shown m. abscessus to be the current dominant ntm and to be associated with evidence of clinical decline . as in previous studies , we found marked geographic variation in prevalence : olivier et al\n. found higher rates in coastal centers in the united states ( 9 ) , and roux et al . found the highest prevalence in west and southwest france ( 10 ) .\nthe higher prevalence in the south of the united kingdom could be caused by different sampling rates , but we found no systematic difference in screening policy between different uk regions .\nclimatic differences are relatively small across a small temperate island such as the united kingdom .\ngeology could be another factor ; ntm acquisition has been linked with water from aquifers ( 12,14 ) which are present mainly in the younger rocks in southeastern united kingdom .\nthe varied threshold for instigating ntm treatment is perhaps not surprising in view of the lack of evidence to guide this .\nalthough there is no clear evidence to justify treatment on positive cultures alone , some centers may have lowered their threshold in the hope that ( by analogy with pseudomonas aeruginosa ) aggressive early treatment might lead to eradication .\nrefusal of lung transplantation is clearly an issue and appears to affect the threshold for treatment , though the rationale for refusal by transplant centers remains controversial ( 15 ) .\nthis survey highlights the growing importance of ntm as a cf pathogen , the importance of routine , standardized surveillance , and the need to find out how best to manage ntm in cf .\nthis will require further research into environmental , microbial , and host factors influencing acquisition and disease progression of ntm in the cf population .", "role": "user" }, { "content": "incidence of pulmonary infection with nontuberculous mycobacteria ( ntm ) is increasing among persons with cystic fibrosis ( cf ) . \n we assessed prevalence and management in cf centers in the united kingdom and found 5.0% of 3,805 adults and 3.3% of 3,317 children had recently been diagnosed with ntm . \n of those , 44% of adults and 47% of children received treatment .", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\nerg protein expression has been recently suggested to be reflective of erg gene rearrangements in prostate cancer ( pca ) documenting remarkable concordance between the two [ 16 ] .\nthe rearrangements between the androgen receptor - regulated gene tmprss2 ( 21q22.3 ) and members of the ets family member of transcription factor gene , most commonly erg ( 21q22.2 ) , are among the most common genetic alterations detected in prostate cancer [ 711 ] .\nerg gene rearrangements have been detected in roughly half ( 4060% ) of pca of surgical cohorts compared to a rate of 12%15% in incidental or watchful waiting cohorts [ 7 , 1218 ] .\nprevious studies investigating the prognostic significance of erg gene rearrangements have revealed mixed results [ 1922 ] .\nhowever , it is becoming more evident that erg gene rearrangements signify a molecular subtype of pca .\nsome studies investigating the significance of erg protein expression in localized pca failed to show association with adverse clinical outcome [ 23 , 24 ] . however , a recent report by our group demonstrated an association of erg expression with lethal disease in patients with unsuspected and advanced / castrate resistant disease who were treated by transurethral resection of prostate . moreover , we documented significant association between erg expression and both gleason score and tumor volume .\nstudies from our group and others have also linked erg status to responsiveness to hormonal therapy , and longer progression time to castration resistant disease , compared to men with no erg expression [ 24 , 25 ] . in the current study , we investigated the association of erg protein expression to clinical - pathological parameters in a cohort of men with localized prostate cancer .\nthe study cohort consisted of 198 patients who were treated by retropubic radical prostatectomy for localized prostate cancer with a mean followup of 4.8 years ( range 015.8 ) .\nclinical progression was defined as a postoperative serum psa elevation of > 0.2 ng / ml .\nprostate samples were embedded onto three tissue microarray ( tma ) blocks using a manual tissue arrayer ( beecher instruments , silver spring , md , usa ) .\none to nine cores ( average 3.3 ) , 0.6 mm in diameter , were sampled including benign , high grade intraepithelial neoplasia ( hgpin ) , and prostate cancer ( pca ) . after construction ,\n4 m sections were cut and stained with haematoxylin and eosin on the initial slides to verify the histological diagnosis .\nbriefly , 4 m thick sections from formalin - fixed paraffin - embedded tissue blocks were stained with ventana autostainer .\nprior to the staining , heat - induced antigen retrieval was carried out by vegetable steamer in sodium citrate antigen retrieval buffer ( 10 mm ph 6.0 ) for 40 minutes and then cooled down to room temperature for about 20 minutes .\nthe slides were incubated for 60 minutes at 37c with erg rabbit monoclonal antibody ( epitomics , clone epr 3864 ) at 1 : 50 dilution . a ventana iview dab detection kit ( ventana tucson , az , usa )\nthe diagnoses of all tma cores were confirmed by the three study pathologists ( lht , cw , and tab ) .\nfor each patient , the two predominant patterns were sampled and included on the tmas for analysis .\nerg protein expression was assessed semiquantitatively using 3-tiered system ( 0 , negative ; 1 , low ; 2 , high ) .\ncases with either 1 or 2 intensity were considered positive based on previous correlation with erg gene rearrangement as detected by fluorescent in situ hybridization ( data not shown ) .\nthe erg antibody was consistently strongly expressed in endothelial cells , which acted as internal control for expression and intensity level .\npatient characteristics were presented as frequencies and percentages for categorical variables and as means and ranges for continuous variables .\nchi - square tests were used to test for associations between erg protein expression and gleason score , surgical margin , and pathological stage . the kaplan - meier approach along with the log - rank test was used for the survival analyses to test the association between erg expression and serum psa relapse . in all statistical tests ,\nmean patients ' age of this cohort was 64 years ( range 42.780.5 years ) with average follow - up time of 4.8 years ( range 0.015.8 months ) .\ntable 1 demonstrates patients ' demographics of the study cohort with respect to erg expression .\noverall , there were no significant differences between the two subgroups ( erg pos & erg neg ) of patients except for pathological stage , with 37% of erg positive tumors detected in pt3 versus 24% in pt2 . to investigate erg expression in different diagnostic categories , we characterized erg expression based on individual cores sampled .\nwhen we accounted for foamy type pca morphology , the rate of erg expression was 15/84 ( 17.9% ) , compared to 302/704 ( 42.9% ) in acinar pca ( cases with no foamy type morphology ) ( p < 0.001 ) .\nthere was no difference in high erg intensity between foamy type and acinar pca ( data not shown ) . however , mean intensity level of erg in acinar pca was significantly higher than foamy type pca , 1.01 1.27 versus 0.37 0.83 ( p < 0.001 ) .\nerg intensity levels in hgpin were comparable to those in foamy type pca but slightly lower ( 0.13 0.56 ) but significantly lower than those in acinar pca ( p < 0.001 ) ( figure 1 ) .\nerg expression was noted in 106/280 ( 37.8% ) , 175/463 ( 37.8% ) , and 37/108 ( 34.2% ) of gleason scores 6 , 7 , and 810 , respectively . \nfigure 2 demonstrates examples of erg expression in tissue samples and the distribution of erg in relation to gleason score .\nwhen investigating relations between erg expression and pathological parameters , there was significant association between erg expression and higher disease stage . in this cohort , erg expression was present in 50/131 ( 38.1% ) patients with pt2 versus 30/55 ( 54.5% ) patients with pt3 ( p = 0.04 ) .\na similar association was also noted between erg expression and extra - capsular extension . in this cohort , 52/134 ( 38.8% )\nerg positive patients demonstrated organ confined disease versus 29/53 ( 54.7% ) erg positive patients showing extra - capsular extension ( p = 0.04 ) .\nsimilar trends were noted between erg expression and seminal vesicle invasion , but this was not statistically significant ( p = 0.10 ) ( data not shown ) .\nno significant association was noted between overall erg positivity and positive surgical margins ( table 1 ) .\nsimilarly , no association was observed with postsurgical psa levels when assessed by univariate or multivariate analysis ( figure 3 ) . although not informative due to limited patients ' numbers , the association between erg expression and higher stage disease was more pronounced in patients with higher gs . in this cohort ,\nnone of the patients with gs > 7 and erg positive ( 0/7 ) were of stage pt2 compared to 47% ( 7/15 ) of erg negative patients who were of pt2 stage ( p = 0.02 ) ( table 2 ) .\nthis study reports on the potential significance of erg protein expression in localized prostate cancer .\nerg gene rearrangements and erg expression have been documented in roughly 50% of localized prostate and locally advanced castrate resistant prostate cancer compared to 12%15% in watchful waiting or incidental cohorts [ 16 , 17 , 22 , 25 , 29 ] . published reports on the significance of erg expression to patients ' outcome are conflicting with some showing association with adverse outcome , while others document no association .\nsome suggest that it indicates a better prognosis [ 16 , 22 , 25 , 2933 ] .\nhowever , it is proposed that erg signifies a molecular class of prostate cancer and may play a role in disease progression within those tumors .\nthis pathway is closely linked to increased rate of pten genomic deletions as well as increased erg expression or erg gene rearrangements [ 34 , 35 ] .\nerg gene rearrangements and erg expression are associated with adverse outcome and lethal disease in watchful waiting or expectant cohorts [ 16 , 25 ] .\nmoreover , patients with erg overexpression demonstrated shorter progression times to castrate resistance , needing surgical intervention ( channel turp ) .\nin localized prostate cancer , the majority of the reported data suggest no prognostic implication for erg rearrangements or erg overexpression in relation to psa relapse or the recurrence of local disease [ 22 , 36 , 37 ] .\nhowever , two earlier reports suggested adverse association of erg rearrangements with psa relapse after radical prostatectomy [ 20 , 31 ] . in nam 's study ,\nyashimoto 's group noted that the adverse prognostic association was linked to pten genomic deletions . of note , a study by reid et al .\ndocumented that erg gene rearrangements in addition to pten genomic deletions had actually favorable outcomes compared to pten deletion alone .\nthese observations suggest that the method utilized in determining erg status , the inclusion or exclusion of other genomic aberration , and the cohort chosen may be the reason for the different results obtained in various studies investigating the role of erg in prostate cancer .\nour results support previous observations showing no prognostic relationship between erg overexpression and clinical outcome in localized prostate cancer .\nhowever , in contrast to earlier studies , we document significant association between erg expression and some pathological parameters . in this cohort , patients whose tumors were erg positive were at higher risk of exhibiting extra - prostatic extension and increased disease stage compared to patients whose tumors did not express erg .\nspecifically , all patients with gs > 7 and erg expression showed pt3 stage disease compared to none of pt2 . however , this data is limited by the number of patients within each gs subgroup and need further confirmation .\nmore importantly , in addition to not documenting any clinical prognostic significance for erg expression , we did not observe any association between erg expression and other pathological parameters such as gleason score or surgical margins , which further diminishes any potential prognostic significance for erg expression , at least in localized pca .\nanother issue worth mentioning regarding erg is that , erg gene rearrangements have been previously associated with specific histopathological features and detected more frequently in some morphologic variants of prostate cancer than others . in this study , we confirm lower rates of erg expression in tumors with foamy / xanthomatous morphology which demonstrated lower mean expression intensities compared to acinar pca .\nthe significance of this is not yet known , but suggests that those two types of tumors may be different at the molecular level . in conclusion , this study demonstrates significant association between erg expression and extra - prostatic extension and higher pathological stage in localized prostate cancer .\nmoreover , the lack of association with any other pathological parameters also significantly diminishes any potential clinical application of erg expression , at least in men with localized prostate cancer .", "role": "user" }, { "content": "background . \n the prognostic significance of erg expression in prostate cancer ( pca ) has generated mixed results . \n we sought to investigate the prognostic significance of erg expression in a localized cohort of men with pca . \n material and methods . \n we investigated erg protein expression in a cohort of 198 men with localized pca . \n erg expression was correlated with patients ' clinical outcome and several pathological parameters , including gleason score ( gs ) , pathological stage , surgical margin , and extra - capsular extension . results . \n erg expression was detected in 86/198 ( 43.4% ) patients exclusively in neoplastic epithelium . \n overall , erg mean expression intensity was 1.01 1.27 versus 0.37 0.83 in acinar pca compared to foamy type pca ( p < 0.001 ) . in hgpin , erg intensity levels were comparable to those in foamy type pca ( 0.13 0.56 ) but significantly lower than those in acinar pca ( p < 0.001 ) . \n erg expression was significantly associated with extra - prostatic extension and higher pathological stage and showed a trend toward seminal vesicle invasion . \n herein , erg expression was documented in 50/131 ( 38.1% ) patients with pt2 versus 30/55 ( 54.5% ) patients with pt3 ( p = 0.04 ) . \n erg association with higher pathological stage was more pronounced in patients with gs > 7 . \n grouping patients into those with gs 7 versus > 7 , there was no significant association between erg expression and gs . \n similarly , no association was present in relation to either surgical margins or postsurgical serum psa levels . conclusion . \n we report significant association between erg protein levels and extra - prostatic extension and higher pathological stage . \n erg expression is not associated with adverse clinical outcome and is of limited prognostic value in localized pca .", "role": "assistant" } ]

[ { "content": "Analyze the provided paragraph from a scientific document. Your goal is to identify and extract relevant entities.\n\nFormat your findings as a JSON object, where each key represents a category of entities, and the corresponding value is a list of entities identified in that category. If no entities are found for a category, return an empty list.\n\nFocus on precision and ensure that the output is strictly in JSON format.\n\nDocument:\n\nChemotactic Behaviors of Vibrio cholerae Cells Vibrio cholerae, the causative agent of cholera, swims in aqueous environments with a single polar flagellum. In a spatial gradient of a chemical, the bacterium can migrate in \" favorable \" directions, a property that is termed chemotaxis. The chemotaxis of V. cholerae is not only critical for survival in various environments and but also is implicated in pathogenicity. In this chapter, we describe how to characterize the chemotactic behaviors of V. cholerae: these methods include swarm assay, temporal stimulation assay, capillary assay, and receptor methylation assay.", "role": "user" }, { "content": "{\"AnatomicalStructure\": [\"Cells\", \"flagellum\"], \"Bacterium\": [\"bacterium\", \"Vibrio cholerae\", \"V. cholerae\"], \"BiologicFunction\": [\"chemotactic behaviors\", \"chemotaxis\", \"Chemotactic Behaviors\", \"cholera\"], \"BiomedicalOccupationOrDiscipline\": [], \"BodySubstance\": [], \"BodySystem\": [], \"Chemical\": [\"chemical\"], \"ClinicalAttribute\": [], \"Eukaryote\": [], \"Finding\": [], \"Food\": [], \"HealthCareActivity\": [\"swarm assay\", \"receptor methylation assay\", \"capillary assay\", \"temporal stimulation assay\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [], \"MedicalDevice\": [], \"Organization\": [], \"PopulationGroup\": [], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [], \"SpatialConcept\": [\"directions\", \"spatial\", \"environments\"], \"Virus\": []}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: social distancing does help prevent coronavirus (COVID-19\n\nResearch Abstract:\nBackground: The Greek authorities implemented the strong social distancing measures within the first few weeks after the first confirmed case of the virus to curtail the COVID-19 growth rate.\nObjectives: To estimate the effect of the two-stage strong social distancing measures, the closure of all non-essential shopping centers and businesses on March 16 and the shelter in place orders (SIPOs) on March 23 on the COVID-19 growth rate in Greece Methods: We obtained data on COVID-19 cases in Greece from February 26th through May 4th from publicly available sources.\nAn interrupted time-series regression analysis was used to estimate the effect of the measures on the exponential growth of confirmed COVID-19 cases, controlling for the number of daily testing, and weekly fixed-effects.\nResults: The growth rate of the COVID-19 cases in the pre-policies implementation period was positive as expected (p=0.003).\nBased on the estimates of the interrupted time-series, our results indicate that the SIPO on March 23 significantly slowed the growth rate of COVID-19 in Greece (p=0.04).\nHowever, we did not find evidence on the effectiveness of standalone and partial measures such as the non-essential business closures implemented on March 16 on the COVID-19 spread reduction.\nDiscussion: The combined social distancing measures implemented by the Greek authorities within the first few weeks after the first confirmed case of the virus reduced the COVID-19 growth rate.\nThese findings provide evidence and highlight the effectiveness of these measures to flatten the curve and to slow the spread of the virus.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Discussion: The combined social distancing measures implemented by the Greek authorities within the first few weeks after the first confirmed case of the virus reduced the COVID-19 growth rate.\"]}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: SIFT Meets CNN: A Decade Survey of Instance Retrieval \nChapter Title: Pipeline \n1. Abstract of Cited Paper (BIB001): The state of the art in visual object retrieval from large databases is achieved by systems that are inspired by text retrieval. A key component of these approaches is that local regions of images are characterized using high-dimensional descriptors which are then mapped to ldquovisual wordsrdquo selected from a discrete vocabulary.This paper explores techniques to map each visual region to a weighted set of words, allowing the inclusion of features which were lost in the quantization stage of previous systems. The set of visual words is obtained by selecting words based on proximity in descriptor space. We describe how this representation may be incorporated into a standard tf-idf architecture, and how spatial verification is modified in the case of this soft-assignment. We evaluate our method on the standard Oxford Buildings dataset, and introduce a new dataset for evaluation. Our results exceed the current state of the art retrieval performance on these datasets, particularly on queries with poor initial recall where techniques like query expansion suffer. Overall we show that soft-assignment is always beneficial for retrieval with large vocabularies, at a cost of increased storage requirements for the index. \n2. Abstract of Cited Paper (BIB002): We address the problem of image search on a very large scale, where three constraints have to be considered jointly: the accuracy of the search, its efficiency, and the memory usage of the representation. We first propose a simple yet efficient way of aggregating local image descriptors into a vector of limited dimension, which can be viewed as a simplification of the Fisher kernel representation. We then show how to jointly optimize the dimension reduction and the indexing algorithm, so that it best preserves the quality of vector comparison. The evaluation shows that our approach significantly outperforms the state of the art: the search accuracy is comparable to the bag-of-features approach for an image representation that fits in 20 bytes. Searching a 10 million image dataset takes about 50ms. \n3. Abstract of Cited Paper (BIB003): The Fisher kernel (FK) is a generic framework which combines the benefits of generative and discriminative approaches. In the context of image classification the FK was shown to extend the popular bag-of-visual-words (BOV) by going beyond count statistics. However, in practice, this enriched representation has not yet shown its superiority over the BOV. In the first part we show that with several well-motivated modifications over the original framework we can boost the accuracy of the FK. On PASCAL VOC 2007 we increase the Average Precision (AP) from 47.9% to 58.3%. Similarly, we demonstrate state-of-the-art accuracy on CalTech 256. A major advantage is that these results are obtained using only SIFT descriptors and costless linear classifiers. Equipped with this representation, we can now explore image classification on a larger scale. In the second part, as an application, we compare two abundant resources of labeled images to learn classifiers: ImageNet and Flickr groups. In an evaluation involving hundreds of thousands of training images we show that classifiers learned on Flickr groups perform surprisingly well (although they were not intended for this purpose) and that they can complement classifiers learned on more carefully annotated datasets.\n\nReview Chapter:", "role": "user" }, { "content": "The pipeline of SIFT-based retrieval is introduced in Fig. 2 . Local Feature Extraction. Suppose we have a gallery G consisting of N images. Given a feature detector, we extract local descriptors from the regions around the sparse interest points or dense patches. We denote the local descriptors of D detected regions in an image as ff i g D i¼i ; f i 2 R p . Codebook Training. SIFT-based methods train a codebook offline. Each visual word in the codebook lies in the center of a subspace, called the \"Voronoi cell\". A larger codebook corresponds to a finer partitioning, resulting in more discriminative visual words and vice versa. Suppose that a pool of local descriptors F ff i g M i¼1 are computed from an unlabeled training set. The baseline approach, i.e., k-means, partitions the M points into K clusters; the K visual words thus constitute a codebook of size K. Feature Encoding. A local descriptor f i 2 R p is mapped into a feature embedding g i 2 R l through the feature encoding process, f i ! g i . When k-means clustering is used, f i can be encoded according to its distances to the visual words. For large codebooks, hard , BIB001 and soft quantization BIB002 are good choices. In the former, the resulting embedding g i has only one non-zero entry; in the latter, f i can be quantized to a small number of visual words. A global signature is produced after a sum-pooling of all the embeddings of local features. For medium-sized codebooks, additional binary signatures can be generated to preserve the original information. When using small codebooks, popular encoding schemes include vector of locally aggregated descriptors (VLAD) BIB003 , Fisher vector (FV) BIB004 , etc.", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\nunderstanding the developmental patterns of vegetative and reproductive organs and factors that influence those patterns is of critical importance for conserving rare plants .\nwe recently determined that leaf and leaflet expansion of the endangered cycas micronesica were influenced by spatial and temporal factors , but reproductive organ expansion was unaffected or only minimally influenced by the same factors .\nwe pointed out that empirical approaches for fitting models to organ growth and development may be used to inform horticultural or conservation questions of other rare cycad taxa . here\nwe argue that this approach may improve our understanding of the evolutionary and developmental biology of cycads .\nwhile slow to gain traction in botany , especially in studies of gymnosperms ( but see refs . 2 and 3 )\n, evo - devo has become one of the most promising and productive perspectives in biology .\nthis should not be surprising given that development describes processes within a generation and evolution describes processes among generations .\nin writing about fossil cycads , mamay first suggested that angiosperm carpels evolved from megasporophylls , possibly of cycads . in more modern terms , examining regulatory genes , frohlich suggested that angiosperm carpels evolved from microsporophylls .\nthese two hypotheses are probably incommensurate given that female and male strobili of cycads are homologous , unlike strobili of all other extant gymnosperms .\ncycad megastrobili and microstrobili are effectively a telescoped flush of leaves ( fig . 1 ) .\nboth female and male strobili are still highly modified , so we still expect different developmental pathways in vegetative leaves , megastrobili and microstrobili .\ndevelopment in cycads is undoubtedly modular , as in other gymnosperms , although maybe not as modular as in angiosperms .\nthus ontogeny of various cycad organs should progress differently from other organs in the same individual plant .\nwe expect different developmental timing in vegetative vs. reproductive organs because cycad strobili are likely highly endoploid .\nthermogenesis probably requires extra mitochondria , as we see in several skunk cabbage ( symplocarpus ) species .\nwhile almost exclusively documented in angiosperms , plants have plenty of endoploidy , especially succulent plants , which might include stems and strobilus axes in cycads . furthermore , animal tissues with high metabolic demand are often highly endoploid , such as heart muscles , flight muscles and liver cells .\nwe suspect that endoploidy provides a way around otherwise rate - limiting production of mrna .\nefforts to confirm endoploidy in cycad strobili are warranted because endoploidy alters developmental rates insofar as mitotic cycle rates are inversely proportional to ploidy levels and probably inversely proportional to chromosomal content per nucleus , i.e. , c - values .\nthere are four modes of evolutionary response to changing environments : ( 1 ) environmental tracking , ( 2 ) phenotypic plasticity , ( 3 ) bet hedging , and ( 4 ) extinction . a priori ,\nwe expect greater environmental tracking and phenotypic plasticity in vegetative structures because the individual plant can not grow without leaves . however , we expect more bet hedging ( risk aversion ) in reproductive organ production for any perennial plant ; especially in cycas micronesica , which makes large investments in both female and male strobili . but these are all mechanisms by which organisms evolve via selection . by contrast , gorelick and olson argued that drift should play a disproportionate role in cycad evolution compared with selection because of the peculiar genomic architecture and small population sizes ( see also ref .\nsimilarly , lynch and conery hypothesized that large genome size , which we see in cycads , may be maladaptive .\nthus developmental rates of different plant parts may be nothing more that what gould and lewontin mistakenly called spandrels .\nmaybe there are no adaptationist explanations nor fitness benefits to the developmental patterns we described . or , alternatively , maybe these developmental patterns are nothing more than a corollary of endoploidy levels , which we presume are greater in thermogenic cones than in other plant parts .\ncycads are a threatened group of plants worldwide for which recovery plans have already been proposed or implemented for some taxa ( e.g. , see ref .\n. a full understanding of evolutionary developmental trajectories of cycads may be a prerequisite for restoring habitats during recovery efforts .\nthus far , we have only examined phenology and evolutionary responses in the most basal genus of cycads , cycas , with its disaggregated female strobili .\nbecause of the putative recent ancestry of all extant cycads , we anticipate similarities among all living cycads , which may not be due to any selective advantage .\ndoes plasticity of cycad male cone development differ from that of other gymnosperms ? because cycad male cones are presumably not homologous with those of other extant gymnosperms , the relative roles of selection and drift may not be the same in evolution of cycads vs. other gymnosperms . given that cycads are the most basal of living seed plants , it is incumbent upon us to better understand these fascinating plants .\nmeasurement of effective population sizes , plasticity , heterochrony , and endoploidy will help immensely in answering these evolutionary questions about cycads and may well help in their conservation .\nfigure 1 . a cycas seemannii megastrobilus ( or indeterminate strobilus sensu in ref .\n28 ) emerges as a flush of megasporophylls bearing naked ovules , which are almost certainly homologous to the pinnately compound vegetative leaves .\nthe genus cycas contain some species with pinnately compound megasporophylls , e.g. , c. revoluta and c. pectinata , while all members of the genus have new flushes of vegetative leaves that emerge from the center of the megastrobilus , as seen in this figure , further indicating homology between sporophylls and vegetative leaves in cycads .", "role": "user" }, { "content": "we recently described lack of phenotypic plasticity in reproductive organ development and substantial plasticity in vegetative organ development for the cycad cycas micronesica . \n is there an evo - devo explanation for the disparity in phenotypic plasticity of vegetative vs. reproductive organs ? despite modularity , might evolution of cycad phenology be controlled more by drift than selection ?", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nTypical recommender systems push K items at once in the result page in the form of a feed, in which the selection and the order of the items are important for user experience. In this paper, we formalize the K-item recommendation problem as taking an unordered set of candidate items as input, and exporting an ordered list of selected items as output. The goal is to maximize the overall utility, e.g. the click through rate, of the whole list. As one solution to the K-item recommendation problem under this proposition, we proposed a new ranking framework called the Evaluator-Generator framework. In this framework, the Evaluator is trained on user logs to precisely predict the expected feedback of each item by fully considering its intra-list correlations with other co-exposed items. On the other hand, the Generator will generate different sequences from which the Evaluator will choose one sequence as the final recommendation. In our experiments, both the offline analysis and the online test show the effectiveness of our proposed framework. Furthermore, we show that the offline behavior of the Evaluator is consistent with the realistic online environment.\n\nCited Works Summary:\n[1]: Recommender systems can mitigate the information overload problem by suggesting users' personalized items. In real-world recommendations such as e-commerce, a typical interaction between the system and its users is - users are recommended a page of items and provide feedback; and then the system recommends a new page of items. To effectively capture such interaction for recommendations, we need to solve two key problems - (1) how to update recommending strategy according to user's real-time feedback, and 2) how to generate a page of items with proper display, which pose tremendous challenges to traditional recommender systems. In this paper, we study the problem of page-wise recommendations aiming to address aforementioned two challenges simultaneously. In particular, we propose a principled approach to jointly generate a set of complementary items and the corresponding strategy to display them in a 2-D page; and propose a novel page-wise recommendation framework based on deep reinforcement learning, DeepPage, which can optimize a page of items with proper display based on real-time feedback from users. The experimental results based on a real-world e-commerce dataset demonstrate the effectiveness of the proposed framework.\n\n[2]: The goal of search result diversification is to select a subset of documents from the candidate set to satisfy as many different subtopics as possible. In general, it is a problem of subset selection and selecting an optimal subset of documents is NP-hard. Existing methods usually formalize the problem as ranking the documents with greedy sequential document selection. At each of the ranking position the document that can provide the largest amount of additional information is selected. It is obvious that the greedy selections inevitably produce suboptimal rankings. In this paper we propose to partially alleviate the problem with a Monte Carlo tree search (MCTS) enhanced Markov decision process (MDP), referred to as M @math Div. In M @math Div, the construction of diverse ranking is formalized as an MDP process where each action corresponds to selecting a document for one ranking position. Given an MDP state which consists of the query, selected documents, and candidates, a recurrent neural network is utilized to produce the policy function for guiding the document selection and the value function for predicting the whole ranking quality. The produced raw policy and value are then strengthened with MCTS through exploring the possible rankings at the subsequent positions, achieving a better search policy for decision-making. Experimental results based on the TREC benchmarks showed that M @math Div can significantly outperform the state-of-the-art baselines based on greedy sequential document selection, indicating the effectiveness of the exploratory decision-making mechanism in M @math Div.\n\n[3]: In this paper, we propose a novel Deep Reinforcement Learning framework for news recommendation. Online personalized news recommendation is a highly challenging problem due to the dynamic nature of news features and user preferences. Although some online recommendation models have been proposed to address the dynamic nature of news recommendation, these methods have three major issues. First, they only try to model current reward (e.g., Click Through Rate). Second, very few work consider to use user feedback other than click no click labels (e.g., how frequent user returns) to help improve recommendation. Third, these methods tend to keep recommending similar news to users, which may cause users to get bored. Therefore, to address the aforementioned challenges, we propose a Deep Q-Learning based recommendation framework, which can model future reward explicitly. We further consider user return pattern as a supplement to click no click label in order to capture more user feedback information. In addition, an effective exploration strategy is incorporated to find new attractive news for users. Extensive experiments are conducted on the offline dataset and online production environment of Chinese Bing News and have shown the superior performance of our methods.", "role": "user" }, { "content": "Some recent works have been addresses long-term rewards in recommender systems. [2] also work on intra-list correlations, which applies policy gradient and Monte Carlo Tree Search(MCTS) to optimize the @math -NDCG in diversified ranking for the global optimum. Other works pursues long-term rewards in inter-list recommendations ( [1] , [3] ). Though [1] also proposed treating a page of recommendation list as a whole, the intra-list correlations are not well modelled and analyzed in their work. Also their work is not testified on realistic online RS. In this paper, we more thoroughly investigates the general form of the intra-list correlations. We formalize the utility of the whole list as our final target, but we have also used item-level feedbacks. This has not been sufficiently studied in the above works.", "role": "assistant" } ]

[ { "content": "Examine the provided biomedical text and determine the answer to the question. Your response should be either \"yes\" or \"no\" based on the information given.\n\nQuestion: Is Sotrovimab effective for COVID-19?\n\nText: It seems that monoclonal antibodies (e.g., low dosage bamlanivimab, baricitinib, imatinib, and sotrovimab) are a better choice for treating severe or non-severe COVID-19 patients.\nThe Food and Drug Administration has granted emergency use authorization to sotrovimab for the treatment of mild to moderate COVID-19 in patients at increased risk for progression to severe illness.\nEarly Treatment for Covid-19 with SARS-CoV-2 Neutralizing Antibody Sotrovimab.\nSotrovimab is a pan-sarbecovirus monoclonal antibody that was designed to prevent progression of Covid-19 in high-risk patients early in the course of disease\nCONCLUSIONS: Among high-risk patients with mild-to-moderate Covid-19, sotrovimab reduced the risk of disease progression.\nThe Food and Drug Administration has granted emergency use authorization to sotrovimab for the treatment of mild to moderate COVID-19 in patients at increased risk for progression to severe illness.Sotrovimab is a monoclonal antibody that works directly against the spike protein of SARS-CoV-2 to block its attachment and entry into a human cell.\nIn patients with non-severe covid-19, casirivimab-imdevimab probably reduces hospitalisation; bamlanivimab-etesevimab, bamlanivimab, and sotrovimab may reduce hospitalisation. Convalescen\nms that monoclonal antibodies (e.g., low dosage bamlanivimab, baricitinib, imatinib, and sotrovimab) are a better choice for treating severe or non-severe COVID-19 patients. Clini\nEarly Treatment for Covid-19 with SARS-CoV-2 Neutralizing Antibody Sotrovimab\nThe Food and Drug Administration has granted emergency use authorization to sotrovimab for the treatment of mild to moderate COVID-19 in patients at increased risk for progression to severe illness", "role": "user" }, { "content": "yes", "role": "assistant" } ]

[ { "content": "Examine the following abstract and identify distinct entities. Focus on extracting entities related to participants, interventions, and outcomes.\n\nPresent your findings in a JSON format like: {\"Participant\": [\"example entity\", ...], \"Intervention\": [\"example entity\", ...], \"Outcome\": [\"example entity\", ...]}. If no entities are found for a category, use an empty list.\n\nAbstract Content:\n\nSupplementation with iron and riboflavin enhances dark adaptation response to vitamin A-fortified rice in iron-deficient , pregnant , nightblind Nepali women . BACKGROUND Nightblindness affects 16-52 % of pregnant women in areas of Nepal and in some cases persists after vitamin A treatment . Iron and riboflavin affect vitamin A utilization and photoreceptor function , respectively , and pilot data in the study population showed a high prevalence of iron and riboflavin deficiencies . OBJECTIVE The objective was to assess the effect of supplemental iron and riboflavin on pupillary threshold ( PT ) and plasma retinol in nightblind , pregnant Nepali women given vitamin A-fortified rice . DESIGN Nightblind pregnant women were randomly assigned to receive , 6 d/wk under supervision for 6 wk , a vitamin A-fortified rice curry dish providing 850 microg retinal activity equivalents/d with either a 30-mg Fe and 6-mg riboflavin ( FeR + VA ) capsule or a placebo control ( VA only ) capsule . Hemoglobin , erythrocyte riboflavin , and plasma ferritin and retinol were measured before and after the intervention . Dark adaptation was assessed by PT score . RESULTS Women who were iron deficient at baseline ( n=38 ) had significantly greater improvement in PT score with iron and riboflavin supplementation than without ( P=0.05 ) . Iron and riboflavin supplements significantly reduced the prevalences of riboflavin deficiency ( from 60 % to 6 % ; P < 0.0001 ) , iron deficiency anemia ( from 35 % to 15 % ; P < 0.007 ) , and abnormal PT ( from 87 % to 30 % ; P < 0.05 ) from baseline . Mean increases in erythrocyte riboflavin ( P < 0.0001 ) and plasma ferritin ( P=0.01 ) were greater in the FeR + VA group than in the VA only group . CONCLUSIONS Iron deficiency may limit the efficacy of vitamin A to normalize dark adaptation in pregnant Nepali women . Further studies are needed to assess the effect of simultaneous delivery of iron and vitamin A for the treatment of nightblindness .", "role": "user" }, { "content": "{\"Intervention\": [\"iron\", \"30-mg Fe\", \"6-mg riboflavin\", \"vitamin A-fortified rice\", \"supplemental iron and riboflavin\", \"Supplementation with iron and riboflavin\", \"riboflavin\", \"Iron\", \"vitamin A\", \"vitamin A-fortified rice curry dish\", \"placebo control\"], \"Outcome\": [\"riboflavin deficiency\", \"abnormal PT\", \"plasma ferritin\", \"PT score with iron and riboflavin supplementation\", \"iron deficiency anemia\", \"Hemoglobin , erythrocyte riboflavin , and plasma ferritin and retinol\"], \"Participant\": [\"women\", \"Nightblind pregnant\", \"iron-deficient , pregnant , nightblind\", \"pregnant\"]}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Alcohol does not disinfect the mouth or provide protection.\n\nResearch Abstract:\nAmong the basic protective measures against COVID-19, the need to wash hands frequently and in a prolonged way using soap, and to regularly use alcohol-based hand sanitizers is well established for the whole population.\nHealthcare workers in general, and particularly those involved in the direct care of COVID-19 patients, have to wear personal protective equipment (PPE) daily for many hours and also accomplish general preventive measurements outside their work.\nCutaneous adverse reactions can develop that need to be prevented, identified and therapeutically managed.\nAccording to the data reported by Lin et al 1 , based in the experience from healthcare workers in Wuhan, adverse skin reactions were reported in 74% of responders (n=376) to a general survey.\nThe most commonly reported types of eruptions were skin dryness or desquamation (68.6%), papules or erythema (60.4%) and maceration (52,9%).", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Among the basic protective measures against COVID-19, the need to wash hands frequently and in a prolonged way using soap, and to regularly use alcohol-based hand sanitizers is well established for the whole population.\"]}", "role": "assistant" } ]

[ { "content": "Explore the following research question and associated terms. Identify the most suitable dataset from the list provided. Use the dataset descriptions to guide your choice.\n\nInquiry: I want to train a weakly supervised system for action recognition from video.\n\nKeywords: weakly supervised action recognition video\n\nDataset Information:\nDiDeMo: The Distinct Describable Moments (DiDeMo) dataset is one of the largest and most diverse datasets for the temporal localization of events in videos given natural language descriptions. The videos are collected from Flickr and each video is trimmed to a maximum of 30 seconds.\nEPIC-KITCHENS-100: This paper introduces the pipeline to scale the largest dataset in egocentric vision EPIC-KITCHENS. The effort culminates in EPIC-KITCHENS-100, a collection of 100 hours, 20M frames, 90K actions in 700 variable-length videos, capturing long-term unscripted activities in 45 environments, using head-mounted cameras.\nBreakfast: The Breakfast Actions Dataset comprises of 10 actions related to breakfast preparation, performed by 52 different individuals in 18 different kitchens. The dataset is one of the largest fully annotated datasets available.\nDCASE 2018 Task 4: DCASE2018 Task 4 is a dataset for large-scale weakly labeled semi-supervised sound event detection in domestic environments. The data are YouTube video excerpts focusing on domestic context which could be used for example in ambient assisted living applications.\n\nAvailable Datasets: A: DiDeMo B: EPIC-KITCHENS-100 C: Breakfast D: DCASE 2018 Task 4", "role": "user" }, { "content": "Breakfast", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Dataset search: a survey \nChapter Title: Current dataset search implementations \n1. Abstract of Cited Paper (BIB001): The Open Data movement has become a driver for publicly available data on the Web. More and more data—from governments and public institutions but also from the private sector—are made available online and are mainly published in so-called Open Data portals. However, with the increasing number of published resources, there is a number of concerns with regards to the quality of the data sources and the corresponding metadata, which compromise the searchability, discoverability, and usability of resources. ::: In order to get a more complete picture of the severity of these issues, the present work aims at developing a generic metadata quality assessment framework for various Open Data portals: We treat data portals independently from the portal software frameworks by mapping the specific metadata of three widely used portal software frameworks (CKAN, Socrata, OpenDataSoft) to the standardized Data Catalog Vocabulary metadata schema. We subsequently define several quality metrics, which can be evaluated automatically and in an efficient manner. Finally, we report findings based on monitoring a set of over 260 Open Data portals with 1.1M datasets. This includes the discussion of general quality issues, for example, the retrievability of data, and the analysis of our specific quality metrics. \n2. Abstract of Cited Paper (BIB002): Intuitively, most datasets found on governmental Open Data portals are organized by spatio-temporal criteria, that is, single datasets provide data for a certain region, valid for a certain time period. Likewise, for many use cases (such as, for instance, data journalism and fact checking) a pre-dominant need is to scope down the relevant datasets to a particular period or region. Rich spatio-temporal annotations are therefore a crucial need to enable semantic search for (and across) Open Data portals along those dimensions, ::: yet -- to the best of our knowledge -- no working solution exists. To this end, in the present paper we (i) present a scalable approach to construct a spatio-temporal knowledge graph that hierarchically structures geographical as well as temporal entities, (ii) annotate a large corpus of tabular datasets from open data portals with entities from this knowledge graph, and (iii) enable structured, spatio-temporal search and querying over Open Data catalogs, both via a search interface as well as via a SPARQL endpoint, available at http://data.wu.ac.at/odgraphsearch/\n\nReview Chapter:", "role": "user" }, { "content": "There are many functioning versions of dataset search in production today. In this section, we break down the set of dataset search services that exist according to their focus and how they deal with datasets. We distinguish between the two scenarios discussed in Examples 1 and 2 and between centralized and decentralized architectures. For the latter, the search engine needs a way to discover the datasets as well as handle user queries and present results. Table 1 matches the implementations discussed to the technology described in Sect. 2. Note that at this time, we can find no examples of tabular search being used commercially. The common theme of current dataset search strategies, both on the web and within the boundaries of a repository, is the reliance on dataset publishers tagging their data with appropriate information in the correct format. Because current dataset search only uses the metadata of a dataset, it is imperative that these metadata descriptions are correct and maintained. Other, domain-specific solutions function in similar ways. Especially for scientific datasets there are initiatives aiming to support the creation of better and more unified metadata, such as for instance CEDAR by the Metadata Center 2 or 'Data in Brief' submissions supported by Elsevier. BIB001 In aid of better searches, there are several attempts at monitoring and working over data portals to provide a metaanalysis. For instance, the Open Data Portal Watch BIB003 BIB002 currently watches 254 open data portals. Once a week, the metadata from all watched portals is fetched, the quality of the metadata computed, and the site updated to allow a cohesive search across the open data. Similarly, the European Data Portal 4 harvests metadata of public sector datasets available on public data portals across European countries, in addition to educating about open data publishing.", "role": "assistant" } ]

[ { "content": "Analyze the following sentence to identify chemical entities of interest. List these entities in a JSON array format. If no entities are found, return an empty array.\n\nText to Analyze:\ng:Detailofutricle;bar=10mum.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "Analyze the provided paragraph from a scientific document. Your goal is to identify and extract relevant entities.\n\nFormat your findings as a JSON object, where each key represents a category of entities, and the corresponding value is a list of entities identified in that category. If no entities are found for a category, return an empty list.\n\nFocus on precision and ensure that the output is strictly in JSON format.\n\nDocument:\n\nCrop -to- wild gene flow and its fitness consequences for a wild fruit tree: Towards a comprehensive conservation strategy of the wild apple in Europe Crop -to- wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crab-apple fruit tree in particular, is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: (i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crab apples in agrosystems and in forests, (ii) the impact of the level of M. domestica ancestry on individual tree fitness and (iii) pollen dispersal abilities in relation to crop -to- wild gene flow. We found substantial contemporary crop -to- wild gene flow in crab-apple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4 km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programmes was found to suffer from poor genetic diversity, introgressions and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.", "role": "user" }, { "content": "{\"AnatomicalStructure\": [\"genetic\"], \"Bacterium\": [], \"BiologicFunction\": [\"gene flow\", \"fitness\", \"introgressions\", \"hybridization\", \"wild gene flow\", \"growth\"], \"BiomedicalOccupationOrDiscipline\": [], \"BodySubstance\": [], \"BodySystem\": [], \"Chemical\": [\"microsatellite markers\"], \"ClinicalAttribute\": [], \"Eukaryote\": [\"trees\", \"crab apples\", \"crop\", \"crab-apple fruit tree\", \"pollen\", \"replanting\", \"seedlings\", \"Malus domestica\", \"individual tree\", \"M. sylvestris\", \"Malus sylvestris\", \"crab-apple\", \"M. domestica\", \"Crop\", \"wild\", \"seeds\", \"wild seeds\", \"tree populations\", \"seed\", \"wild apple\", \"tree\"], \"Finding\": [], \"Food\": [\"wild fruit\"], \"HealthCareActivity\": [\"paternity analyses\"], \"InjuryOrPoisoning\": [], \"IntellectualProduct\": [\"species\"], \"MedicalDevice\": [], \"Organization\": [], \"PopulationGroup\": [], \"ProfessionalOrOccupationalGroup\": [], \"ResearchActivity\": [\"experiments\"], \"SpatialConcept\": [\"habitat\", \"Europe\", \"agrosystems\", \"European\", \"French\"], \"Virus\": []}", "role": "assistant" } ]

[ { "content": "Analyze the given paragraph from COVID-19 research. Determine the relevant topics discussed in the text. Your response should be a JSON array containing the identified topics. Ensure the output is a valid JSON array with no additional commentary.\n\nText:\n\nA large proportion of deaths worldwide have occurred among elderly living in nursing homes. Sweden is no exception with a comparable proportion making up around half of all deaths. The elderly, frail individuals living in nursing homes are among the most vulnerable and with the highest risk to die of covid-19. In spite of that we see almost two-thirds of the infected are still alive with a majority recovering fully after receiving treatment at the nursing home. Of 8 057 residents living in nursing homes in Stockholm, 1 464 (18 %) individuals have so far been diagnosed with covid-19 and 532 have died (6 % of all residents). Importantly, this means that a great majority of the residents are still alive including almost two-thirds (932/1 464) of the infected individuals.", "role": "user" }, { "content": "[\"Prevention\"]", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nSize information from the centered and oriented outlines was removed with a uniform scaling of the pseudolandmark configurations to unit centroid size (Benazzi et al., 2011a, b, 2012).", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nFree-field stimuli were simulated by filtering signals through head-related transfer functions (HRTFs) measured in one cat by Musicant et al. (1990).", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Severe heart damage has occurred in young, healthy people, but is rare. There may be more cases of mild effects of COVID-19 on the heart that can be diagnosed with special imaging tests, including in younger people with mild or minimal symptoms; however, the long-term significance of these mild effects on the heart are unknown.\n\nResearch Abstract:\nBACKGROUND: A novel coronavirus disease (COVID-19) in Wuhan has caused an outbreak and become a major public health issue in China and great concern from international community.\nMyocarditis and myocardial injury were suspected and may even be considered as one of the leading causes for death of COVID-19 patients.\nTherefore, we focused on the condition of the heart, and sought to provide firsthand evidence for whether myocarditis and myocardial injury were caused by COVID-19.\nMETHODS: We enrolled patients with confirmed diagnosis of COVID-19 retrospectively and collected heart-related clinical data, mainly including cardiac imaging findings, laboratory results and clinical outcomes.\nSerial tests of cardiac markers were traced for the analysis of potential myocardial injury/myocarditis.\nRESULTS: 112 COVID-19 patients were enrolled in our study.\nThere was evidence of myocardial injury in COVID-19 patients and 14 (12.5%) patients had presented abnormalities similar to myocarditis.\nMost of patients had normal levels of troponin at admission, that in 42 (37.5%) patients increased during hospitalization, especially in those that died.\nTroponin levels were significantly increased in the week preceding the death.\n15 (13.4%) patients have presented signs of pulmonary hypertension.\nTypical signs of myocarditis were absent on echocardiography and electrocardiogram.\nCONCLUSIONS: The clinical evidence in our study suggested that myocardial injury is more likely related to systemic consequences rather than direct damage by the 2019 novel coronavirus.\nThe elevation in cardiac markers was probably due to secondary and systemic consequences and can be considered as the warning sign for recent adverse clinical outcomes of the patients.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: In the first in a series of conversations on the science of COVID-19, we learn how the hot weather is affecting the movement of the novel coronavirus.\n\nResearch Abstract:\nThis paper investigates the correlation between the high level of coronavirus SARS-CoV-2 infection accelerated transmission and lethality, and surface air pollution in Milan metropolitan area, Lombardy region in Italy.\nFor January-April 2020 period, time series of daily average inhalable gaseous pollutants ozone (O3) and nitrogen dioxide (NO2), together climate variables (air temperature, relative humidity, wind speed, precipitation rate, atmospheric pressure field and Planetary Boundary Layer) were analyzed.\nIn spite of being considered primarily transmitted by indoor bioaerosols droplets and infected surfaces or direct human-to-human personal contacts, it seems that high levels of urban air pollution, and climate conditions have a significant impact on SARS-CoV-2 diffusion.\nExhibited positive correlations of ambient ozone levels and negative correlations of NO2 with the increased rates of COVID-19 infections (Total number, Daily New positive and Total Deaths cases), can be attributed to airborne bioaerosols distribution.\nThe results show positive correlation of daily averaged O3 with air temperature and inversely correlations with relative humidity and precipitation rates.\nViral genome contains distinctive features, including a unique N-terminal fragment within the spike protein, which allows coronavirus attachment on ambient air pollutants.\nAt this moment it is not clear if through airborne diffusion, in the presence of outdoor and indoor aerosols, this protein \"spike\" of the new COVID-19 is involved in the infectious agent transmission from a reservoir to a susceptible host during the highest nosocomial outbreak in some agglomerated industrialized urban areas like Milan is.\nAlso, in spite of collected data for cold season (winter-early spring) period, when usually ozone levels have lower values than in summer, the findings of this study support possibility as O3 can acts as a COVID-19 virus incubator.\nBeing a novel pandemic coronavirus version, it might be ongoing during summer conditions associated with higher air temperatures, low relative humidity and precipitation levels.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Popularity-Based Video Caching Techniques for Cache-Enabled Networks: A Survey \nChapter Title: I. INTRODUCTION \n1. Abstract of Cited Paper (BIB001): Driven by the visions of Internet of Things and 5G communications, recent years have seen a paradigm shift in mobile computing, from the centralized Mobile Cloud Computing towards Mobile Edge Computing (MEC). The main feature of MEC is to push mobile computing, network control and storage to the network edges (e.g., base stations and access points) so as to enable computation-intensive and latency-critical applications at the resource-limited mobile devices. MEC promises dramatic reduction in latency and mobile energy consumption, tackling the key challenges for materializing 5G vision. The promised gains of MEC have motivated extensive efforts in both academia and industry on developing the technology. A main thrust of MEC research is to seamlessly merge the two disciplines of wireless communications and mobile computing, resulting in a wide-range of new designs ranging from techniques for computation offloading to network architectures. This paper provides a comprehensive survey of the state-of-the-art MEC research with a focus on joint radio-and-computational resource management. We also present a research outlook consisting of a set of promising directions for MEC research, including MEC system deployment, cache-enabled MEC, mobility management for MEC, green MEC, as well as privacy-aware MEC. Advancements in these directions will facilitate the transformation of MEC from theory to practice. Finally, we introduce recent standardization efforts on MEC as well as some typical MEC application scenarios.\n\nReview Chapter:", "role": "user" }, { "content": "The data explosion and persistent user requests have increased pressure on the network backbone. Social media is a growing primary source of data traffic, wherein every minute users around the world post more than 500 million tweets, like ∼4.6 billion posts on Facebook, upload ∼85 million videos onto YouTube, and watch 5 billion YouTube videos. BIB001 The end-users demand ultrafast network connections, high data transfer rates, and minimal service delays. The latter influences the retention rate of website users, given that websites may lose more than half of their mobile visitors if the page takes longer than three seconds to load . The associate editor coordinating the review of this manuscript and approving it for publication was Kostas Psannis. https://socialpilot.co/blog/125-amazing-social-media-statistics-know-2016/ 2 https://fortunelords.com/youtube-statistics/ This soaring demand requires a paradigm shift towards the development of key enabling techniques for the next generation of wireless networks. In this respect, the fifth generation (5G) network promises to meet the increasing demand for online data streaming by integrating advanced technologies in a cooperative and optimal manner. This includes the development of denser small-cell base stations (SBSs) along with massive multiple-input and multiple-output deployment, beamforming, and broadcasting using millimeter waves. These technologies bring their own complexities and challenges in addition to the inconvenience when scaling up the network, because more base stations and nodes are required in the mobile packet core network BIB001 . In this regard, edge caching is a favorable method for Internet service providers (ISPs) and content providers because it is less expensive, helps to reduce the overall network traffic and does not require network modifications. Edge caching barters expensive bandwidth resources by the redundant and affordable network storage. It transfers content to nodes near the endusers in order to reduce delivery latency and bandwidth usage, lighten the load on the original server, increase the cache hit rate, and improve users quality of experience (QoE) BIB002 .", "role": "assistant" } ]

[ { "content": "Analyze the following sentence to identify chemical entities of interest. List these entities in a JSON array format. If no entities are found, return an empty array.\n\nText to Analyze:\nAbcg8/sterolin-2deficientmicealsoallowustoexaminetheroleofthisproteininbiliarysterolsecretion.", "role": "user" }, { "content": "[\"protein\", \"sterol\"]", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nSemi-supervised learning, i.e. jointly learning from labeled an unlabeled samples, is an active research topic due to its key role on relaxing human annotation constraints. In the context of image classification, recent advances to learn from unlabeled samples are mainly focused on consistency regularization methods that encourage invariant predictions for different perturbations of unlabeled samples. We, conversely, propose to learn from unlabeled data by generating soft pseudo-labels using the network predictions. We show that a naive pseudo-labeling overfits to incorrect pseudo-labels due to the so-called confirmation bias and demonstrate that label noise and mixup augmentation are effective regularization techniques for reducing it. The proposed approach achieves state-of-the-art results in CIFAR-10 100 and Mini-Imaget despite being much simpler than other state-of-the-art. These results demonstrate that pseudo-labeling can outperform consistency regularization methods, while the opposite was supposed in previous work. Source code is available at this https URL .\n\nCited Works Summary:\n[1]: Semi-supervised learning (SSL) provides a powerful framework for leveraging unlabeled data when labels are limited or expensive to obtain. SSL algorithms based on deep neural networks have recently proven successful on standard benchmark tasks. However, we argue that these benchmarks fail to address many issues that these algorithms would face in real-world applications. After creating a unified reimplementation of various widely-used SSL techniques, we test them in a suite of experiments designed to address these issues. We find that the performance of simple baselines which do not use unlabeled data is often underreported, that SSL methods differ in sensitivity to the amount of labeled and unlabeled data, and that performance can degrade substantially when the unlabeled dataset contains out-of-class examples. To help guide SSL research towards real-world applicability, we make our unified reimplemention and evaluation platform publicly available.\n\n[2]: Semi-supervised learning is becoming increasingly important because it can combine data carefully labeled by humans with abundant unlabeled data to train deep neural networks. Classic methods on semi-supervised learning that have focused on transductive learning have not been fully exploited in the inductive framework followed by modern deep learning. The same holds for the manifold assumption---that similar examples should get the same prediction. In this work, we employ a transductive label propagation method that is based on the manifold assumption to make predictions on the entire dataset and use these predictions to generate pseudo-labels for the unlabeled data and train a deep neural network. At the core of the transductive method lies a nearest neighbor graph of the dataset that we create based on the embeddings of the same network.Therefore our learning process iterates between these two steps. We improve performance on several datasets especially in the few labels regime and show that our work is complementary to current state of the art.", "role": "user" }, { "content": "Semi-supervised learning for image classification is an active research topic [1] ; this section focuses on reviewing work closely related to ours, discussing methods that use deep learning with mini-batch optimization over large image collections. Previous work on semi-supervised deep learning differ in whether they use consistency regularization or pseudo-labeling to learn from the unlabeled set [2] , while they all share the use of a cross-entropy loss (or similar) on labeled data.", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nMcCartney and Lessios (2004) found evidence that the bindin of E. lucunter (but not of E. viridis) evolves under strong selection.", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "Review the provided sections from a computer science paper and distill the primary contribution into a single sentence. Provide only the summary sentence.\n\nSections:\n\nPeople ask questions that are far richer, more informative, and more creative than current AI systems.\nWe propose a neural program generation framework for modeling human question asking, which represents questions as formal programs and generates programs with an encoder-decoder based deep neural network.\nFrom extensive experiments using an information-search game, we show that our method can ask optimal questions in synthetic settings, and predict which questions humans are likely to ask in unconstrained settings.\nWe also propose a novel grammar-based question generation framework trained with reinforcement learning, which is able to generate creative questions without supervised data.\nPeople can ask rich, creative questions to learn efficiently about their environment.\nQuestion asking is central to human learning yet it is a tremendous challenge for computational models.\nThere is always an infinite set of possible questions that one can ask, leading to challenges both in representing the space of questions and in searching for the right question to ask.\nMachine learning has been used to address aspects of this challenge.\nTraditional methods have used heuristic rules designed by humans (Heilman & Smith, 2010; Chali & Hasan, 2015) , which are usually restricted to a specific domain.\nRecently, neural network approaches have also been proposed, including retrieval methods which select the best question from past experience (Mostafazadeh et al., 2016 ) and encoder-decoder frameworks which map visual or linguistic inputs to questions (Serban et al., 2016; Mostafazadeh et al., 2016; Yuan et al., 2017; Yao et al., 2018) .\nWhile effective in some settings, these approaches do not consider settings where the questions are asked about partially unobservable states.\nBesides, these methods are heavily data-driven, limiting the diversity of generated questions and requiring large training sets for different goals and contexts.\nThere is still a large gap between how people and machines ask questions.\nRecent work has aimed to narrow this gap by taking inspiration from cognitive science.\nFor instance, Lee et al. (2018) incorporates aspects of \"theory of mind\" (Premack & Woodruff, 1978) in question asking by simulating potential answers to the questions, but the approach relies on imperfect agents for natural language understanding which may lead to error propagation.\nRelated to our approach, Rothe et al. (2017) proposed a powerful question-asking framework by modeling questions as symbolic programs, but their algorithm relies on hand-designed program features and requires expensive calculations to ask questions.\nWe use \"neural program generation\" to bridge symbolic program generation and deep neural networks, bringing together some of the best qualities of both approaches.\nSymbolic programs provide a compositional \"language of thought\" (Fodor, 1975) for creatively synthesizing which questions to ask, allowing the model to construct new ideas based on familiar building blocks.\nCompared to natural language, programs are precise in their semantics, have clearer internal structure, and require a much smaller vocabulary, making them an attractive representation for question answering systems as well (Johnson et al., 2017; Yi et al., 2018; Mao et al., 2019) .\nHowever, there has been much less work using program synthesis for question asking, which requires searching through infinitely many questions (where many questions may be informative) rather than producing a single correct answer to a question.\nDeep neural networks allow for rapid question-synthesis using encoder-decoder modeling, eliminating the need for the expensive symbolic search and feature evaluations in Rothe et al. (2017) .\nTogether, the questions can be synthesized quickly and evaluated formally for quality groundtruth board partly revealed board example questions\nHow long is the red ship?\n(size Red)\nIs purple ship horizontal?\n(== (orient Purple)\nH) Do all three ships have the same size?\n(=== (map (λ x (size x)) (set AllShips)))\nFigure 1: The Battleship task.\nBlue, red, and purple tiles are ships, dark gray tiles are water, and light gray tiles are hidden.\nThe agent can see a partly revealed board, and should ask a question to seek information about the hidden board.\nExample questions and translated programs are shown on the right.\nWe recommend viewing the figures in color.\n(e.g. the expected information gain), which as we show can be used to train question asking systems using reinforcement learning.\nIn this paper, we develop a neural program generation model for asking questions in an informationsearch game similar to \"Battleship\" used in previous work (Gureckis & Markant, 2009; Rothe et al., 2017; .\nThe model uses a convolutional encoder to represent the game state, and a Transformer decoder (Vaswani et al., 2017) for generating questions.\nBuilding on the work of Rothe et al. (2017) , the model uses a grammar-enhanced question asking framework, such that questions as programs are formed through derivation using a context free grammar.\nImportantly, we show that the model can be trained from human demonstrations of good questions using supervised learning, along with a data augmentation procedure that leverages previous work to produce additional human-like questions for training.\nOur model can also be trained without such demonstrations using reinforcement learning.\nWe evaluate the model on several aspects of human question asking, including reasoning about optimal questions in synthetic scenarios, density estimation based on free-form question asking, and creative generation of genuinely new questions.\nTo summarize, our paper makes three main contributions:\n1) We propose a neural network for modeling human question-asking behavior,\n2) We propose a novel reinforcement learning framework for generating creative human-like questions by exploiting the power of programs, and\n3) We evaluate different properties of our methods extensively through three different experiments.\nWe train our model in a fully supervised fashion.\nAccuracy for the counting and missing tile tasks is shown in Figure 3 .\nThe full neural program generation model shows strong reasoning abilities, achieving high accuracy for both the counting and missing tile tasks, respectively.\nWe also perform ablation analysis of the encoder filters of the model, and provide the results in Appendix D.\nThe results for the compositionality task are summarized in Table 1 .\nWhen no training data regarding the held out question type is provided, the model cannot generalize to situations systematically different from training data, exactly as pointed out in previous work on the compositional skills of encoder-decoder models (Lake & Baroni, 2018) .\nHowever, when the number of additional training data increases, the model quickly incorporates the new question type while maintaining high accuracy on the familiar question tasks.\nOn the last row of Table 1 , we compare our model with another version where the decoder is replaced by two linear transformation operations which directly classify the ship type and location (details in Appendix B.1).\nThis model has 33.0% transfer accuracy on compositional scenarios never seen during training.\nThis suggests that the model has the potential to generalize to unseen scenarios if the task can be decomposed to subtasks and combined together.\nWe evaluate the log-likelihood of reference questions generated by our full model as well as some lesioned variants of the full model, including a model without pretraining, a model with the Transformer decoder replaced by an LSTM decoder, a model with the convolutional encoder replaced by a simple MLP encoder, and a model that only has a decoder (unconditional language model).\nThough the method from Rothe et al. (2017) also works on this task, here we cannot compare with their method for two reasons.\nOne is that our dataset is constructed using their method, so the likelihood of their method should be an upper bound in our evaluation setting.\nAdditionally, they can only approximate the log-likelihood due to an intractable normalizing constant, and thus it difficult to directly compare with our methods.\nTwo different evaluation sets are used, one is sampled from the same process on new boards, the other is a small set of questions collected from human annotators.\nIn order to calculate the log-likelihood of human questions, we use translated versions of these questions that were used in previous work (Rothe et al., 2017) , and filtered some human questions that score poorly according to the generative model used for training the neural network (Appendix B.2).\nA summary of the results is shown in Table 2a .\nThe full model performs best on both datasets, suggesting that pretraining, the Transformer decoder, and the convolutional encoder are all important components of the approach.\nHowever, we find that the model without an encoder performs reasonably well too, even out-performing the full model with a LSTM-decoder on the human-produced questions.\nThis suggests that while contextual information from the board leads to improvements, it is not the most important factor for predicting human questions.\nTo further investigate the role of contextual information and whether or not the model can utilize it effectively, we conduct another analysis.\nIntuitively, if there is little uncertainty about the locations of the ships, observing the board is critical since there are fewer good questions to ask.\nTo examine this factor, we divide the scenarios based on the entropy of the hypothesis space of possible ship locations into a low entropy set (bottom 30%), medium entropy set (40% in the middle), and high entropy set (top 30%).\nWe evaluate different models on the split sets of sampled data and report the results in Table 2b .\nWhen the entropy is high, it is easier to ask a generally good question like \"how long is the red ship\" without information of the board, so the importance of the encoder is reduced.\nIf entropy is low, the models with access to the board has substantially higher log-likelihood than the model without encoder.\nAlso, the first experiment (section 5.1) would be impossible without an encoder.\nTogether, this implies that our model can capture important context-sensitive characteristics of how people ask questions.\nThe models are evaluated on 2000 randomly sampled boards, and the results are shown in Table 3 .\nNote that any ungrammatical questions are excluded when we calculate the number of unique questions.\nFirst, when the text-based model is evaluated on new contexts, 96.3% of the questions it generates were included in the training data.\nWe also find that the average EIG and the ratio of EIG>0 is worse than the supervised model trained on programs.\nSome of these deficiencies are due to the very limited text-based training data, but using programs instead can help overcome these limitations.\nWith the program-based framework, we can sample new boards and questions to create a much larger dataset with executable program representations.\nThis self-supervised training helps to boost performance, especially when combined with grammar-enhanced RL.\nFrom the table, the grammar-enhanced RL model is able to generate informative and creative questions.\nIt can be trained from scratch without examples of human questions, and produces many novel questions with high EIG.\nIn contrast, the supervised model rarely produces new questions beyond the training set.\nThe sequence-level RL model is also comparatively weak at generating novel questions, perhaps because it is also pre-trained on human questions.\nIt also more frequently generates ungrammatical questions.\nWe also provide examples in Figure 4 to show the diversity of questions generated by the grammar enhanced model, and more in the supplementary materials.\nFigure 4a shows novel questions the model produces, which includes clever questions such as \"Where is the bottom right of all the purple and blue tiles?\" or \"What is the size of the blue ship minus the purple ship?\", while it can also sometimes generates meaningless questions such as \"Is the blue ship shorter than itself?\"\nAdditional examples of generated questions are provided in Appendix B. Is any ship two tiles long?\n(> (++ (map (lambda x (== (size x) 2)) (set AllShips))) 0)\nAre there any ships in row 1?\n(> (++ (map (lambda y (and (== (rowL y) 1) (not (== (color y) Water)))) (set AllTiles))) 0)\nIs part of a ship on tile 4-6?\n(not (== (color 4-6)\nWater)) What is the size of the blue ship?\n(setSize (coloredTiles Blue))\nWhat is the size of the purple ship?\n(size Purple)\nWhich column is the first part of the blue ship?\n(colL (topleft (coloredTiles Blue)))\nWhat is the orientation of the blue ship?\nWith the grammar enhanced framework, we can also guide the model to ask different types of questions, consistent with the goal-directed nature and flexibility of human question asking.\nThe model can be queried for certain types of questions by providing different start conditions to the model.\nInstead of starting derivation from the start symbol \"A\", we can start derivation from a intermediate state such as \"B\" for Boolean questions or a more complicated \"(and B B)\" for composition of two Boolean questions.\nIn Figure 4b , we show examples where the model is asked to generate four specific types of questions: true/false questions, number questions, location-related questions, and compositional true/false questions.\nWe see that the model can flexibly adapt to new constraints and generate meaningful questions.\nIn Figure 4c , we compare the model generated questions with human questions, each randomlysampled from the model outputs and the human dataset.\nThese examples again demonstrate that our model is able to generate clever and human-like questions.\nHowever, we also find that people sometimes generate questions with quantifiers such as \"any\" and \"all\", which are operationalized in program form with lambda functions.\nThese questions are complicated in representation and not favored by our model, showing a current limitation in our model's capacity.\nWe introduce a neural program generation framework for question asking task under partially unobservable settings, which is able to generate creative human-like questions with human question demonstrations by supervised learning or without demonstrations by grammar-enhanced reinforcement learning.\nPrograms provide models with a \"machine language of thought\" for compositional thinking, and neural networks provide an efficient means of question generation.\nWe demonstrate the effectiveness of our method in extensive experiments covering a range of human question asking abilities.\nThe current model has important limitations.\nIt cannot generalize to systematically different scenarios, and it sometimes generates meaningless questions.\nWe plan to further explore the model's compositional abilities in future work.\nAnother promising direction is to model question asking and question answering jointly within one framework, which could guide the model to a richer sense of the question semantics.\nBesides, allowing the agent to iteratively ask questions and try to win the game is another interesting future direction.\nWe would also like to use our framework in dialog systems and open-ended question asking scenarios, allowing such systems to synthesize informative and creative questions.", "role": "user" }, { "content": "We introduce a model of human question asking that combines neural networks and symbolic programs, which can learn to generate good questions with or without supervised examples.", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nLearning robot control policies from physics simulations is of great interest to the robotics community as it may render the learning process faster, cheaper, and safer by alleviating the need for expensive real-world experiments. However, the direct transfer of learned behavior from simulation to reality is a major challenge. Optimizing a policy on a slightly faulty simulator can easily lead to the maximization of the 'Simulation Optimization Bias' (SOB). In this case, the optimizer exploits modeling errors of the simulator such that the resulting behavior can potentially damage the robot. We tackle this challenge by applying domain randomization, i.e., randomizing the parameters of the physics simulations during learning. We propose an algorithm called Simulation-based Policy Optimization with Transferability Assessment (SPOTA) which uses an estimator of the SOB to formulate a stopping criterion for training. The introduced estimator quantifies the over-fitting to the set of domains experienced while training. Our experimental results in two different environments show that the new simulation-based policy search algorithm is able to learn a control policy exclusively from a randomized simulator, which can be applied directly to real system without any additional training on the latter.\n\nCited Works Summary:\n[1]: Does optimization systematically lead to solutions that appear better than they actually turn out to be when implemented? The answer can be yes if there are errors in estimating objective function coefficients. Even if such errors are unbiased, the calculated value of the objective function for the optimal solution will, in an expected value sense, overstate that solution's true performance. This presupposes that errors in the constraint set are relatively unimportant. The existence of such a bias is shown by proof; Monte Carlo simulations of two realistic water resources optimization problems show its significance for water planners. The most important implication is that the estimated net benefits of model solutions may be exaggerated compared to existing water systems, whose performance is generally known with more accuracy.\n\n[2]: A stochastic program SP with solution value z^* can be approximately solved by sampling n realizations of the program's stochastic parameters, and by solving the resulting ''approximating problem'' for (x^*\"n,z^*\"n). We show that, in expectation, z^*\"n is a lower bound on z^* and that this bound monotonically improves as n increases. The first result is used to construct confidence intervals on the optimality gap for any candidate solution x@^ to SP, e.g., x@^=x^*\"n. A sampling procedure based on common random numbers ensures nonnegative gap estimates and provides significant variance reduction over naive sampling on four test problems.\n\n[3]: Monte Carlo methods have extensively been used and studied in the area of stochastic programming. Their convergence properties typically consider global minimizers or first-order critical points of the sample average approximation (SAA) problems and minimizers of the true problem, and show that the former converge to the latter for increasing sample size. However, the assumption of global minimization essentially restricts the scope of these results to convex problems. We review and extend these results in two directions: we allow for local SAA minimizers of possibly nonconvex problems and prove, under suitable conditions, almost sure convergence of local second-order solutions of the SAA problem to second-order critical points of the true problem. We also apply this new theory to the estimation of mixed logit models for discrete choice analysis. New useful convergence properties are derived in this context, both for the constrained and unconstrained cases, and associated estimates of the simulation bias and variance are proposed.\n\n[4]: The stochastic root-finding problem (SRFP) is that of solving a nonlinear system of equations using only a simulation that provides estimates of the functions at requested points. Equivalently, SRFPs seek locations where an unknown vector function attains a given target using only a simulation capable of providing estimates of the function. SRFPs find application in a wide variety of physical settings. We develop a family of retrospective-approximation (RA) algorithms called Bounding RA that efficiently solves a certain class of multidimensional SRFPs. During each iteration, Bounding RA generates and solves a sample-path problem by identifying a polytope of stipulated diameter, with an image that bounds the given target to within stipulated tolerance. Across iterations, the stipulations become increasingly stringent, resulting in a sequence of shrinking polytopes that approach the correct solution. Efficiency results from: (i) the RA structure, (ii) the idea of using bounding polytopes to exploit problem structure, and (iii) careful step-size and direction choice during algorithm evolution. Bounding RA has good finite-time performance that is robust with respect to the location of the initial solution, and algorithm parameter values. Empirical tests suggest that Bounding RA outperforms Simultaneous Perturbation Stochastic Approximation (SPSA), which is arguably the best-known algorithm for solving SRFPs.\n\n[5]: Determining whether a solution is of high quality (optimal or near optimal) is fundamental in optimization theory and algorithms. In this paper, we develop Monte Carlo sampling-based procedures for assessing solution quality in stochastic programs. Quality is defined via the optimality gap and our procedures' output is a confidence interval on this gap. We review a multiple-replications procedure that requires solution of, say, 30 optimization problems and then, we present a result that justifies a computationally simplified single-replication procedure that only requires solving one optimization problem. Even though the single replication procedure is computationally significantly less demanding, the resulting confidence interval might have low coverage probability for small sample sizes for some problems. We provide variants of this procedure that require two replications instead of one and that perform better empirically. We present computational results for a newsvendor problem and for two-stage stochastic linear programs from the literature. We also discuss when the procedures perform well and when they fail, and we propose using ɛ-optimal solutions to strengthen the performance of our procedures.\n\n[6]: This chapter reviews the principles of sample average approximation (SAA) for solving simulation optimization problems. We provide an accessible overview of the area and survey interesting recent developments. We explain when one might want to use SAA and when one might expect it to provide good-quality solutions. We also review some of the key theoretical properties of the solutions obtained through SAA. We contrast SAA with stochastic approximation (SA) methods in terms of the computational effort required to obtain solutions of a given quality, explaining why SA “wins” asymptotically. However, an extension of SAA known as retrospective optimization can match the asymptotic convergence rate of SA, at least up to a multiplicative constant.", "role": "user" }, { "content": "Hobbs & Hepenstal [1] proved for linear programs that optimization is optimistically biased, given that there are errors in estimating the objective function coefficients. Furthermore, they demonstrated the optimistic bias of a nonlinear program, and mentioned the effect of errors on the parameters of linear constraints. The optimization problem introduced in belongs to the class of SP for which the assumption required in [1] are guaranteed to hold. The most common approaches to solve convex SP are sample average approximation methods, including: (i) the MRP and its derivatives [2] [5] which assess a solution's quality by comparing with sampled alternative solutions, and (ii) RA [4] [6] which iteratively improved the solution by lowering the error tolerance. Bastin al [3] extended the existing convergence guarantees from convex to non-convex SP , showing almost sure convergence of the minimizers.", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\nthe association of drinking water hardness and cardiovascular diseases ( cvds ) has been studied since more than five decades ago .\na study in england and wales showed that cardiovascular death - rates had a favorable effect in towns with harder water and had an adverse effect in towns with softer water .\nanother studies showed that high levels of drinking water hardness can be protective against cvd .\nhowever , a review of ecological studies showed that the results are inconsistent between studies .\na meta - analysis revealed a negative association between concentration of magnesium in water and cvd mortality .\nmoreover , another review showed protective role of magnesium concentration in water against cvd in some case - control studies and one cohort study , but the analytical studies showed little evidence about the association of calcium and magnesium levels in drinking water and cvd risk .\nwater hardness may be also associated with cvd risk factors , for instance positive correlations of water magnesium and calcium with blood pressure is documented . in the netherlands ,\nanother study found no overall association between calcium , magnesium or total hardness and ischemic heart disease or stroke mortality .\nwater hardness may be also associated with cvd risk factors , for instance positive correlations of water magnesium and calcium with blood pressure is documented .\ncase - control and cohort studies are more useful than ecological epidemiologicalstudies for investigating cause- and - effect relationships .\nthe guidelines for drinking - water quality of the world health organization in 2011 reported that one of the case - control studies addressed the association between calcium and acute myocardial infarction and three reported the association between calcium and death from cvds .\nthe aim of this study is to investigate the association of calcium and magnesium concentration of drinking water with cvds in urban and rural areas of a city in iran .\nthis case - control study was conducted in 2012 in khansar county in isfahan province , iran .\nits area is 900 km and it includes 18 towns , 3 villages and one central city .\nwe used the official data of the provincial health center regarding the chemical analysis data of urban and rural areas including the hardness , calcium and magnesium content of drinking water .\ndata of patients hospitalized for cvd in the only specialty hospital of the city was gathered . by using the population of these areas , we calculated the relative frequency of cvd in urban and rural areas .\nwe compared the frequency and relative frequency of cvds in the population studied according to the concentrations of ca and mg hardness in drinking water in 2010 and 2011 .\nwe compared the frequency and relative frequency of cvds in the population studied according to the concentrations of ca and mg hardness in drinking water in 2010 and 2011 .\nthe findings of the study in 2010 and 2011 are reported in table 1 . in 2010 ,\nthe increase in the calcium hardness above 72 mg / l , the prevalence of cvds in 1000 population decreased [ figure 1a ] ; in 2011 this decrease in cvds was observed for calcium hardness of more than 75 mg / l [ figure 1b ] . in 2010 , the level of mg hardness in water ranged from 23 to 57 mg / l . by increasing mg hardness level above 31 mg / l in 2010 [ figure 2a ] and above 26 mg / l in 2011 [ figure 2b ] , the number of cvd in 1000 people decrease .\ncharacteristics of variables studied in 2010 and 2011 cardiovascular patients in 1000 people according to the calcium hardness in water in ( a ) 2010 and ( b ) 2011 cardiovascular patients in 1000 people according to the magnesium hardness in water in ( a ) 2010 and ( b ) 2011\nour study suggests favorable protective effects of water hardness , mainly water magnesium content , on cvds .\nseveral epidemiological studies have confirmed a negative association between water hardness and cvd among adults .\nhowever , some other studies did not confirm such relationship controversial results exist on the association of water hardness with cvd and their risk factors among the adult population .\nthe health effects of hard water are mainly considered to be because of the effects of its dissolved salts , primarily ca and mg .\nsome studies documented that the softer the water , the higher the cvd death - rates and suggested that water ca may have such protective role .\nmost previous studies showed a significant inverse association between mortality from cvd and water levels of mg , but not ca levels .\na review of the current literature reported that 10 of the 19 geographical studies published since 1979 , found a significant association , but two geographical studies from sweden , reported no association .\nmoreover , one of the six case - control studies that considered ca , found significant protective effect of high ca levels ( > 70 mg / l ) in drinking water .\nmg is a protective element against soft - tissue calcification and has a role in prevention from myocardial infarction .\nmany , but not all , of the geographical correlation , cohort and case - control studies suggested that a high mg water concentration protects against cvd mortality .\nlikewise , a recent review confirmed the protective effects of water hardness , notably its ca level against many chronic diseases including cvds . the main limitation of the current study is its cross - sectional nature , thus the associations documented in this study should be considered with caution .\nthe main limitation of the current study is its cross - sectional nature , thus the associations documented in this study should be considered with caution .\nwater hardness , as well as calcium and magnesium content of drinking water may have a protective role against cvds .\nfurther experimental studies are necessary to determine the underlying mechanisms and longitudinal studies are required to study the clinical impacts of the current findings .", "role": "user" }, { "content": "background : the aim of this study is to investigate the association of calcium and magnesium concentration of drinking water with cardiovascular disease ( cvds ) in urban and rural areas of a city in iran.methods:this case - control study was conducted in 2012 in khansar county in isfahan province , iran . \n we used the official data of the provincial health center regarding the chemical analysis data of urban and rural areas including the hardness , calcium and magnesium content of drinking water . \n data of patients hospitalized for cvd in the only specialty hospital of the city was gathered for the years of 2010 and 2011.results:in 2010 , water calcium content above 72 mg / l was associated with reduced number of cvds in 1000 population ; whereas in 2011 this decrease in cvds was observed for calcium levels of more than 75 mg / l . in 2010 , the level of water mg content ranged from 23 to 57 mg / l . by increasing mg hardness level above 31 mg / l in 2010 and above 26 mg / l in 2011 were associated with decreased number of cvds in 1000 people . \n decrease.conclusions:our study suggests favorable protective effects of water hardness , mainly water magnesium content , on cvds . \n water hardness , as well as calcium and magnesium content of drinking water may have a protective role against cvds . \n further experimental studies are necessary to determine the underlying mechanisms and longitudinal studies are required to study the clinical impacts of the current findings .", "role": "assistant" } ]

[ { "content": "Explore the following research question and associated terms. Identify the most suitable dataset from the list provided. Use the dataset descriptions to guide your choice.\n\nInquiry: The aim of this paper is to improve the recommendation accuracy of a user-based collaborative filtering\n\nKeywords: recommendation\n\nDataset Information:\nContentWise Impressions: The ContentWise Impressions dataset is a collection of implicit interactions and impressions of movies and TV series from an Over-The-Top media service, which delivers its media contents over the Internet. The dataset is distinguished from other already available multimedia recommendation datasets by the availability of impressions, i.e., the recommendations shown to the user, its size, and by being open-source.\nReDial: ReDial (Recommendation Dialogues) is an annotated dataset of dialogues, where users recommend movies to each other. The dataset consists of over 10,000 conversations centered around the theme of providing movie recommendations.\nJester: 6.5 million anonymous ratings of jokes by users of the Jester Joke Recommender System.\nCookie: The dataset is constructed from an Amazon review corpus by integrating both user-agent dialogue and custom knowledge graphs for recommendation.\n\nAvailable Datasets: A: ContentWise Impressions B: ReDial C: Jester D: Cookie", "role": "user" }, { "content": "Jester", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\ntrue metastases from solid tumors in lung , skin ( melanoma ) , gastrointestinal tract , kidney , testes , and endocrine glands are reported only in 0.2% of all surgical prostatic specimens and 2.9% of all male postmortems .\nlung is the most common primary site of metastases to the prostate . in all series direct spread of bladder carcinoma\nclinical context , morphological features , and immunohistochemical localization of prostate specific antigen ( psa ) are supposed to clarify the differential diagnosis between a secondary and a primary tumor .\nwe report an unusual and rare case of secondary signet ring cell carcinoma ( srcc ) of prostate in which the clinical data pointed toward the diagnosis of a primary srcc .\nsignet ring cell morphology was also not helpful as incidence of primary srcc was more than that of secondary srcc in prostate .\nimmunohistochemistry ( ihc ) for psa not only proved the case to be a secondary srcc but also initiated the process for diagnosis of the occult primary malignancy in the patients stomach .\na 74-year - old male patient presented with frequency of micturition , dysuria , and features of urinary outlet obstruction developing progressively over a period of last 3 months .\nhe was a smoker , occasional drinker , and complained of no other features of clinical interest except infrequent dyspepsia .\ntransrectal ultrasonography showed grade iii prostatomegaly measuring 5.54.24.8 cm ( 58 g ) , with suspicious hypoechoic areas in the peripheral zone and residual urine of 80 ml .\nserum total psa level was 9.71 ng / ml and free - to - total psa ratio was 10.8 . on digital rectal examination\nthe prostate was elastic , slightly hard , painless , and with prominent retroprostatic sulci .\ncystoscopic examination found no primary abnormality of the bladder and extensive transurethral resection of prostate ( turp ) was performed under anesthesia with resultant specimen measuring 45 g. histopathology revealed nests and singly infiltrating poorly differentiated , hyperchromatic , pleomorphic adenocarcinoma cells majority of which were of signet ring morphology [ figures 13 ] .\nindividual cells and cell nests were seen lying haphazardly among bundles of smooth muscle fibers and also within lymphovascular spaces but no perineural invasion , mucinous fibroplasia or glomerulations were noted . initial diagnosis of signet ring variant of invasive prostatic adenocarcinoma with gleason score 4 + 5=9 was thought of but ihc for psa [ figure 3 ( inset ) ] and carcinoembryonic antigen ( cea ) were simultaneously performed as primary prostatic signet ring cell adenocarcinoma is rare and it is mandatory to exclude other mucinous tumors of non - prostatic origin based on morphology and immunohistochemistry and if necessary using clinical information .\nthe globoid optically clear cytoplasm of the signet ring cells were stained positively with alcian blue at ph 2.5 confirming the contents as acid mucin [ figure 1 ( inset ) ] .\ngastric endoscopic biopsy was subsequently performed 2 weeks after turp and histopathology showed infiltrating signet ring cell carcinoma of stomach .\n( inset : same signet ring cells with positive alcian blue stain at ph 2.5 . ) signet ring cells lying haphazardly among bundles of smooth muscle fibers .\nsome primary adenocarcinomas of the prostate will have a signet - ring - cell appearance , yet the vacuoles do not contain intracytoplasmic mucin . these vacuolated cells may be present as singly invasive cells , in single glands , and in sheets . only a few cases of prostate cancer have been reported with mucin positive signet ring cells .\none should exclude other mucinous tumors of nonprostatic origin based on morphology and immunohistochemistry and if necessary using clinical information .\nimmunohistochemical stain for psa is diagnostically helpful in distinguishing prostatic adenocarcinomas from other neoplasms secondarily involving the prostate and establishing prostatic origin in metastatic carcinomas of unknown primary .\na minority of higher grade prostatic adenocarcinomas are psa negative , although some of these tumors have been shown to express psa mrna .\nsome prostatic adenocarcinomas lose psa immunoreactivity following androgen deprivation or radiation therapy . in gastric signet ring cell carcinoma ( who classification )\nmore than 50% of the tumor consists of isolated or small groups of malignant cells containing intracytoplasmic acid mucin that stain with alcian blue at ph 2.5 .\nthe present case once again underlines the fact that metastatic src carcinoma although rare should be considered as a differential before diagnosing a primary src carcinoma of prostate .\na detailed clinical examination and special attention to any prior history of mild symptoms like dyspepsia might lead to the performance of an upper gastrointestinal endoscopy which can help in much earlier detection of a primary gastric tumor .\nthe most important feature for differentiation in this case with an occult primary was psa immunostain supplemented by an alcian blue stain at ph 2.5 .\ndr . tapas moitra , associate professor , department of urology , north bengal medical college , sushrutanagar , darjeeling .", "role": "user" }, { "content": "true metastases to prostate from solid tumors are reported only in 0.2% of all surgical prostatic specimens and 2.9% of all male postmortems . \n clinical context , morphological features , and immunohistochemical localization of prostate specific antigen ( psa ) are supposed to clarify the differential diagnosis between a secondary and a primary tumor . \n we report an unusual and rare case of secondary signet ring cell carcinoma ( srcc ) of prostate in which the clinical data and signet ring cell morphology pointed toward the diagnosis of a primary srcc . \n immunohistochemistry ( ihc ) for psa not only proved the case to be a secondary srcc but also initiated the process for diagnosis of the occult primary malignancy in the patients stomach .", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: A SURVEY OF CONTENTION BASED MEDIUM ACCESS CONTROL (MAC) PROTOCOLS IN WIRELESS LAN \nChapter Title: Fig 6: Virtual Carrier Sensing Mechanism \n1. Abstract of Cited Paper (BIB001): The Carrier Sense Multiple Access with Collision Av oidance (CSMA/CA) based Medium Access Control (MAC) protocol uses a short request-to-send (RTS) and clear-to-send (CTS) contr ol packets prior of actual data packet transmission . The function of the CSMA/CA based MAC protocol in wireless communication is to facilitate wireless nodes (i.e. laptop, PC, smart p hones and etc) to access a wireless medium efficiently. Besides, it is also efficiently manage the wireless medium when more wire less nodes involving in transmission activity in the network. This protocol allows all wireless nodes in the network to commun icate between each other without collision. Since collisions may only occurr ed on the RTS control packets thus it can reduce th e actual data collision on the medium. The RTS/CTS control handshake provides bett er performance and reduce the duration of collision especially when long data packets are transmitted over wireless medium. Howev er, even though the CSMA/CA based MAC protocol work ing effectively and provides better throughput performance over single hop communication but it performance degrade signif icantly when directly applied in multihop Wireless Mesh Network (WMN). Th e reason behind this poor performance is due to the inefficient packet delivery of CSMA/CA based MAC protocol in multihop network. The exchange of RTS and CTS signaling that required at each hop throughout the multihop network eventually will cause the larg e overheads and subsequently degrade network throug hput. Therefore, in this paper, an enhancement of RTS/CTS handshake has been proposed in order reduces the signaling overheads and ultimately allows a smooth packet delivery in the multihop network with out any collision. In this work, the multihop netw ork performances are evaluated analytically in terms of throughput and overhead. I t is proven that the new method of RTS/CTS handshak e provides significant improvement in throughput and overhead.\n\nReview Chapter:", "role": "user" }, { "content": "The use of RTS/CTS control packets mechanism prevent the larger DATA packet from involve in collision. For example, if two or more nodes initiate the packet transmission at the same time, then it will lead to the collision. However, if both transmitting nodes use the RTS/CTS mechanism before the DATA packet transmission could commence, thus the collision only will be occurred among RTS control packets. Therefore, the DATA-DATA collisions can be prevented through the usage of RTS/CTS mechanism in DCF CSMA/CA protocol. The collision among the RTS and CTS control packets are acceptable in the network because their sizes are too small. Thus the bandwidth loss due to this collision is small compare to DATA-DATA collision. This approach improves the system performance by reducing the bandwidth loss BIB001 BIB002 .", "role": "assistant" } ]

[ { "content": "Analyze the given text to identify specific entities. Focus on extracting relevant data.\n\nProvide your findings in JSON format. Each category should list the entities found.\n\nText:\n\nThermochemistry of uracils. Experimental and computational enthalpies of formation of 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyluracils. We describe in the current paper an experimental and computational study of three methylated uracils, in particular, the 5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyl derivatives. The values of the standard (p(0) = 0.1 MPa) molar enthalpies of formation in the gas phase at T = 298.15 K have been determined. The energies of combustion were measured by static bomb combustion calorimetry, and from the results obtained, the standard molar enthalpies of formation in the crystalline state at T = 298.15 K were calculated. The enthalpies of sublimation were determined using the transpiration method in a saturated N(2) stream. Values of -(376.2 ± 2.6), -(355.9 ± 3.0), and -(381.7 ± 2.8) kJ·mol(-1) for the gas-phase enthalpies of formation at T = 298.15 K of 5,6-dimethyluracil, 1,3,5-trimethyluracil, and 1,3,5,6-tetramethyluracil, respectively, were obtained from the experimental thermochemical study. An extended theoretical study with the G3 and the G4 quantum-chemical methods has been carried out for all the possible methylated uracils. There is a very good agreement between experimental and calculated enthalpies of formation for the three derivatives studied. A Free-Wilson analysis on G4-calculated enthalpies of formation has been carried out, and the contribution of methylation in the different positions of the uracil ring has been estimated.", "role": "user" }, { "content": "{\"Chemical\": [\"methylated uracils\", \"1,3,5,6-tetramethyluracil\", \"1,3,5-trimethyluracil\", \"N(2)\", \"5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyluracils\", \"5,6-dimethyl-, 1,3,5-trimethyl-, and 1,3,5,6-tetramethyl\", \"uracils\", \"5,6-dimethyluracil\"]}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Network Coding Meets Multimedia: a Review \nChapter Title: B. Network Coding for P2P Live Streaming \n1. Abstract of Cited Paper (BIB001): Digital media companies have recently started embracing peer-assisted distribution networks as an alternative to traditional client-server architectures [5]. Such Peer-to-Peer (P2P) architectures ensure a fast and scalable delivery of media content. However, their drawback is that users need to often wait for the full video to be downloaded before they can start watching it. While a lot of effort has gone into optimizing the distribution of large video files using P2P swarming techniques, little research has been done on how to ensure a small start-up time and a sustainable playback rate to enable a play-asyou-download experience. In this work, we address the challenges underlying the problem of near Video-on-Demand (nVoD) using P2P swarming systems, and provide evidence that high-quality nVoD is feasible. In particular, we investigate the scheduling problem of efficiently disseminating the blocks of a video file in a P2P mesh-based system, and show that pre-fetching and network coding techniques can provide significant benefits. Our results show that, for videos which are 120 minutes in duration, 10 minutes (≈ 8% of the video’s length) of buffering at start-up can enable playback rates that are close (up to 80 − 90%) to the access link capacity, even under dynamic changes of the user population. \n2. Abstract of Cited Paper (BIB002): In recent literature, network coding has emerged as a promising information theoretic approach to improve the performance of both peer-to-peer and wireless networks. It has been widely accepted and acknowledged that network coding can theoretically improve network throughput of multicast sessions in directed acyclic graphs, achieving their cut-set capacity bounds. Recent studies have also supported the claim that network coding is beneficial for large-scale peer-to-peer content distribution, as it solves the problem of locating the last missing blocks to complete the download. We seek to perform a reality check of using network coding for peer-to-peer live multimedia streaming. We start with the following critical question: How helpful is network coding in peer-to-peer streaming? To address this question, we first implement the decoding process using Gauss-Jordan elimination, such that it can be performed while coded blocks are progressively received. We then implement a realistic testbed, called Lava, with actual network traffic to meticulously evaluate the benefits and tradeoffs involved in using network coding in peer-to-peer streaming. We present the architectural design challenges in implementing network coding for the purpose of streaming, along with a pull-based peer-to-peer live streaming protocol in our comparison studies. Our experimental results show that network coding makes it possible to perform streaming with a finer granularity, which reduces the redundancy of bandwidth usage, improves resilience to network dynamics, and is most instrumental when the bandwidth supply barely meets the streaming demand. \n3. Abstract of Cited Paper (BIB003): In recent literature, network coding has emerged as a promising information theoretic approach to improve the performance of both peer-to-peer (P2P) and wireless networks. It has been widely accepted and acknowledged that network coding can theoretically improve network throughput of multicast sessions in directed acyclic graphs, achieving their cut-set capacity bounds. Recent studies have also supported the claim that network coding is beneficial for large-scale P2P content distribution, as it solves the problem of locating the last missing blocks to complete the download. We seek to perform a reality check of using network coding for P2P live multimedia streaming. We start with the following critical question: How helpful is network coding in P2P streaming? To address this question, we first implement the decoding process using Gauss-Jordan elimination, such that it can be performed while coded blocks are progressively received. We then implement a realistic testbed, called Lava, with actual network traffic to meticulously evaluate the benefits and tradeoffs involved in using network coding in P2P streaming. We present the architectural design challenges in implementing network coding for the purpose of streaming, along with a pull-based P2P live streaming protocol in our comparison studies. Our experimental results show that network coding makes it possible to perform streaming with a finer granularity, which reduces the redundancy of bandwidth usage, improves resilience to network dynamics, and is most instrumental when the bandwidth supply barely meets the streaming demand. \n4. Abstract of Cited Paper (BIB004): In information theory, it has been shown that network coding can effectively improve the throughput of multicast communication sessions in directed acyclic graphs. More practically, random network coding is also instrumental towards improving the downloading performance in BitTorrent-like peer-to-peer content distribution sessions. Live peer-to-peer streaming, however, poses unique challenges to the use of network coding, due to its strict timing and bandwidth constraints. In this paper, we revisit the complete spectrum in the design space of live peer-to-peer streaming protocols, with a sole objective of taking full advantage of random network coding. We present R2, our new streaming algorithm designed from scratch to incorporate random network coding with a randomized push algorithm. R2 is designed to improve the performance of live streaming in terms of initial buffering delays, resilience to peer dynamics, as well as reduced bandwidth costs on dedicated streaming servers, all of which are beyond the basic requirement of stable streaming playback. On an experimental testbed consisting of dozens of dual-CPU cluster servers, we thoroughly evaluate R2 with an actual implementation, real network traffic, and emulated peer upload capacities, in comparisons with a typical live streaming protocol (both without and with network coding), representing the current state-of-the-art in real-world streaming applications. \n5. Abstract of Cited Paper (BIB005): A key challenge faced by peer-to-peer (P2P) video-on-demand (VoD) systems is their ability, or lack thereof, to provide DVD-like functionality, such as pause, forward and backward seeking (or jumps). Such operations can significantly degrade the performance of a P2P system as arbitrary video segmentsmay need to be served timely on demand. Currently, little is known of the impact that these operations can have on the swarm efficiency, user experience and server load. In this paper, we design and implement a novel P2P system called Kangaroo, which supports DVD-like jumps. Using a carefully designed peer topology management, hybrid block scheduling algorithms, and a smart tracker, Kangaroo provides low buffering times and high swarming throughput under jump operations, without the need for overly provisioned peers or server. We experimentally evaluate the performance of the system using live VoD traces captured from a large commercial IPTV network. \n6. Abstract of Cited Paper (BIB006): Video-on-demand (VoD) service on the Internet has been surprisingly popular during these years. And it is being greatly enhanced by the emergence and maturation of both the peer-to-peer (P2P) schema and network coding (NC) technology. P2P-based solution can make VoD systems obtain high scalability. The introduction of network coding improves the content distributing efficiency of the system. Meanwhile, digital video cassette recording (VCR) functionality provides users more freedom to choose playback mode while viewing video-clips. Designed a video segmentation-aided VCR support for P2P VoD system without network coding; and in ,we designed a P2P VoD system with scene-segmentation and network coding, which is called SonicVoD. In this paper, we will place our detailed design for SonicVoD and introduce some extensions for it. \n7. Abstract of Cited Paper (BIB007): Since the inception of network coding in information theory, we have witnessed a sharp increase of research interest in its applications in communications and networking, where the focus has been on more practical aspects. However, thus far, network coding has not been deployed in real-world commercial systems in operation at a large scale, and in a production setting. In this paper, we present the objectives, rationale, and design in the first production deployment of random network coding, where it has been used in the past year as the cornerstone of a large-scale production on-demand streaming system, operated by UUSee Inc., delivering thousands of on-demand video channels to millions of unique visitors each month. To achieve a thorough understanding of the performance of network coding, we have collected 200 Gigabytes worth of real-world traces throughout the 17-day Summer Olympic Games in August 2008, and present our lessons learned after an in-depth trace-driven analysis.\n\nReview Chapter:", "role": "user" }, { "content": "NC has been one of the key enabling technologies that marks a significant design shift in P2P multimedia streaming. The highly visible Avalanche project has demonstrated the first practical use of NC in P2P file sharing systems. It showed that all pieces of information are treated equally with NC. Without the need to identify and distribute the \"rarest piece\" first, the control protocols are greatly simplified since the need for data reconciliation is eliminated. The simplified protocol along with the coded data swarming concept lead to a faster download rate with a minimal coding operation overhead. It has been shown that the performance benefits provided by NC correspond to a 2-3 times higher throughput compared to a system that does not use NC at all . In addition, the residual bandwidth at peers can be utilized to transmit small encoded blocks. Due to the great performance gain brought by NC in P2P file sharing systems, network researchers and developers are extending its application to P2P live multimedia streaming systems. The benefits and trade-offs of NC in P2P live streaming have been studied in BIB003 , BIB004 . These studies shows that the use of NC leads to better bandwidth utilization and better resiliency to network dynamics. Furthermore, under limited bandwidth, NC-enabled streaming systems offer better performance than conventional streaming systems do. We analyze now in more details the benefits of NC in P2P live streaming. With NC, video segments are divided into blocks and then encoded, as shown in Figure 6 . Peers exchange small coded blocks rather than the large raw segments. Hence, a peer may download coded blocks of a segment from multiple seeds simultaneously without using any protocol to coordinate the seeds. Once a peer completely decodes the segment, it informs all its seeds by sending short messages to terminate the transmission of the segment. Without using NC, a peer has to explicitly request individual segments from the seeds. As mentioned in Section III, the delay introduced by NC operations can increase the delivery time of video segments, which is critical in multimedia streaming sessions. In order to minimize this overhead, progressive decoding has been introduced in BIB003 , BIB004 . With progressive decoding, as illustrated in Figure 7 , a peer can start decoding as soon as the first coded block is received. Then, it progressively decodes the new coded blocks as soon as they are received. In this process, the decoding time overlaps with the time required to receive the coded blocks, thus mitigating the coding delay within the transmission time of a segment. The application of NC fundamentally changes the way segments are shared among peers, and the uniform importance of each coded block within a segment greatly simplifies the data reconciliation process. A peer no longer relies on a single seed for a given segment. It can simultaneously receive different blocks of a segment from multiple seeds. Consequently, the system is more resilient to network dynamics since the departure of one seed only affects a small portion of a segment, which can be quickly recovered with data from other seeds. The delivery of small coded blocks also makes good use of upload capacity, even for peers with very small residual upload capacity. This effectively leads to faster delivery of segments and better playback quality. These fundamental changes encourage a re-design of the P2P live streaming system to take full advantage of NC. To this end, the authors in BIB005 have redesigned the P2P streaming protocol, R 2 , which incorporates random NC with a randomized push algorithm. Unlike the \"static\" push-based design using predetermined trees in BIB001 , a peer in R 2 randomly chooses a downstream peer and pushes coded blocks for a segment that is found missing without the need for any explicit request. We finally note that the R 2 design has been adapted by UUSee BIB008 , hence it represents the first real-world deployment of NC. C. Network coding for P2P Video-on-Demand Video-on-Demand (VoD) is a special case of live streaming, where the constraint of synchronized playback among peers is relaxed. VoD users enjoy the flexibility of watching arbitrary video segments at any time, including DVD-like playback operations: play, pause, chapter selection, fast forward, and rewind. P2P VoD has been widely deployed BIB008 , [50] , BIB006 , [68] , but it has received less attention in the research community compared to P2P live streaming services. Many works have focused on the ability to support asynchronous playback but not the full set of VCR/DVD-like features. RedCarpet BIB002 is the first work incorporating NC into a P2P VoD system that achieves a better playback quality with a simple protocol. Annapureddy et al. have then addressed the challenge of providing VoD using P2P mesh-based network. They have also shown that it is possible to provide high quality VoD using an algorithm combining NC, optimized resource allocation and overlay topology management. SonicVoD BIB007 and UUSee BIB008 are the two latest implementations of NC in real P2P streaming applications. Measurements from UUSee BIB008 confirm that NC can significantly reduce the initial delay and server bandwidth cost in the streaming architecture. They also show that, when multiple seeds proactively push coded blocks to neighbouring peers, more blocks than necessary for decoding may be transmitted, resulting in a waste of resources. This calls for an early breaking mechanism, proposed in BIB008 , so that a peer can effectively stop the seeds from sending coded blocks when it is about to receive sufficiently many blocks for decoding. Despite the success of NC, the performance gain provided by NC has yet to be quantified. SonicVoD BIB007 has provided a comparison study to this end, but the evaluation results are questionable. NC enabled VoD applications cannot achieve smooth playback until the bandwidth provision is equvalent to at least twice the streaming rate, and the baseline VoD applications can never achieve smooth playback. In reality, the streaming protocol cannot be that inefficient in its bandwidth utilization. Therefore, the comparison results are yet to be confirmed. More in-depth work on NC for P2P VoD is to be performed.", "role": "assistant" } ]

[ { "content": "Explore the following research question and associated terms. Identify the most suitable dataset from the list provided. Use the dataset descriptions to guide your choice.\n\nInquiry: I'm trying to build a model for head and body pose estimation.\n\nKeywords: head body pose estimation video\n\nDataset Information:\nSALSA: A novel dataset facilitating multimodal and Synergetic sociAL Scene Analysis.\nPoseTrack: The PoseTrack dataset is a large-scale benchmark for multi-person pose estimation and tracking in videos. It requires not only pose estimation in single frames, but also temporal tracking across frames.\nMSRC-12: The Microsoft Research Cambridge-12 Kinect gesture data set consists of sequences of human movements, represented as body-part locations, and the associated gesture to be recognized by the system. The data set includes 594 sequences and 719,359 frames—approximately six hours and 40 minutes—collected from 30 people performing 12 gestures.\nCOCO-WholeBody: COCO-WholeBody is an extension of COCO dataset with whole-body annotations. There are 4 types of bounding boxes (person box, face box, left-hand box, and right-hand box) and 133 keypoints (17 for body, 6 for feet, 68 for face and 42 for hands) annotations for each person in the image.\n\nAvailable Datasets: A: SALSA B: PoseTrack C: MSRC-12 D: COCO-WholeBody", "role": "user" }, { "content": "SALSA", "role": "assistant" } ]

[ { "content": "Analyze the following sentence to identify chemical entities of interest. List these entities in a JSON array format. If no entities are found, return an empty array.\n\nText to Analyze:\n(f)darkfielddoublefilterexposureofanE10chimera.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "Analyze the following sentence to identify chemical entities of interest. List these entities in a JSON array format. If no entities are found, return an empty array.\n\nText to Analyze:\n60xmagnification.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "Analyze the given text to identify specific entities. Focus on extracting relevant data.\n\nProvide your findings in JSON format. Each category should list the entities found.\n\nText:\n\nSyntheses and in vitro evaluations of uncharged reactivators for human acetylcholinesterase inhibited by organophosphorus nerve agents. Organophosphorus nerve agents (OPNAs) are highly toxic compounds that represent a threat to both military and civilian populations. They cause an irreversible inhibition of acetylcholinesterase (AChE), by the formation of a covalent P-O bond with the catalytic serine. Among the present treatment of nerve agents poisoning, pyridinium and bis-pyridinium aldoximes are used to reactivate this inhibited enzyme but these compounds do not readily cross the blood brain barrier (BBB) due to their permanent cationic charge and thus cannot efficiently reactivate cholinesterases in the central nervous system (CNS). In this study, a series of seven new uncharged oximes reactivators have been synthesized and their in vitro ability to reactivate VX and tabun-inhibited human acetylcholinesterase (hAChE) has been evaluated. The dissociation constant KD of inhibited enzyme-oxime complex, the reactivity rate constant kr and the second order reactivation rate constant kr2 have been determined and have been compared to reference oximes HI-6, Obidoxime and 2-Pralidoxime (2-PAM). Regarding the reactivation of VX-inhibited hAChE, all compounds show a better reactivation potency than those of 2-PAM, nevertheless they are less efficient than obidoxime and HI-6. Moreover, one of seven described compounds presents an ability to reactivate tabun-inhibited hAChE equivalent to those of 2-PAM.", "role": "user" }, { "content": "{\"Chemical\": [\"HI-6\", \"organophosphorus\", \"Obidoxime\", \"2-Pralidoxime\", \"Organophosphorus\", \"2-PAM\", \"oximes\", \"P-O\", \"tabun\", \"serine\", \"pyridinium and bis-pyridinium aldoximes\", \"obidoxime\", \"oxime\"]}", "role": "assistant" } ]

[ { "content": "Examine the provided text and determine the interactions between chemical entities and genes. Focus on identifying any connections present.\n\nPresent your findings in a structured JSON format. Each relationship should be represented as an array entry. If no interactions are detected, return an empty array.\n\nText Content:\n\nThe mannose 6-phosphate-binding sites of M6P/IGF2R determine its capacity to suppress matrix invasion by squamous cell carcinoma cells. The M6P (mannose 6-phosphate) /IGF2R (insulin-like growth factor II receptor) interacts with a variety of factors that impinge on tumour invasion and metastasis. It has been shown that expression of wild-type M6P/IGF2R reduces the tumorigenic and invasive properties of receptor-deficient SCC-VII squamous cell carcinoma cells. We have now used mutant forms of M6P/IGF2R to assess the relevance of the different ligand-binding sites of the receptor for its biological activities in this cellular system. The results of the present study demonstrate that M6P/IGF2R does not require a functional binding site for insulin-like growth factor II for inhibition of anchorage-independent growth and matrix invasion by SCC-VII cells. In contrast, the simultaneous mutation of both M6P-binding sites is sufficient to impair all cellular functions of the receptor tested. These findings highlight that the interaction between M6P/IGF2R and M6P-modified ligands is not only important for intracellular accumulation of lysosomal enzymes and formation of dense lysosomes, but is also crucial for the ability of the receptor to suppress SCC-VII growth and invasion. The present study also shows that some of the biological activities of M6P/IGF2R in SCC-VII cells strongly depend on a functional M6P-binding site within domain 3, thus providing further evidence for the non-redundant cellular functions of the individual carbohydrate-binding domains of the receptor.", "role": "user" }, { "content": "[[\"M6P\", \"PART-OF\", \"insulin-like growth factor II receptor\"]]", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: At the moment, [social distancing is] the only tool available to fight the spread of the coronavirus\n\nResearch Abstract:\nThe Australian and New Zealand governments both initiated strict social distancing measures in response to the COVID-19 pandemic in late March.\nIt remains difficult to quantify the impact this had in reducing the spread of the virus.\nBayesian structural time series model provide a model to quantify the scenario in which these government-level interventions were not placed.\nOur models predict these strict social distancing measures caused a 79% and 61% reduction in the daily cases of COVID-19 across Australia and New Zealand respectively.\nThis provides both evidence and impetus for governments considering similar measures in response to COVID-19 and other pandemics.", "role": "user" }, { "content": "{\"verdict\": \"CONTRADICT\", \"evidence\": [\"Our models predict these strict social distancing measures caused a 79% and 61% reduction in the daily cases of COVID-19 across Australia and New Zealand respectively.\", \"This provides both evidence and impetus for governments considering similar measures in response to COVID-19 and other pandemics.\"]}", "role": "assistant" } ]

[ { "content": "Examine the provided text and determine the interactions between chemical entities and genes. Focus on identifying any connections present.\n\nPresent your findings in a structured JSON format. Each relationship should be represented as an array entry. If no interactions are detected, return an empty array.\n\nText Content:\n\nEffect of water extracts from edible myrtaceae plants on uptake of 2- (n- (7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino) -2-deoxyglucose in TNF-α-treated FL83B mouse hepatocytes. This study investigated the glucose uptake activity of the water extracts from the leaves and fruit of edible Myrtaceae plants, including guava (Psidium guajava Linn.), wax apples [ Syzygium samarangense (Blume) Merr. and L.M. Perry ], Pu-Tau [ Syzygium jambo (L.) Alston ], and Kan-Shi Pu-Tau (Syzygium cumini Linn.) in FL83B mouse hepatocytes. The fluorescent dye 2- (n- (7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino) -2-deoxyglucose was used to estimate the uptake ability of the cells. Glucose uptake test showed that pink wax apple fruit extract (PWFE) exhibits the highest glucose uptake activity, at an increment of 21% in the insulin-resistant FL83B mouse hepatocytes as compared with the TNF-α-treated control group. Vescalagin was isolated using column chromatography of PWFE. This compound, at the concentration of 6.25   µg/mL, exhibits the same glucose uptake improvement in insulin-resistant cells as PWFE at a 100-µg/mL dose. We postulate that vescalagin is an active component in PWFE that may alleviate the insulin resistance in mouse hepatocytes.", "role": "user" }, { "content": "[[\"vescalagin\", \"INDIRECT-REGULATOR\", \"insulin\"]]", "role": "assistant" } ]

[ { "content": "Transform the following sections from a biomedical study into a simple summary for the general public. Focus on making the information accessible and easy to understand.\n\nResearch Heading: Associative Mechanisms Allow for Social Learning and Cultural Transmission of String Pulling in an Insect\nContent:\nAbstract:\nSocial insects make elaborate use of simple mechanisms to achieve seemingly complex behavior and may thus provide a unique resource to discover the basic cognitive elements required for culture, i. e., group-specific behaviors that spread from “innovators” to others in the group via social learning. We first explored whether bumblebees can learn a nonnatural object manipulation task by using string pulling to access a reward that was presented out of reach. Only a small minority “innovated” and solved the task spontaneously, but most bees were able to learn to pull a string when trained in a stepwise manner. In addition, naïve bees learnt the task by observing a trained demonstrator from a distance. Learning the behavior relied on a combination of simple associative mechanisms and trial-and-error learning and did not require “insight”: naïve bees failed a “coiled-string experiment, ” in which they did not receive instant visual feedback of the target moving closer when tugging on the string. In cultural diffusion experiments, the skill spread rapidly from a single knowledgeable individual to the majority of a colony’s foragers. We observed that there were several sequential sets( “generations”) of learners, so that previously naïve observers could first acquire the technique by interacting with skilled individuals and, subsequently, themselves become demonstrators for the next “generation” of learners, so that the longevity of the skill in the population could outlast the lives of informed foragers. This suggests that, so long as animals have a basic toolkit of associative and motor learning processes, the key ingredients for the cultural spread of unusual skills are already in place and do not require sophisticated cognition.\nIntroduction:\nSocial learning is widespread in animals[1, 2] and can enable novel behavior routines, sometimes introduced by a single “innovator, ” to spread among individuals in a group[1–5]. Examples are potato washing and termite fishing in primates, pinecone stripping in rodents and milk bottle opening in birds[6–10]. Such phenomena in animals have received considerable attention because researchers hoped to discover the key evolutionary ingredients of the cultural processes that define us as humans[11–13]. Social learning can lead to group-specific behavior patterns that are shared by a large number of animals in an area[13–15]. Two key components of culture-like phenomena in animals include spreading of a new behavior via social learning as well as persistence of the behavior in groups for extended periods of time[5, 12, 14, 16, 17]. Individuals that picked up the information from the initial demonstrator( s) can themselves become demonstrators to uninformed individuals[18], a process by which such group-specific phenomena can, at least in principle, persist across many generations[5, 19]. In some cases, culture-like phenomena such as beach hunting in killer whales( Orcinus orca)[17] and lexigram communication in bonobos( Pan paniscus)[20] require relatively sophisticated learning mechanisms, for example imitation and/or teaching[21–23]. In insects, seemingly complex processes of social information acquisition, for example the gradual consensus building that occurs when honeybee swarms decide on new nesting locations[24], can sometimes instead be mediated by relatively simple learning mechanisms[25, 26], suggesting that cultural processes may not necessarily require sophisticated learning abilities[27–29]. The spread of novel foraging techniques by means of a formal transmission chain experiment[5], in which an experimentally induced innovation is seeded into a group and the subsequent spread is monitored in a social network analysis, has never been explored in an insect. We suggest that doing so provides a unique opportunity for the exploration of the basic cognitive elements required for culture[18, 30]. A variety of impressive cognitive skills in social bees has been described, such as object categorization, simple spatial concepts, and numerosity, as well as social learning skills by which bees can acquire information about valuable food sources by observing conspecifics[25, 26, 31–33]. Scholars in comparative cognition have advocated testing animal intelligence by exploring the flexibility and innovative skills in solving tasks that are relatively remote from the animal’s natural behavior[34, 35]. Here, we explore whether bumblebees( Bombus terrestris) have the capacity to learn a string pulling task[36]. We also test whether naïve observers can acquire this technique through observation of trained demonstrators, as occurs in naturally widespread foraging techniques[37, 38]. Finally, we explore whether and how swiftly such an experimentally introduced innovation can spread through a bumblebee colony. To do this, we used an “open group diffusion” paradigm( forager pairings were not determined by the experimenter)[39] to determine whether diffusion( or transmission) chains that begin with a trained bee follow a sequence in which observers successively become models for a subsequent observer in the chain[5].\nDiscussion:\nHere, we show that an invertebrate can be trained to solve a string pulling task, and that a minority can even solve such a task without stepwise training or observation of skilled demonstrators. String pulling is a popular problem-solving paradigm to investigate cognitive abilities in vertebrates[45], in part because scientists in comparative cognition have been interested in exploring the limits of animal intelligence and behavioral flexibility by facing subjects with tasks that are outside their natural repertoires[35, 36]. Although there are natural analogues to many standard laboratory tests in animal cognition, string pulling is indeed relatively remote from most animal’s daily behavioral routines. There is no question that many animals regularly pull objects( including bees—e. g., to remove debris or corpses from their nests), but, specifically, the act of object pulling with the purpose of obtaining a food reward, and the learning of such techniques, is not commonly observed in many animals’ daily lives. As one aspect of exploring animal intelligence, string pulling tasks have been used to test the understanding of means–end relationship: the capacity to mentally model the string as a means to reach an end( the reward) and to understand the connection between the string and the reward. However, most animals appear instead to use perceptual feedback to solve string tasks[45]. Our results indicate that bees may not be different from birds, dogs, or apes in this respect. Bumblebees relied on the perceptual feedback provided by their actions, resulting in target movement to learn string pulling, and failed, for example, in an experiment in which the string was coiled, and therefore tugging on it did not result in immediate feedback. However, through experience, bees eventually learnt to associate the string with the reward and solved the task without the need for feedback. Nonetheless, this would not allow bees to solve tasks requiring means–end understanding such as the discrimination of connected and disconnected strings. More than a century of research in social learning in animals has revealed a plethora of evidence that animals, from primates and cetaceans to birds and fish, can acquire novel skills by observing the actions of others[1, 3, 5, 6, 30, 51]. Growing evidence also shows that insects can glean critical information about their environment by observing others[52–54]. Here, we show that uninformed bumblebees can learn a novel and highly unnatural foraging technique, string pulling, by observation. To this end, our bees used a combination of simple forms of learning. Consistent with a previous study[55], during observation, bees were able to pick up the location of a new access to the reward( local enhancement of flower position). In addition, we showed that the observers were attracted to the string( stimulus enhancement). A recent study showed that learning about rewarding flowers from conspecifics resulted in stimulus enhancement, whilst learning from nonsocial or model demonstrators resulted in local enhancement[46]. In contrast, our results suggest that observers can use both forms of information independently of the cue type. In addition, the results of the coiled-string experiment also indicate that trial-and-error learning was involved in learning the technique. That is, when observing the demonstrations, the observers did not learn the specific sequence of actions used by the demonstrator with the string but simply knew to go to the correct location where the string was accessible. They had to learn the technique of how to move the target( blue flower) closer by individual exploration. These results suggest that the combination of relatively simple forms of social learning and trial-and-error learning can mediate the social learning of novel skills[19, 29, 56]. In this sense, our study adds to the growing evidence that simple principles of “asocial” associative learning can also account for many aspects of social learning[29, 53]. For instance, observational learning about flower colors in bumblebees can emerge through the simple Pavlovian ability to integrate two learned associations( second-order conditioning)[28]. This mechanism has more commonly been explored in nonsocial learning and is also common to social and solitary species[28, 57]. Moreover, social learning ability and asocial learning ability covary across and within species[57]. Overall, this suggests that social and asocial learning are mediated by the same “generic” mechanism[29, 57]. The use of generic mechanisms in learning generates the possibility to combine different forms of learning, allowing bees to use local as well as stimulus enhancement and trial-and-error learning to learn string pulling by observation. Even if social and asocial learning rely on common associative learning mechanisms, the sensory filters that allow animals to recognize conspecifics can guide attention of observers to valuable resources[58]. This may explain why observer bees were not able to solve the task in the “ghost experiment. ” Without the presence of a visible demonstrator, the motivation or the attention paid by the observer to the flower movement and the string may not have been sufficient to learn the critical information required to solve the string task[57], or, indeed, bees may not have paid attention to the action of the moving flower. Consistent with this, a recent report on learning in bees suggested that the specific attention directed to mobile salient cues provided by conspecifics could explain the dissociation of social and asocial learning[53]. The spread of novel foraging techniques has often been viewed as evidence that animals have the basic cognitive tools needed for cultural transmission of skills[34, 41, 59]. From an evolutionary perspective, culture should allow for the passing along of advantageous information through generations of learners. Here, we show that a novel, experimentally seeded foraging technique can spread through social learning by observation in bee populations. Moreover, we report that the novel routine persisted in the population for longer than the original knowledgeable individual served as a demonstrator, so that successive learning “generations” became demonstrators. Though these sequential sets of learners are not true biological generations, these results indicate that, just as in birds[60] and mammals[61], an experimentally introduced innovative behavior can spread via cultural transmission in social insect groups and potentially be retained over long periods. Together with recent work documenting social learning in fruit flies[62], our results suggest that insects possess the essential cognitive elements for cultural transmission. It may be asked what the natural relevance of our findings is, or whether there is likely to be a natural analogue of the cultural transmission of a unique foraging routine as we have described in bumblebees. This may be unlikely to be the case, but our results indicate that this is a question of opportunity rather than a question of whether or not bumblebees have the cognitive toolkit to exhibit culture-like processes. We found that when the appropriate social and ecological conditions are present, culture can be mediated by the use of a combination of simple forms of learning[28, 63]. Thus, cultural transmission does not require the high cognitive sophistication specific to humans, nor is it a distinctive feature of humans. It may well be that the absence of such cultural transmission phenomena in bees and other animals in the wild simply reflects the absence of natural opportunities. For example, the spread of the milk bottle opening “culture” in some British songbirds in the 20th century only arose because humans created a “niche” for the behavioral spread of this technique to become useful( by depositing accessible milk bottles on doorsteps of households hours before they were collected)[6]. If a majority of United Kingdom households presented artificial flowers that require unusual manipulation techniques to pollinators, especially at times of dearth, it is equally conceivable that these manipulation techniques would spread socially through pollinator populations. If nature presented such challenges, and if bee foraging activities were not discontinued during winter months, it is clear from our work that bees have the learning capacities to affect long-term, group-specific behavior patterns. More sophisticated forms of social learning and cognitive mechanisms specific to human culture may well have evolved from simpler forms of learning and cognition as described here. Human culture exhibits unparalleled complexity and diversity, and is unambiguously cumulative in character[21, 64]. The combination of high-fidelity transmission( e. g., via imitation, teaching, language) of beneficial modifications of cultural knowledge with the ability to identify “who knows” these modifications with greater accuracy and precision by metacognitive representation promotes cumulative culture in humans[63]. Despite the obvious differences between humans and other animals, understanding social learning and culture in animals holds a key to understanding the evolutionary roots of the peculiarities of social learning and culture in humans. It is clear from our study and others on cultural diffusion in animals that once experimenters create the conditions under which such diffusion is beneficial( often via allowing access to desirable nutrition via man-made devices that must be operated in specific ways), they can be instantly observed in many animals. Early tool-using hominids are likely to have created the conditions for themselves that favored the further evolutionary fine-tuning of social learning processes that results in high-fidelity transmission and cumulative culture[21, 64]. Our findings add to the accumulating evidence suggesting that the capacity of culture may be within most animals with a relatively basic toolkit of learning processes as described here, in turn shedding light on the evolutionary precursors of the more sophisticated forms of culture in humans.", "role": "user" }, { "content": "Social insects make use of simple mechanisms to achieve many seemingly complex behaviors and thus may be able to provide a unique resource for uncovering the basic cognitive elements required for culture . Here , we first show that bumblebees can be trained to pull a string to access a reward , but most could not learn on their own . Naïve bees learned how to pull strings by observing trained demonstrators from a distance . Learning the behavior through observation relied on bees paying attention to both the string and the position of the trained demonstrator bee while pulling the string . We then tested whether bees could pass this information to others during a semi-natural situation involving several colonies . We found that once one bee knew how to string pull , over time , most of the foraging bees learned from the initially trained bee or from bees who had learned from the trained bee , even after the initial demonstrator was no longer available . These results suggest that learning a nonnatural task in bumblebees can spread culturally through populations .", "role": "assistant" } ]

[ { "content": "Examine the text below and extract disease-related entities. Present your findings in a structured JSON format.\n\nYour response should be a JSON object with keys as entity types and values as lists of entities. If no entities are found, return an empty list for that type.\n\nContent:\n\nSpontaneous reversion of novel Lesch-Nyhan mutation by HPRT gene rearrangement. Molecular analysis of an unusual patient with the Lesch-Nyhan syndrome has suggested that the mutation is due to a partial HPRT gene duplication. We now report the cloning and sequencing of the mutant HPRT cDNA which shows the precise duplication of exons 2 and 3. This mutation is the result of an internal duplication of 16-20 kilobases of the gene. The structure of the mutant gene suggests that the duplication was not generated by a single unequal crossing-over event between two normal HPRT alleles. Growth of Epstein-Barr virus-transformed lymphoblasts from this patient in selective medium has permitted isolation of spontaneous HPRT + revertants of this mutation. The reversion event involves a second major HPRT gene rearrangement where most or all of the duplicated portion of the mutant gene is deleted. The original mutation therefore has the potential for spontaneous somatic reversion. This may explain the relatively mild symptoms of the Lesch-Nyhan syndrome exhibited by this patient..", "role": "user" }, { "content": "{\"Disease\": [\"Epstein-Barr\", \"Lesch-Nyhan syndrome\", \"Lesch-Nyhan\"]}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Viruses, like the novel coronavirus, may also aggravate preexisting diabetic systems leading to added challenges managing blood sugar levels and worse outcomes.\n\nResearch Abstract:\nObjective: To undertake a review and critical appraisal of published/preprint reports that offer methods of determining the effects of hypertension, diabetes, stroke, cancer, kidney issues, and high-cholesterol on COVID-19 disease severity.\nData sources: Google Scholar, PubMed, COVID-19 Open Research Dataset: a resource of over 128,000 scholarly articles, including over 59,000 articles with full text related to COVID-19, SARS-CoV-2, and coronaviruses.\nMethods: A search was conducted by two authors independently on the freely available COVID-19 Open Research Dataset (CORD-19).\nWe developed an automated search engine to screen a total of 59,000 articles in a few seconds.\nThe search engine was built using a retrieval function that ranks a set of documents based on the query terms appearing in each document regardless of their proximity within the document.\nFiltering of the articles was then undertaken using keywords and questions, e.g. \"Effects of diabetes on COVID/normal coronavirus/SARS-CoV-2/nCoV/COVID-19 disease severity, mortality?\".\nThe search terms were repeated for all the comorbidities considered in this paper.\nAdditional articles were retrieved by searching via Google Scholar and PubMed.\nFindings: A total of 54 articles were considered for a full review.\nIt was observed that diabetes, hypertension, and cholesterol levels possess an apparent relation to COVID-19 severity.\nOther comorbidities, such as cancer, kidney disease, and stroke, must be further evaluated to determine a strong relationship to the virus.\nReports associating cancer, kidney disease, and stroke with COVID-19 should be carefully interpreted, not only because of the size of the samples, but also because patients could be old, have a history of smoking, or have any other clinical condition suggesting that these factors might be associated with the poor COVID-19 outcomes rather than the comorbidity itself.\nSuch reports could lead many oncologists and physicians to change their treatment strategies without solid evidence and recommendations.\nFurther research regarding this relationship and its clinical management is warranted.\nAdditionally, treatment options must be examined further to provide optimal treatment and ensure better outcomes for patients suffering from these comorbidities.\nIt should be noted that, whether definitive measurements exist or not, the care of patients as well as the research involved should be largely prioritized to tackle this deadly pandemic.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Analyze the following sentence to identify chemical entities of interest. List these entities in a JSON array format. If no entities are found, return an empty array.\n\nText to Analyze:\nThemeanplateletcountsfromwildtypeandanxA7-/-mutantmicearedeterminedas674x103/muland774x103/mul,respectively.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "Analyze the following excerpt from a biomedical text. Identify the relevant information needed to respond to the inquiry. Provide only the necessary details in your answer.\n\nContext: The models suggested that without a vaccine, school closures would be unlikely to affect the pandemic, an estimated 35 000 to 60 000 ventilators would be needed, up to an estimated 7.3 billion surgical masks or respirators would be required, and perhaps most important, if vaccine development did not start before the virus was introduced, it was unlikely that a significant number of hospitalizations and deaths could be averted due to the time it takes to develop, test, manufacture, and distribute a vaccine. It is impossible to know what will happen so early in this novel 2019 coronavirus (2019-nCoV) epidemic. The scope, morbidity, and mortality will depend on the combination of severity and transmissibility. Numerous experts have “nowcasted” how many cases have occurred and forecasted how many cases will likely occur. A recent study suggests rapid person to person transmission can occur.8 Disease modelers have estimated R0 to be 2.2.9 The University of Hong Kong estimates the outbreak could infect more than 150 000 persons per day in China at its peak. Is 2019-nCoV infection severe? To date approximately 14% of cases of 2019-nCoV have been described as severe by WHO, with a case-fatality rate of 2.1%.10 Estimates of severity are usually higher in the beginning of an epidemic due to the identification of the most severely affected cases and decline as the epidemic progresses. However, because many infected persons have not yet recovered and may still die, the case-fatality rate and severity could be underestimated. On January 30, 2020, WHO officially declared the 2019-nCoV epidemic as a Public Health Emergency of International Concern, indicating its concern that countries aside from China could be affected by 2019-nCoV. In preparing for possible sustained transmission of 2019-nCoV beyond China, applicable lessons from previous experiences with epidemics/pandemics of respiratory viruses should be carefully considered to better control and mitigate potential consequences. Influenza preparedness plans have been developed that aim to stop, slow, or limit the spread of an influenza pandemic to the United States. These plans address limiting domestic spread and mitigating disease but also sustaining infrastructure and reducing the adverse effects of the pandemic on the economy and society. These plans would be useful to enact during the 2019-nCoV epidemic should the United States experience sustained transmission. Countries have been successful in the past and there is nothing yet to predict that this time it is likely to be worse. Effective prevention and control will not be easy if there is sustained transmission and will require the full attention of public health, federal and local governments, the private sector, and every citizen. Back to topArticle Information\nCorresponding Author: David L. Swerdlow, MD, Clinical Epidemiology Lead, Medical Development and Scientific/Clinical Affairs, Pfizer Vaccines, 500 Arcola Rd, Collegeville, PA 19426 ([email protected]). Published Online: February 11, 2020. doi:10.1001/jama.2020.1960\n\nConflict of Interest Disclosures: Dr Swerdlow reports owning stock and stock options in Pfizer Inc. Dr Swerdlow also reports providing a one-time consultation consisting of an overview of SARS and MERS epidemiology to GLG Consulting and receiving an honorarium. Dr Finelli reports owning stock in Merck and Co.\n\nFunding/Support: Pfizer Inc provided salary support for Dr Swerdlow. Role of the Funder/Sponsor: Pfizer Inc reviewed the manuscript and approved the decision to submit the manuscript for publication. References\n1. Swerdlow DL, Finelli L, Bridges CB. 2009 H1N1 influenza pandemic: field and epidemiologic investigations in the United States at the start of the first pandemic of the 21st century. Clin Infect Dis. 2011;52(suppl 1):S1-S3. doi:10.1093/cid/ciq005PubMedGoogle ScholarCrossref\n2. Balcan D, Hu H, Goncalves B, et al. Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility. BMC Medicine. 2009;7(45). doi:10.1186/1741-7015-7-45\n3. Dawood FS, Iuliano AD, Reed C, et al. Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study. Lancet Infect Dis. 2012;12(9):687-695. doi:10.1016/S1473-3099(12)70121-4PubMedGoogle ScholarCrossref\n4. Chowell G, Castillo-Chavez C, Fenimore PW, Kribs-Zaleta CM, Arriola L, Hyman JM. Model parameters and outbreak control for SARS. Emerg Infect Dis. 2004;10(7):1258-1263. doi:10.3201/eid1007.030647PubMedGoogle ScholarCrossref\n5. Killerby ME, Biggs HM, Midgley CM, Gerber SI, Watson JT. Middle East respiratory syndrome coronavirus transmission. Emerg Infect Dis. 2020;26(2):191-198. doi:10.3201/eid2602.190697PubMedGoogle ScholarCrossref\n6. Rasmussen SA, Watson AK, Swerdlow DL. Middle East respiratory syndrome (MERS). Microbiol Spectr. 2016;4(3). doi:10.1128/microbiolspec.EI10-0020-2016PubMedGoogle Scholar\n7. Swerdlow DL, Pillai SK, Meltzer MI, eds. CDC modeling efforts in response to a potential public health emergency: influenza A(H7N9) as an example. Clin Infect Dis. 2015;60(suppl):S1-S63. https://academic.oup.com/cid/issue/60/suppl_1.Google Scholar\n8. Wang D, Hu B, Hu C, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan, China. JAMA. Published online February 7, 2020. doi:10.1001/jama.2020.1585\nArticlePubMedGoogle Scholar\n9. Li Q, Guan X, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Engl J Med. Published online January 29, 2020. doi:10.1056/NEJMoa2001316PubMedGoogle Scholar\n10. World Health Organization. Novel coronavirus (2019-nCoV) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/. Accessed February 4, 2020. Comment\n2 Comments for this articleEXPAND ALL\nFebruary 12, 2020\nUnderstanding R and Disease Control\nOz Mansoor | Public Health Physician, Wellington\nThe message, that we need to prepare for a pandemic is vital. But the article misreports some key ideas. Firstly, SARS was not controlled \"because a high proportion of cases were severe.\" While that helped , it was because cases were not infectious before some days after symptom onset (usually in the second week of illness). This gave more time for case identification and isolation. And most cases did not pass on infection to anybody, but a few spread to many. When all such individuals were identified and isolated, spread stopped. Unfortunately, the new virusappears to be spreading from people much earlier in the course of illness, and even with mild symptoms - which was never documented for SARS. However, it is not clear that it is any different or better at spread between people, and perhaps with the same pattern of most cases not causing further spread. Secondly, the R0, the basic reproduction number, is correctly described as the average number of infections each case causes. But it lacks two key ideas: 1) the 0 after the R implies the native state, which is a fully susceptible population and without any control measures. R is the effectiive number and can include the impact of control measures. To claim that it was the lack of transmissibility, rather than the control measures that ended SARS, is not based on any evidence. And it ignores the heroic efforts of affected countries. Elimination of SARS demonstrated the potential of globally coordinated collective action, as well as the damage caused by ignorance and prejudice. Most seem to have already forgotten the lessons of SARS.CONFLICT OF INTEREST: Worked for WHO/WPRO in SARS responseREAD MORE\nFebruary 24, 2020\nCOVID 19: a global presence and not only a new pathogen? Giuliano Ramadori, Professor of Medicine | University Clinic, Göttingen, Germany\nIn the winter season there comes the time of upper and lower respiratory tract infections characterised by cough, dyspnea and eventually fever (influenza-like illness).Some of the patients, especially older people living alone affected by the disease ,may need hospitalization and eventually intensive care. In many of the cases who are hospitalized nasal and/or tracheal fluid are examined for viral or bacterial agents. Only in less than 50% of the cases influenza viruses are considered to be the cause of the disease.In the rest of the cases diagnostic procedure for human coronaviruses is not performed routinely. One of the fourdifferent Human Coronaviruses (HuCoV: 229E,NL 63,0C43 and HKU1) can however be found in up to 30% ofpatients negative for influenza viruses (1). Chinese scientists in Wuhan, who had to deal with an increasing number of acute respiratory tract diseases resembling viral pneumonia, performed deep sequencing analysis from samples taken from the lower respiratory tract and found a \"novel\" coronavirus. The sequence of the complete genome was made public. At the same time, however, the notice from Wuhan brought to mind the SARS- and MERS-epidemics. The measures taken by the Chinese- and WHO-authorities are now well known. Recently about 150 new cases have been identified in northern Italy and health authorities are still looking for case 0 (the source). Is it possible that COVID-19 was already existent in Italy -- and not only in Italy but possibly everywhere in the world -- and that newly available nucleotide sequence allows now to find the cause of previously undefined influenza-like illness? REFERENCE\n\n1. Benezit F et al.\n\nInquiry: How many surgical masks or respirators have past studies projected will be required for a pandemic in the United States?", "role": "user" }, { "content": "an estimated 7.3 billion", "role": "assistant" } ]

[ { "content": "Transform the following sections from a biomedical study into a simple summary for the general public. Focus on making the information accessible and easy to understand.\n\nResearch Heading: Neurally Encoding Time for Olfactory Navigation\nContent:\nAbstract:\nAccurately encoding time is one of the fundamental challenges faced by the nervous system in mediating behavior. We recently reported that some animals have a specialized population of rhythmically active neurons in their olfactory organs with the potential to peripherally encode temporal information about odor encounters. If these neurons do indeed encode the timing of odor arrivals, it should be possible to demonstrate that this capacity has some functional significance. Here we show how this sensory input can profoundly influence an animal’s ability to locate the source of odor cues in realistic turbulent environments—a common task faced by species that rely on olfactory cues for navigation. Using detailed data from a turbulent plume created in the laboratory, we reconstruct the spatiotemporal behavior of a real odor field. We use recurrence theory to show that information about position relative to the source of the odor plume is embedded in the timing between odor pulses. Then, using a parameterized computational model, we show how an animal can use populations of rhythmically active neurons to capture and encode this temporal information in real time, and use it to efficiently navigate to an odor source. Our results demonstrate that the capacity to accurately encode temporal information about sensory cues may be crucial for efficient olfactory navigation. More generally, our results suggest a mechanism for extracting and encoding temporal information from the sensory environment that could have broad utility for neural information processing.\nIntroduction:\nThere are four fundamental dimensions to all sensory modalities—quality, quantity, space and time. While the quality and quantity dimensions of olfaction are well appreciated and increasingly understood, it has long been assumed that olfaction yields little information about space and time. In contrast, in vision and audition, neural encoding of space and time information provides effective perception of the dynamic world[1, 2], commonly referred to as ‘scene analysis’[3]. Since olfaction presumably is the oldest sensory system( e. g.,[4]), it would be surprising if animals relying heavily on olfaction did not evolve some version of ‘olfactory scene analysis’ as an edge for survival[5]. Indeed, many animals, including humans( e. g.[6]) are capable of using odor cues to navigate. The best-studied example of this type of navigation is known as olfactory search, a behavior in which animals locate the source of an odor emitted by food or potential mates( e. g.,[7–11]). For all but the smallest animals, searches take place in turbulent air or water. The considerable difficulties associated with finding an odor source in turbulence have been well documented( see e. g.,[12–14]). The question is, how do organizational features inherent in the olfactory system allow animals to accomplish this task? Past studies of olfactory search have generally either proposed navigational algorithms and demonstrated their efficiency in idealized environments( e. g.,[12, 13, 15]), or studied behavioral responses to controlled scent stimuli( e. g.,[10, 16, 17]). These studies have yielded general principles of search and greater knowledge of the behavioral responses of searchers to odor cues. Yet, it is still not clear what features of odor cues animals actually measure, neurally encode, and use for navigation. Here, we suggest that reverse-engineering search strategies from the neurophysiology of the olfactory system may provide a way forward. In vision, the relative motion of objects provides information about the spatial structure of the environment and animals use this information to navigate. The head related transfer function serves a similar purpose in audition. In the case of olfaction, the time intervals between odor encounters inherent in the structure of odor plumes( i. e., odor intermittency) can vary dramatically with distance to odor sources and therefore appear to be candidate cues for olfactory navigation( e. g.,[14, 18]). If this is generally the case, one could hypothesize the existence of a specialized sensory subsystem that could capture and represent timing of past odor encounters. We recently demonstrated[19] that a subset of olfactory receptor neurons( ORNs)—known as ‘bursting’ ORNs( bORNs) because they spontaneously and rhythmically oscillate and are entrained by odorants—have the capacity to encode time intervals between odor encounters. bORNs have been identified in a diverse range of animals including arthropods[20], amphibians[21], and mammals[21–24], suggesting that they may provide an important and basic function in the olfactory system. The finding that bORNs appear to be capable of capturing information about the timing of odor encounters supports the hypothesis that animals have evolved a functionally distinct sensory subsystem with the capacity to accurately measure and encode the times between odor arrivals. However, whether this capability is related to the navigational challenges that animals face in natural odor environments, and precisely how it could influence search behavior is an open question. We address this question in what follows. Bursting olfactory receptor neurons exhibit several functional properties that suggest they may serve to measure and encode the timing of odor cues. Unlike canonical, tonic ORNs whose activity follows the concentration of a stimulus or the rate of change in concentration[25], bORNs burst spontaneously, even in the absence of odor stimulation, in addition to bursting in response to odors. Each bORN’s spontaneous activity is characterized by a distinct intrinsic bursting frequency( Fig 1A), and whether a bORN responds to an odor stimulus depends on when the odorant arrives relative to its inherent bursting cycle( Fig 1A). The probability that a bORN will burst in response to an odor increases strongly as a function of the time since its last burst τ( Fig 1A and 1B). The bORN’s probability of responding to a stimulus can be characterized by two functions: the evoked response probability( Fig 1B, blue curve and points) and the probability of going τ seconds without bursting spontaneously( Fig 1B, red curve). The composition of these two functions gives rise to a ‘time entrainment tuning curve’ for that bORN( Fig 1B, green curve). The population of bORNs is heterogeneous, creating an ensemble sensitivity to a wide range of odor arrival periodicities that can extend from hundreds of milliseconds to tens of seconds( Fig 1C). As a population, bORNs encode in their pattern of bursting the time since the last odor was encountered( Fig 1D). This neurally encoded time interval can be decoded using a simple maximum likelihood procedure, implemented, for example, with a winner take all operation on the population of neurons that receives axonal projections from the bORNs( Fig 1E). Unlike other proposed methods for neurally encoding time intervals, which require precise fine-tuning of ensembles of neurons( e. g.,[26, 27]), bORN-based encoding requires no such fine-tuning and yields low variance in the estimate of time, even for long time-intervals between odor encounters[19]. This means that the time since the last odor encounter can be measured, encoded, and decoded with high accuracy, even when odors arrive infrequently. bORNs represent a sensory-specific timing mechanism[28] that provide animals that have them[21–24, 29] with the ability to peripherally encode the time intervals between odor encounters. The central hypothesis we test in this manuscript is whether bORNs provide a neural mechanism for extracting useful navigational information in natural turbulent odor environments. Here we combine a model based on neurophysiological measurements obtained from the spiny lobster Panulirus argus[19] with detailed data from a real turbulent plume to show that populations of bORNs can directly measure properties of odor intermittency that are useful for navigation. We use detailed data on the concentration of a fluorescein dye from planar laser-induced fluorescence( PLIF) recordings from a turbulent plume[18] to rigorously characterize the timing of odor arrivals. Our analysis shows that, at scales relevant to animals searching for odor sources, there is sufficient information in the timing of odor arrivals to distinguish different locations in the plume. Finally, we use a computational model parameterized with experimental measurements from P. argus bORNs and the turbulent plume data to show that a searching animal with paired olfactory organs can quickly locate an odor source using the real-time measurements of odor intermittency captured by bORNs.\nDiscussion:\nOur results suggest that bursting olfactory receptor neurons serve a crucial but previously unappreciated role in olfactory navigation by accurately encoding the time intervals between odor encounters. In real turbulent odor plumes like the one studied here, there is structure in the sequence of odor arrivals at any given location( e. g., Fig 3;[14, 18]) and this structure is strongly correlated with position relative to the odor source. Navigational information contained in this structure can be captured by a simple metric: recurrence time( the T 1 ¯ and T 2 ¯ metrics discussed above, Fig 4). bORNs are capable of collectively encoding the time since the last odor encounter( Fig 1) and this quantity is precisely a low-dimensional stochastic estimate of recurrence time. The implication is that the lobster has evolved a specialized sensory subsystem that is highly sensitive to changes in the local structure of turbulent odor plumes[39, 40]. A searcher employing a simple heuristic that uses only the information captured by bORNs can quickly and reliably locate an odor source in a realistic turbulent plume( Fig 5). This demonstrates that the interval between odor encounters is useful for solving the online navigational problem animals actually face when searching a turbulent environment—to locate the source without wasting time waiting in places where the likelihood of encountering an odor is low[12, 15]. Recurrence times are ideally suited to this task because, unlike other metrics that are typically applied to time series analysis, recurrence times are highly sensitive to changes in the rate of arrival of odor pulses( i. e., nonstationarity of the attractor,[39]), which occur when the searcher actively moves through the plume as it samples odors. Though a searcher could also use measurements of odor concentration, strategies based on concentration estimates alone perform poorly( Fig 5, Fig C in S1 Appendix) suggesting, counterintuitively, that the most important navigational information captured by the olfactory system may come in the form of measurement of time rather than measurement of concentration. It is likely that our findings apply to other species of olfactory searchers in different types of turbulent odor environments( e. g., air versus water). Using a very different approach from that taken here, Celani et al.[14] applied methods from statistical fluid dynamics to characterize the features of odor transport in idealized turbulent plumes that are believed to be most relevant for olfactory navigation. While the mean odor concentration and the probability distribution of concentration varies systematically with position relative to an odor source, the manner in which these statistical features of the plume change with distance to the source are strongly influenced by properties of the plume such as the mean speed of advection( i. e. flow rate) and the amount of odorant released at the source. By contrast, the duration of time intervals during which the odor is below a detection threshold( analogous to the T ^ 2 statistic defined above) depends far less strongly on the details of the environment, which implies that there is information embedded in this statistic that can be extracted without knowledge of the properties of the flow and odor source. A second advantage of navigating using odor inter-arrival times is that these intervals decay rapidly with distance from the plume mid line( e. g. Fig 3), whereas other features of the odor field do not[14]. The statistical fluid dynamics approach is complementary to our method of empirically characterizing the dynamics of odor concentration using dynamical systems theory. Moreover, the results of[14] suggest that our general conclusion—that odor inter-arrival times are a sensitive metric for navigating odor plumes, and therefore, that bORNs can encode useful navigational information—is likely to extend to environments that differ substantially from the laboratory plume studied here( e. g. different flow speeds, odor concentrations, air vs. water, differences in chemical diffusivity). Animals that engage in olfactory search also use information from other sensory modalities to guide search behavior. For example, male moths locate females using measurements of prevailing winds in addition to measurements of the pheromones females emit[14] and mosquitos combine visual and thermal cues with CO2 detection to localize hosts[46]. In the case of most species that navigate using olfactory cues, it remains to be shown precisely how information from multiple sensory modalities is integrated to govern movement decisions. Various strategies for olfactory navigation have been proposed( e. g., the “mapless” scheme of[45], the “infotaxis” scheme of[13], the signal-modulated random walks studied in[15, 32]), but at present, the behavioral and neurophysiological data necessary to evaluate such navigational strategies and compare them to one another is lacking. However, the utility of odor inter-arrival times and the existence of a sensory subsystem capable of measuring them directly strongly suggest that temporal information inherent in the olfactory signal itself is fundamental to the search process. The presence of bORNs in animals as phylogenetically diverse as arthropods[20], amphibians[21], and mammals[21–24] suggests that the dynamic encoding of temporal information these neurons provide may even be fundamental to olfactory navigation. Taken together, our results reveal a neural mechanism for extracting and encoding navigational information from a noisy sequence of odor encounters. They add to an increasing understanding of how complex olfactory data are captured, encoded, and relayed through the brain[17, 47, 48]. Our results argue strongly that the ability of bORNs to encode time not only has behavioral significance, but that the dimension of time, and through time, the dimension of space, is inherent in olfaction. Thus, olfactory scene analysis is not limited to the sensory dimensions of quality and quantity( e. g.,[49]) but also appears to employ the spatial and temporal dimensions. This would make olfaction not unlike vision and audition, where visual and auditory scene analyses effectively combine space and time information to disambiguate the external world.", "role": "user" }, { "content": "Many animals navigate turbulent environments using odor cues , a behavior known as olfactory search . We propose a neural mechanism for olfactory search based on evidence that a functional subset of olfactory receptor neurons ( ORNs ) called bursting ORNs or bORNs can encode the time intervals between successive encounters with odor . We show that these time intervals are estimators of the recurrence time , an information-rich statistic of the turbulent flow . Using a computational model parameterized with data from an actual turbulent plume , we demonstrate that a searcher can locate an odor source efficiently using only input from bORNs . These findings provide scientific evidence that the most important navigational information captured by the olfactory system may come in the form of measurements of time .", "role": "assistant" } ]

[ { "content": "Analyze the given paragraph from COVID-19 research. Determine the relevant topics discussed in the text. Your response should be a JSON array containing the identified topics. Ensure the output is a valid JSON array with no additional commentary.\n\nText:\n\nCoronavirus Disease 2019 (COVID-19) has had a devastating impact on the ability of highly trained healthcare providers to render sufficient care, due to both the significant demand on resources and the unique nature of this disease that make it resistant to traditional therapies. This review sought to determine the potential role of phosphodiesterase-5 inhibitors (PDE-5) in the management of COVID-19 by extrapolating relevant data and clinical studies from other related disease states, including acute respiratory distress syndrome, acute lung injury, and high altitude pulmonary edema. Following a literature search, 4 reports were analyzed and included in this review. While the heterogenicity of data and the small number of trials included limit the interpretation and applicability, it was consistently demonstrated that PDE-5 inhibitors lowered pulmonary arterial pressures. The overall benefit of these agents is seemingly dependent upon the etiology of the respiratory failure, which warrants expanded clinical investigation for COVID-19.", "role": "user" }, { "content": "[\"Treatment\", \"Mechanism\"]", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Variability in quality attributes of service-based software systems: A systematic literature review \nChapter Title: Variability \n1. Abstract of Cited Paper (BIB001): Explicit and software-supported Business Process Management has become the core infrastructure of any medium and large organization that has a need to be efficient and effective. The number of processes of a single organization can be very high, furthermore, they might be very similar, be in need of momentary change, or evolve frequently. If the adhoc adaptation and customization of processes is currently the dominant way, it clearly is not the best. In fact, providing tools for supporting the explicit management of variation in processes (due to customization or evolution needs) has a profound impact on the overall life-cycle of processes in organizations. Additionally, with the increasing adoption of Service-Oriented Architectures, the infrastructure to support automatic reconfiguration and adaptation of business process is solid. In this paper, after defining variability in business process management, we consider the requirements for explicit variation handling for (service based) business process systems. eGovernment serves as an illustrative example of reuse. In this case study, all local municipalities need to implement the same general legal process while adapting it to the local business practices and IT infrastructure needs. Finally, an evaluation of existing tools for explicit variability management is provided with respect to the requirements identified.\n\nReview Chapter:", "role": "user" }, { "content": "Variability is understood as the ability of a software artifact to be adapted (e.g., configured, extended) for a specific context, in a preplanned manner [1] . This means, we interpret variability as planned change, rather than change due to errors, maintenance or new unanticipated customer needs. Variability specifies parts of the system and its architecture which remain variable and are not fully defined during design time. Variability allows the development of different versions of an architecture/system. Variability in the architecture is usually introduced through variation points, i.e., locations where change may occur. Variability occurs in different phases of the software life cycle BIB002 . Design time variability defines variability of quality attributes at design time of the architecture. Runtime variability defines variability in quality attributes while the system is running, i.e., after design, implementation, etc. This is particularly relevant for service-based systems as these can be adapted and reconfigured at runtime BIB001 . Handling variability requires explicitly representing variability in software artifacts throughout the lifecycle of a software product. We use the term ''handling'' variability rather than ''managing'' variability. As argued by Svahnberg et al. , managing variability is only one of several activities in the context of handling variability. Managing variability comprises managing dependencies between variabilities, maintenance and continuous population of variant features with new variants, removing features, the distribution of new variants to the installed customer base, etc. Additional activities involved in handling variability include identifying variability (i.e., determining where variability is needed), reasoning, representing and implementing variability (i.e., use a variability realization technique resolve variability at variation points and to implement a certain variant) .", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: public should wear face masks to combat COVID-19\n\nResearch Abstract:\nWe present two models for the COVID-19 pandemic predicting the impact of universal face mask wearing upon the spread of the SARS-CoV-2 virus--one employing a stochastic dynamic network based compartmental SEIR (susceptible-exposed-infectious-recovered) approach, and the other employing individual ABM (agent-based modelling) Monte Carlo simulation--indicating (1) significant impact under (near) universal masking when at least 80% of a population is wearing masks, versus minimal impact when only 50% or less of the population is wearing masks, and (2) significant impact when universal masking is adopted early, by Day 50 of a regional outbreak, versus minimal impact when universal masking is adopted late.\nThese effects hold even at the lower filtering rates of homemade masks.\nTo validate these theoretical models, we compare their predictions against a new empirical data set we have collected that includes whether regions have universal masking cultures or policies, their daily case growth rates, and their percentage reduction from peak daily case growth rates.\nResults show a near perfect correlation between early universal masking and successful suppression of daily case growth rates and/or reduction from peak daily case growth rates, as predicted by our theoretical simulations.\nOur theoretical and empirical results argue for urgent implementation of universal masking.\nAs governments plan how to exit societal lockdowns, it is emerging as a key NPI; a\"mouth-and-nose lockdown\"is far more sustainable than a\"full body lockdown\", on economic, social, and mental health axes.\nAn interactive visualization of the ABM simulation is at http://dek.ai/masks4all.\nWe recommend immediate mask wearing recommendations, official guidelines for correct use, and awareness campaigns to shift masking mindsets away from pure self-protection, towards aspirational goals of responsibly protecting one's community.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"We present two models for the COVID-19 pandemic predicting the impact of universal face mask wearing upon the spread of the SARS-CoV-2 virus--one employing a stochastic dynamic network based compartmental SEIR (susceptible-exposed-infectious-recovered) approach, and the other employing individual ABM (agent-based modelling) Monte Carlo simulation--indicating (1) significant impact under (near) universal masking when at least 80% of a population is wearing masks, versus minimal impact when only 50% or less of the population is wearing masks, and (2) significant impact when universal masking is adopted early, by Day 50 of a regional outbreak, versus minimal impact when universal masking is adopted late.\", \"We recommend immediate mask wearing recommendations, official guidelines for correct use, and awareness campaigns to shift masking mindsets away from pure self-protection, towards aspirational goals of responsibly protecting one's community.\"]}", "role": "assistant" } ]

[ { "content": "Examine the given text from a research paper in the field of NLP. Your task is to identify the role of the citation within the context provided. Focus on understanding the intent behind the citation and classify it accordingly.\n\nSection Title:\nexperiments\n\nText Before Citation:\nThe dialogue state is represented by a cumulative answer analysis which tracks, over multiple turns, the correct, incorrect, and not-yet-mentioned parts 1Other factors such as student confidence could be considered as well (Callaway et al., 2007). Interaction between components is coordinated by the dialogue manager which uses the informationstate approach (Larsson and Traum, 2000).\n\nCitation Text:\nThe dialogue state is represented by a cumulative answer analysis which tracks , over multiple turns , the correct , incorrect , and not-yet-mentioned parts 1Other factors such as student confidence could be considered as well ( Callaway et al. , 2007 ) .\n\nText After Citation:\nof the answer. Once the complete answer has been accumulated, the system accepts it and moves on. Tutor hints can contribute parts of the answer to the cumulative state as well, allowing the system to jointly construct the solution with the student.", "role": "user" }, { "content": "FutureWork", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\n…gene has the potential to challenge oxazolidinone clinical utility as well as other antimicrobial classes (phLOPSA pattern) used in humans or animals (Arias et al., 2008; Kehrenberg and Schwartz, 2006; Kehrenberg et al., 2005, 2007; Long et al., 2006; Mendes et al,, 2008; Schwarz et al., 2000).", "role": "user" }, { "content": "Background", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Wearing a face mask can help prevent the spread of COVID-19\n\nResearch Abstract:\nFace masks are an avenue to curb the spread of coronavirus, but few people in Western societies wear face masks.\nSocial scientists have rarely studied face mask wearing, leaving little guidance for methods to encourage these behaviours.\nIn the current article, we provide an approach to address this issue by developing the 32-item and 8-dimension Face Mask Perceptions Scale (FMPS).\nWe begin by developing an over-representative item list in a qualitative study, wherein participants' responses are used to develop items to ensure content relevance.\nThis item list is then reduced via exploratory factor analysis in a second study, and the eight dimensions of the scale are supported.\nWe also support the validity of the FMPS, as the scale significantly relates to both face mask wearing and health perceptions.\nWe lastly confirm the factor structure of the FMPS in a third study via confirmatory factor analysis.\nFrom these efforts, we identify an avenue that social scientists can aid in preventing coronavirus and illness more broadly - by studying face mask perceptions and behaviours.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Face masks are an avenue to curb the spread of coronavirus, but few people in Western societies wear face masks.\"]}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: An Overview of Reconfigurable Hardware in Embedded Systems \nChapter Title: Scientific data acquisition and analysis \n1. Abstract of Cited Paper (BIB001): Tornado, hazardous weather and flood detection radars demand high-throughput, high-speed data acquisition and processing. Weather-processing systems need to be capable of implementing powerful signal processing algorithms on the raw data collected by the radars. Following processing, data is distributed to the end-user in real-time for timely and accurate detection of imminent weather disasters. Since physical accessibility to such systems is often limited, remote-user based control and reconfiguration of processing capabilities are also essential. A real-time data acquisition, processing and distribution system for weather radar applications that meets these needs is described in this paper. This FPGA-based system has been successfully integrated with a radar optimized for tornado detection and deployed in the field \n2. Abstract of Cited Paper (BIB002): In this paper, we present an implementation of the image compression routine set partitioning in hierarchical trees (SPIHT) in reconfigurable logic. A discussion on why adaptive logic is required, as opposed to an application specific integrated circuit (ASIC), is provided along with background material on the image compression algorithm. We analyzed several discrete wavelet transform (DWT) architectures and selected the folded DWT design. In addition we provide a study on what storage elements are required for each wavelet coefficient. A modification to the original SPIHT algorithm is implemented to parallelize the computation. The architecture of our SPIHT engine is based upon fixed-order SPIHT, developed specifically for use within adaptive hardware. For an N/spl times/N image fixed-order SPIHT may be calculated in N/sup 2//4 cycles. Square images which are powers of 2 up to 1024/spl times/1024 are supported by the architecture. Our system was developed on an Annapolis Microsystems WildStar board populated with Xilinx Virtex-E parts. The system achieves a 450/spl times/ speedup versus a microprocessor solution, with less than a 0.2-db loss in peak signal-to-noise ratio over traditional SPIHT.\n\nReview Chapter:", "role": "user" }, { "content": "Scientific data-acquisition systems receive and preprocess vast quantities of data before archiving or sending the data off for further processing. These systems may be remote or inaccessible, operating on battery or solar power, yet requiring extremely high performance to handle the required volume of data. These systems are increasingly using RH to provide this performance in a flexible medium that can be changed as new approaches to data aggregation and preprocessing are researched. RH has been used in systems proposed or created for weather radar BIB002 , seismic exploration , and adaptive cameras for solar study BIB001 . RH is also used to compress the massive volume of data prior to transmission BIB003 .", "role": "assistant" } ]

[ { "content": "Review the provided collection of medical RCT summaries. Your objective is to distill the essential insights into a brief conclusion. Focus solely on the synthesis of findings without additional commentary. The RCT summaries are as follows:\n\n\n\nReport Title 1:\nComparison of transdermal estradiol and tibolone for the treatment of oophorectomized women with deep residual endometriosis.\nReport Abstract 1:\nTo compare the effect of HRT with transdermal estradiol and that of treatment with tibolone in post-menopausal women with residual endometriosis.\n 21 women with residual pelvic endometriosis after bilateral oophorectomy with or without hysterectomy were enrolled in the study and were randomized to HRT with transdermal estradiol 50 mg twice weekly (n = 10) associated with cyclic medroxyprogesterone acetate 10 mg daily in women who preserved uterus, and to treatment with tibolone 2.5 mg administered orally once a day (n = 11). The duration of both treatments was scheduled to last at least 12 months. Residual endometriosis was located in the bowel wall in four patients, in the rectovaginal septum in six and deeply in the retroperitoneal pelvic space in six. All women were symptomatic before oophorectomy.\n All the women were followed for 12 months. No patient suspended therapy because of side effects. Four patients of the estradiol group experienced moderate pelvic pain during treatment compared with only one patient in the tibolone group. One patient in the estradiol group reported severe dyspareunia.\n Although our series is very small, it seems that tibolone may be a safe hormonal treatment for post-menopausal women with residual endometriosis.", "role": "user" }, { "content": "Hormone replacement therapy for women with endometriosis in post-surgical menopause could result in pain and disease recurrence. However, the evidence in the literature is not strong enough to suggest depriving severely symptomatic patients from this treatment. There is a need for more randomised controlled studies.", "role": "assistant" } ]

[ { "content": "Transform the provided sections of a biomedical research paper into a digestible summary for a general audience. Focus on simplifying complex ideas while retaining key scientific insights.\n\nResearch Title: A critical re-evaluation of fMRI signatures of motor sequence learning\nContent Overview:\nAbstract:\nDespite numerous studies, there is little agreement about what brain changes accompany motor sequence learning, partly because of a general publication bias that favors novel results. We therefore decided to systematically reinvestigate proposed functional magnetic resonance imaging correlates of motor learning in a preregistered longitudinal study with four scanning sessions over 5 weeks of training. Activation decreased more for trained than untrained sequences in premotor and parietal areas, without any evidence of learning-related activation increases. Premotor and parietal regions also exhibited changes in the fine-grained, sequence-specific activation patterns early in learning, which stabilized later. No changes were observed in the primary motor cortex( M1). Overall, our study provides evidence that human motor sequence learning occurs outside of M1. Furthermore, it shows that we cannot expect to find activity increases as an indicator for learning, making subtle changes in activity patterns across weeks the most promising fMRI correlate of training-induced plasticity.\nIntroduction:\nHumans have the remarkable ability to learn complex sequences of movements. While behavioural improvements in sequence learning tasks are easily observable, the underlying neural processes remain elusive. Understanding the neural underpinnings of motor sequence learning could provide clues about more general mechanisms of plasticity in the brain. This motivation has led numerous functional magnetic resonance imaging( fMRI) studies to investigate the brain changes related to motor sequence learning. However, there is little agreement about how and where in the brain learning-related changes are observable. Previous studies include reports of signal increases across various brain regions( Floyer-Lea and Matthews, 2005; Grafton et al., 1995; Hazeltine et al., 1997; Karni et al., 1995; Lehéricy et al., 2005; Penhune and Doyon, 2002), as well as signal decreases( Jenkins et al., 1994; Peters et al., 2017; Toni et al., 1998; Ungerleider et al., 2002; Wiestler and Diedrichsen, 2013), nonlinear changes in activation( Ma et al., 2010; Xiong et al., 2009), spatial shifts in activity( Lehéricy et al., 2006; Steele and Penhune, 2010), changes in multivariate patterns( Wiestler and Diedrichsen, 2013; Wymbs and Grafton, 2015), and changes in inter-regional functional connectivity( Bassett et al., 2015; Bassett et al., 2011; Doyon et al., 2002; Mattar et al., 2016). Additionally, some experiments have matched the speed of performance( Karni et al., 1995; Penhune and Doyon, 2002; Steele and Penhune, 2010; Lehéricy et al., 2005; Seidler et al., 2002; Seidler et al., 2005), while others have not( Bassett et al., 2015; Lutz et al., 2004; Wiestler and Diedrichsen, 2013; Wymbs and Grafton, 2015). Given that fMRI analysis has many degrees of freedom, these inconsistencies may not be too surprising. However, the implicit pressure in the publication system to report findings may also have contributed to a lack of coherency. To address this issue, we designed a comprehensive longitudinal study of motor sequence learning that allowed us to systematically reinvestigate previous findings. In order to increase transparency, we pre-registered the design, as well as all tested hypotheses on the Open Science Framework( Berlot et al., 2017; https://osf. io/etnqc), and make the full dataset available to the research community( Berlot, 2020; OpenNeuro accession number ds002776). The main aim of our study was to systematically evaluate different ideas of how learning-related changes are reflected in the fMRI signal. In the context of motor sequence learning, the most commonly examined brain region is the primary motor cortex( M1). Previous reports of increased M1 activation after long-term learning have been interpreted as additional recruitment of neuronal resources for trained behavior, taken to suggest the skill is represented in M1( Floyer-Lea and Matthews, 2005; Karni et al., 1995; Karni et al., 1998; Lehéricy et al., 2005; Penhune and Doyon, 2002; for a review see Dayan and Cohen, 2011; Figure 1a). Since then, several pieces of evidence have suggested that sequence-specific memory may not reside in M1( Beukema et al., 2019; Wiestler and Diedrichsen, 2013; Yokoi and Diedrichsen, 2019). However, some of these reports studied skill acquisition over a course of a few days, while human skill typically evolves over weeks( and months) of practice. Therefore, including several weeks of practice might be more suitable to test whether, and at what time point, M1 develops skill-specific representations. Outside of M1, learning-related activation changes have been reported in premotor and parietal areas( Grafton et al., 2002; Hardwick et al., 2013; Honda et al., 1998; Penhune and Doyon, 2002; Tamás Kincses et al., 2008; Vahdat et al., 2015), with activation increases commonly interpreted as increased involvement of these areas in the skilled behavior. Yet, recent studies have mostly found that, as the motor skill develops, activation in these areas predominantly decreases( Penhune and Steele, 2012; Wiestler and Diedrichsen, 2013; Wu et al., 2004). Such reductions are harder to interpret as they could reflect a reduced areal involvement in skilled performance or, alternatively, more energy efficient implementation of the same function( Figure 1b; Picard et al., 2013; Poldrack et al., 2005). To complicate things further, regional activity increases and decreases could occur simultaneously in the same area( Figure 1c; Steele and Penhune, 2010). In such a scenario, the net activation in the region would not change, yet, the trained sequences would engage slightly different subpopulations of the region than untrained sequences. A variant of this idea is that each specific sequence becomes associated with dedicated neuronal subpopulation( and hence fMRI activity pattern). Such a representation would form the neural correlate of sequence-specific learning – the part of the skill that does not generalize to novel, untrained motor sequences( Karni et al., 1995). Sequence-specific activation patterns should change early in learning( Figure 1d), when behavior improves most rapidly, and stabilize later, once the skill has consolidated and an optimal pattern is established( Peters et al., 2017). One possible way in which sequence-specific patterns could reorganize is by becoming more distinct from one another( Figure 1e; Wiestler and Diedrichsen, 2013). Having a distinctive code for each sequence might be of particular importance to the system in a trained state, allowing it to produce different dynamical sequences, while avoiding confusion or ‘tangling’ of the different neural trajectories( Russo et al., 2018). To systematically examine the cortical changes associated with motor sequence learning, we carried out a longitudinal study over 5 weeks of training with 4 sessions of high-field( 7 Tesla) fMRI scans. Behavioural performance in the first three scanning sessions was imposed to the same speed of performance. This allowed us to inspect whether examined fMRI metrics reflect brain reorganization, independent of behavioral change. However, controlling for speed incurs the danger of not tapping into neural resources that are necessary for skilled performance( Orban et al., 2010; Poldrack, 2000). We therefore compared the fMRI session with paced performance at the end of behavioural training with one acquired with full speed performance( Figure 2). This manipulation allowed us to systematically assess the role of speed on the fMRI metrics of learning, thereby addressing an important methodological problem faced by virtually every study on motor learning.\nDiscussion:\nThe search for neural substrates of learning is a daunting task: the acquisition of longitudinal data sets is work intensive, and the large dimensionality of possible brain metrics makes the search difficult( Poldrack, 2000). Historically, the question was simplified by studying activation increases in single areas as proxies for motor ‘engram’ localization( Lashley, 1950; Berlot et al., 2018). Here we found no evidence for such activation increases; instead we observed widespread and distributed decreases in activation across cortical areas. In contrast, subtler changes in the distributed patterns of fMRI activity have the potential to provide more direct metrics of plasticity. Increased pattern reorganization( across weeks), and larger pattern separation for trained sequences was found across prefrontal, parietal, and striatal regions. These metrics may be useful as general fMRI correlates of neural reorganization beyond the domain of motor learning.", "role": "user" }, { "content": "It has famously been claimed that it takes 10 , 000 hours to become an expert at something . But while most of us will never become concert pianists , we can all learn new motor skills and improve existing ones – from touch-typing to tennis – by practicing . What happens in the brain to produce these improvements in performance ? Researchers have tried to answer this question by scanning the brains of people as they practice motor skills , but the results have proved inconsistent . Some studies find that specific brain areas become more active as people practice . This could indicate that these areas are ‘storing’ new skills . But others report that brain activity decreases with practice . This might indicate that practice instead makes certain brain areas work more efficiently . It is also unclear where in the brain these learning-related changes occur . Some studies suggest that most occur in the primary motor cortex , or M1 – the area that sends commands to muscles . Others suggest that most changes take place outside of M1 , in areas that plan movements . Berlot et al . set out to resolve these inconsistencies by scanning the brains of healthy volunteers as they learned to play six 9-digit sequences on a keyboard . Each volunteer completed about 4 , 000 training trials over 5 weeks , and had their brain scanned four times . As the weeks passed , the volunteers became faster and more accurate at playing the sequences . However , the activity of their primary motor cortex did not change . By contrast , the activity of areas involved in planning movements decreased throughout training . The patterns of activity for each individual sequence reorganized throughout learning in the areas outside of the M1 . This happened most quickly during the early stages of training when the volunteers showed the fastest improvements in performance . Overall , these findings suggest that when we learn a new skill , activity in the brain areas supporting that skill decrease as the brain becomes more efficient . Increases in brain activity are thus unlikely to reflect the acquired skill . Instead , more subtle changes , in which the brain uses more specific patterns of activity to encode the skill , may underlie improved performance . This may also be true for other types of learning , such as acquiring a new language .", "role": "assistant" } ]

[ { "content": "Analyze the given paragraph from COVID-19 research. Determine the relevant topics discussed in the text. Your response should be a JSON array containing the identified topics. Ensure the output is a valid JSON array with no additional commentary.\n\nText:\n\nPURPOSE: There have not been well-designed survey studies investigating the impact of the coronavirus disease 2019 (COVID-19) pandemic on orthopaedic resident education. METHODS: A 58-question, web-based survey was administered to orthopaedic residents in South Korea. A total of 229 orthopaedic residents from 43 hospitals completed the survey questionnaire. RESULTS: The average working time of 72.7 hours/week before the pandemic was decreased to 65.6 hours/week during the pandemic (p < 0.001). The time working in the operating room was significantly decreased during the pandemic, but not in the emergency centre and outpatient clinic. The education times for lecture and clinical case discussion were decreased during the pandemic (both, p < 0.001), respectively. While the use of traditional teaching methods was decreased, the use of online-based teaching methods was increased (p < 0.001). However, satisfaction level with online-based teaching methods was significantly lower compared with that of traditional teaching methods. The average working time exposed to the patients with COVID-19 was 9.7 hours/week. About 47.6% of orthopaedic residents experienced isolation or quarantine. The average score for quality of life, which was 68.9 out of 100 scores before the pandemic, decreased to 61.7 during the pandemic (p < 0.001). The most stressful factor for orthopaedic residents during the pandemic was family/relative health, followed by their own health and residency program. CONCLUSION: The COVID-19 pandemic had a significant impact on orthopaedic resident education in South Korea. Therefore, flexible and sustainable strategies are necessary to prepare for the future as well as the current pandemic situation.", "role": "user" }, { "content": "[\"Prevention\"]", "role": "assistant" } ]

[ { "content": "Craft a concise summary for a chemistry research paper using the provided title and selected text segments.\n\nHeading:\nMolecular Field Analysis Using Computational-Screening Data in Asymmetric N-Heterocyclic Carbene-Copper Catalysis toward Data-driven in silico Catalyst Optimization\n\nContent Extracts:\n\n<p>Data-driven machine-learning-based optimization of molecular catalysis is an emerging and promising research area. 1 Regression analysis, i.e., quantitative structure-property relationships (QSPR) modeling of catalytic reactions typically correlates molecular descriptors with experimental catalytic activity values. High quality-experimental data suitable for QSPR modeling are, however, not always available. In some cases, experimental data include non-negligible noise derived from various factors, such as side reactions and experimental errors. The use of such data in regression analysis/QSPR can reduce its predictive performance, and in some cases, the information extracted by the analysis may not provide reliable insights into the reactions. The use of computational-screening data obtained through abinitio calculations avoids this potential shortcoming, as the calculated activity data do not include the aforementioned noise. In addition, computational-screening approaches do not require experiments to collect data, thereby enabling data analysis of reactions that involve expensive and synthetically difficult catalysts. Despite these attractive features, reports of data-driven molecular design in molecular catalysis using the QSPR framework with the calculated catalytic-activity values as the target variables are scarce, 2 although virtual screening using transition-state force fields developed via the quantum-guided molecular-mechanics method has been investigated in asymmetric catalysis. 1e,1f,3 As transition-state (TS) DFT calculations with appropriate calculation conditions have become a reliable method to design asymmetric catalytic reactions, 4,5 the use of the calculated selectivity values as target variables for QSPR or quantitative structure-selectivity relationships (QSSR) can be expected to further accelerate the development of asymmetric catalytic reactions. Recently, a QSSR study of the asymmetric propargylation of aryl aldehydes has been reported, 6 in which more than 600 training samples with literature-reported calculated activation-energy values 5 were used. However, the calculation cost of DFT-based TS modeling is high. Therefore, it would be highly desirable to develop a regression-based method that enables molecular design to improve enantioselectivity by analyzing a relatively small set of DFT-based computationalscreening data. Here, we report the data-driven design of chiral catalysts for N-heterocyclic carbene (NHC)-Cu-catalyzed asymmetric carbonyl additions of a silylboronate to aldehydes through molecular-field-based regression analysis 7,8 using the calculated DDG ‡ values and transition-state structures with a total of 30 training samples (Figure 1a). For the initial training dataset, we employed three ring-saturated C2-symmetric NHC ligands (L1-3), which have shown low to moderate enantioselectivity in a previous investigation (Table 1). 7b Moreover, six aromatic aldehydes (S1-6) were selected. We calculated the TSs of a possible enantio-determining step for all combinations of the three catalyst and six substrate structures. We hypothesized that the reaction proceeded via the four-centered reaction mechanism that is frequently observed in related Cu(I)-catalyzed reactions. 8,9 As an example, the TS structure derived from ligand L3 and substrate S1 (L3S1) is shown in Figure 2. The calculated DDG ‡ values exhibited a correlation with the experimental DDG ‡ values (see Figure S9). For data analysis, we employed a 3D-QSSR approach, 1c which we refer to here as molecular field analysis (MFA). MFA is a regression analysis between reaction outcomes and molecular fields calculated from three-dimensional molecular structures. In our previous study, we found that MFA of the intermediates in the enantio-determining step of asymmetric catalytic reactions enabled the extraction and visualization of structural information that led to the design of molecules with improved enantioselectivity (Figure 1b). 10,11 Thus, we were interested in whether MFA between the calculated DDG ‡ values and the TS structures would be able to extract similar information (Figure 1a). The seminal report of the use of MFA in asymmetric catalysis by the Kozlowski group employed TS structures; however, the authors did not use the extracted and visualized information for molecular design, and their target variables were the experimental DDG ‡ values. 12 Our specific goal in this study was to evaluate our approach through the data-driven design of the current optimum NHC ligand L6 in the targeted carbonyl additions 7 starting from a set of 18 training samples (Table 1). As molecular fields, we employed steric indicator fields composed of indicator variables (with values of 0 or 1), as shown in Figure 1. The indicator fields were calculated for each unit cell of a grid space. A unit cell that includes the van der Waals radius of any atom was assigned a value of 1, otherwise, the cell was given a value of 0 (Figures 1 and S2). The indicator fields were calculated from the TS structures of a minor pathway (the R pathway), as we aimed to obtain guidelines for the design of chiral NHC ligands that would destabilize the minor pathway. By correlating the calculated DDG ‡ values and the indicator fields using LASSO 13 or Elastic Net 14 regression according to the reported procedure 15 employing the R package glmnet 16 , we generated a regression model (for more details regarding the MFA, see the SI section 'Details of the molecular field analysis'). The important structural information obtained from the regression coefficients is visualized in the TS structures of L1S1 and L3S1 (Figure 3a and 3b). The blue and red points correspond to positive and negative coefficients (for regression coefficient values with coordinates of unit cells, see Table S5). If molecular structures are located on the blue or red points, the enantioselectivity increases or decreases, respectively. We focused on the blue point observed above the phenyl group of the aldehyde. While the phenyl group on the NHC nitrogen atom of the TS structure L1S1 did not overlap with the blue point, as indicated by the yellow arrow (Figure 3b), the corresponding phenylene moiety of L3S1 did overlap with the blue point, as indicated by the green arrow (Figure 3a). The difference in the position of the phenylene moiety occurs due to steric repulsion between the iPr group of the NHC ligand and the silyl group of L3S1 (for details, see Figure S8), which induces a steric interaction between the phenylene moiety of the NHC ligand and the phenyl group of the aldehyde and destabilizes the R pathway (Figure 2). On the other hand, this steric effect between the ligand and aldehyde does not exist in the S pathway (Figure 2). Inspired by this mechanistic insight, we introduced a phenyl or p-tolyl group in the place of the iPr group of NHC ligand L3 to further destabilize the R pathway by increasing the steric repulsion. The transition-state structures L4S1 and L5S1 overlap at the blue point described above (Figures 3c and S4). The calculated DDG ‡ values for L4S1 (1.8 kcal/mol) and L5S1 (2.2 kcal/mol) are higher than that of the design template L1S1 (0.3 kcal/mol). We experimentally confirmed that the enantioselectivity of the reactions L4S1 (87% ee) and L5S1 (82% ee) are improved relative to the selectivity of L3S1 (73% ee), which exhibited the highest value among the 18 training samples (for more details of the molecular design workflow, see the SI, page S4). Thus, we successfully improved the enantioselectivity through data-driven catalyst design using computationalscreening data. We then performed the MFA again, this time including the data calculated from the designed ligands (30 samples, Table 1). Figure 4a shows the structural information in the TS structure L4S1, in which a blue point that did not overlap with the structure was identified near the 3-position of the aromatic group of the NHC ligand, as indicated by the yellow arrow. Based on this information, we designed L6 and L7, which bear Me or iPr groups at the 3-and 5-positions of the aromatic ring. The structures L6S1 and L7S1 overlapped with the structural information used for the design (Figures 4b, 4c and Figure S5). The calculated DDG ‡ values are higher than that of the design template L4S1 (L4S1: 1.8 kcal/mol; L6S1: 3.3 kcal/mol; L7S1: 2.1 kcal/mol). We then performed the reactions L6S1 and L7S1. To our delight, further improvement of the enantioselectivity was observed (L6S1: 90% ee; L7S1: 96% ee; L4S6: 88% ee, which is the highest value among the 30 training samples). Although DFT calculations are useful to design chiral catalysts, 4,5 DFTbased computational predictions vary vastly depending on the calculation conditions and often fail as replacements for experiments. 17 In this case, we employed the wB97XD functional for the single-point calculations; we also confirmed that MFA using DDG ‡ values obtained via single-point calculations using other representative functionals for the TS calculations in asymmetric catalysis led to the same molecular design as described above (Figures S10-S12). Although we employed 30 training samples to secure the quality and reliability of the regression models, practically, we can in this case successfully design appropriate molecules using a smaller sample size (for details, see Figure S13). In summary, a molecular field analysis (MFA) using computational-screening data and the corresponding transition-state (TS) structures with a relatively small dataset (30 samples) enabled the design of chiral NHC ligands with improved enantioselectivity for the Cu-catalyzed carbonyl addition of a silylboronate. The design of ligands L6 and L7 was achieved through iterative MFA-based molecular design. Further optimization of asymmetric catalysis using this strategy is currently in progress. As the structural information comprises Cartesian coordinates that computers can understand, the combination of our MFA-based strategy and a structure generator could lead to the future development of efficient computational chiral catalyst optimization programs/software, as has been seen in the field of the computational design of drug-like molecules. 18</p>\n\nSupporting Information\n<p>The Supporting Information is available free of charge on the ACS Publications website.</p><p>Experimental details, characterization data for all new compounds, details of calculations and data analysis (PDF)</p><p>Input data for the data analysis (Zip)</p><p>Output data obtained from the data analysis (Zip)</p><p>Coordinates of all the TS structures (XYZ)</p>\n\nCorresponding Author\n<p>Shigeru Yamaguchi − RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.; orcid.org /0000-0003-2304-8448; Email: shigeru.yamaguchi.hw@ riken.jp Hirohisa Ohmiya − Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1192, Japan; orcid.org/0000-0002-1374-1137; Email: [email protected] Kazunori Nagao − Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1192, Japan; orcid.org/0000-0003-3141-5279</p>\n\nNotes\n<p>The authors declare no competing interests.</p>", "role": "user" }, { "content": "A molecular-field-based regression analysis using computational screening data for N-heterocyclic carbene (NHC)-Cu-catalyzed asymmetric carbonyl additions of a silylboronate to aldehydes is reported. A computational screening was performed to collect enantioselectivity data (DDG ‡ : energy differences between the transitions states leading to each enantiomer) via transitionstate (TS) calculations using density functional theory (DFT) methods. A molecular field analysis (MFA) was carried out using the obtained calculated DDG ‡ values and TS structures (30 samples in total). Important structural information for enantioselectivity extracted by the MFA was visualized on the TS structures, which provided insight into an asymmetric induction mechanism. Based on the obtained information, chiral NHC ligands were designed, which showed improved enantioselectivity in these carbonyl additions.", "role": "assistant" } ]

[ { "content": "Given the following biomedical passages, answer the question succinctly. Ensure your response is precise and limited to the answer only.\n\nQuestion: Which disease is included as an additional feature in the Goldberg-Shprintzen syndrome?\n\nPassages: Goldberg-Shprintzen syndrome (GOSHS, MIM #609460) is an autosomal recessive disorder of intellectual disability, specific facial gestalt and Hirschsprung's disease (HSCR).\nGoldberg-Shprintzen syndrome (GOSHS) is a rare clinical disorder characterized by central and enteric nervous system defects.\nThus, our data indicate that KBP is involved in neuronal differentiation and that the central and enteric nervous system defects seen in GOSHS are likely caused by microtubule-related defects.\nMutations in Kif1-binding protein/KIAA1279 (KBP) cause the devastating neurological disorder Goldberg-Shprintzen syndrome (GSS) in humans.\nWe describe a brother and sister with Hirschsprung disease, hypotonia, and ptosis. Their condition resembles that in 2 sibs reported by Goldberg and Shprintzen.\nA 5-year-old girl with Hirschsprung disease, unusual facial appearance, psychomotor retardation, epilepsy, and congenital heart disease is reported\nCranial computed tomography demonstrated abnormal findings that may suggest defective neuronal migration and/or dysgenesis of the brain\nIn 1981, Goldberg and Shprintzen described siblings with short-segment Hirschsprung disease, cleft palate, microcephaly, mild mental retardation, short stature and distinctive facial appearance.\nA consanguineous family with Hirschsprung disease, microcephaly, and mental retardation (Goldberg-Shprintzen syndrome)\nHirschsprung disease, mental retardation, microcephaly, and specific craniofacial dysmorphism were observed in three children from a large, consanguineous, Moroccan family\nThe patient showed dysmorphic facies and weakness of connective tissue, and was scheduled to undergo abdominal surgery.\nShprintzen-Goldberg syndrome (SGS) has considerable phenotypic overlap with MFS and LDS, including aortic aneurysm.\nWe report on maternal half-sibs born to unaffected, non-consanguineous parents with classical Shprintzen-Goldberg syndrome (SGS) who had in addition intestinal malrotation and an aberrant subclavian artery\nkeletal abnormalities common to 3 of them include bowing of long bones (with a variable degree of progression over time), flare of the metaphyses, a large anterior fontanel with persistent patency into the second to fourth years of life, 13 pairs of ribs, distinct vertebral abnormalities which were absent neonatally but evolved by the second year of life, and progressive osteopenia.\nMarfanoid phenotype with craniosynostosis (Shprintzen-Goldberg syndrome) is a rare disorder previously described in only 5 patients.\nMutation in fibrillin-1 and the Marfanoid-craniosynostosis (Shprintzen-Goldberg) syndrome\nAdditional common findings include other craniofacial anomalies, hypotonia, obstructive apnea, foot deformity, and congenital weakness of the abdominal wall\nThe radiological features were characterized by late-onset craniosynostosis, arachnodactyly, undermodeling of short tubular bones, mildly undermodeled and slightly bowed long bones, twisted ribs and tall vertebral bodies with elongated neural arches\nAortic root replacement for annuloaortic ectasia in Shprintzen-Goldberg syndrome: a case report\nAnnuloaortic ectasia due to Shprintzen-Goldberg syndrome (SGS) is reported\nShprintzen-Goldberg syndrome is one of a group of disorders characterized by craniosynostosis and marfanoid habitus\nThe Shprintzen-Goldberg syndrome is an extremely rare syndrome with a characteristic face. This is one of a group of disorders characterized by craniosynostosis and marfanoid features.\nThe Shprintzen-Goldberg syndrome (SGS) is a disorder of unknown cause comprising craniosynostosis, a marfanoid habitus and skeletal, neurological, cardiovascular, and connective-tissue anomalies.\nOther commonly reported manifestations include hypotonia in at least the neonatal period, developmental delay, and inguinal or umbilical hernia.\nShprintzen-Goldberg syndrome is a rare connective tissue disorder characterized by marfanoid habitus and additional dysmorphic stigmata.\nOverall intelligibility, language, articulation, voice and resonance characteristics in a child with Shprintzen-Goldberg syndrome\nShprintzen-Goldberg syndrome (SGS) is a rare disorder characterized by a Marfan-like habitus, mental retardation and craniosynostosis.\nShprintzen-Goldberg syndrome (SGS) is characterized by: craniosynostosis of the coronal, sagittal, or lambdoid sutures; dolichocephaly; distinctive craniofacial features; skeletal changes (dolichostenomelia, arachnodactyly, camptodactyly, pes planus, pectus excavatum or carinatum, scoliosis, joint hypermobility or contractures and C1/C2 spine malformation); neurologic abnormalities; intellectual disability; and brain anomalies (hydrocephalus, dilatation of the lateral ventricles, and Chiari 1 malformation). Cardiovascular anomalies may include mitral valve prolapse, mitral regurgitation/incompetence, aortic regurgitation and aortic root dilatation. Minimal subcutaneous fat, abdominal wall defects, myopia, and cryptorchidism in males, are also characteristic findings.\nSurgical treatment for scoliosis in patients with Shprintzen-Goldberg syndrome.\nShprintzen-Goldberg syndrome (SGS) is characterized by craniosynostosis and marfanoid habitus.\nWe identified, by homozygosity mapping, a novel locus on 10q21.3-q22.1 for Goldberg-Shprintzen syndrome (GOSHS) in a consanguineous Moroccan family. Phenotypic features of GOSHS in this inbred family included microcephaly and mental retardation, which are both central nervous system defects, as well as Hirschsprung disease, an enteric nervous system defect\nWe demonstrate that homozygous nonsense mutations in KIAA1279 at 10q22.1, encoding a protein with two tetratrico peptide repeats, underlie this syndromic form of Hirschsprung disease and generalized polymicrogyria, establishing the importance of KIAA1279 in both enteric and central nervous system development\nWe report on four children in whom was diagnosed a neurocristopathy, associating Hirschsprung's disease with a wide spectrum of neurologic abnormalities. The patients included two children presenting the phenotypic features of the Goldberg-Shprintzen syndrome: distinct dysmorphic facial features, microcephaly, and mental retardation, along with agenesis of the corpus callosum and cortical malformations associated with intractable seizures in one child. The third newborn presented with the Haddad syndrome: short-segment Hirschsprung's disease associated with the congenital central hypoventilation syndrome requiring permanent artificial ventilation\nTherefore, awareness of a possible neurocristopathy associated with neurologic abnormalities should be taken into account in any patient newly diagnosed with Hirschsprung's disease to detect the abnormalities early and promptly manage them", "role": "user" }, { "content": "Craniosynostosis", "role": "assistant" } ]

[ { "content": "Consider the following research inquiry and associated key terms. Review the dataset summaries provided and determine which datasets are suitable for addressing the research question. Base your decision on your understanding of machine learning datasets.\nProvide your answer as a JSON list. For example, for the inquiry \"Semi supervised image classification\", a possible response could be: [\"CIFAR-10\", \"CIFAR-100\"]. Ensure the response contains only the dataset names in JSON format.\n\nResearch Inquiry: We investigate whether a small number of training samples is sufficient for image classification. We empirically demonstrate that there\n\nKey Terms: image classification images\n\nDataset Summaries:\nShiny dataset: The shiny folder contains 8 scenes with challenging view-dependent effects used in our paper. We also provide additional scenes in the shiny_extended folder.\nMaleX: MaleX is a curated dataset of malware and benign Windows executable samples for malware researchers. The dataset contains 1,044,394 Windows executable binaries with 864,669 labelled as malware and 179,725 as benign.\nImageNet: The ImageNet dataset contains 14,197,122 annotated images according to the WordNet hierarchy. Since 2010 the dataset is used in the ImageNet Large Scale Visual Recognition Challenge (ILSVRC), a benchmark in image classification and object detection.\nDOTA: DOTA is a large-scale dataset for object detection in aerial images. It can be used to develop and evaluate object detectors in aerial images.\nSilhouettes: The Caltech 101 Silhouettes dataset consists of 4,100 training samples, 2,264 validation samples and 2,307 test samples. The datast is based on CalTech 101 image annotations.\nMVTecAD: MVTec AD is a dataset for benchmarking anomaly detection methods with a focus on industrial inspection. It contains over 5000 high-resolution images divided into fifteen different object and texture categories.\nCIFAR-10: The CIFAR-10 dataset (Canadian Institute for Advanced Research, 10 classes) is a subset of the Tiny Images dataset and consists of 60000 32x32 color images. The images are labelled with one of 10 mutually exclusive classes: airplane, automobile (but not truck or pickup truck), bird, cat, deer, dog, frog, horse, ship, and truck (but not pickup truck).\n\nDataset Options: A: Shiny dataset B: MaleX C: ImageNet D: DOTA E: Silhouettes F: MVTecAD G: CIFAR-10", "role": "user" }, { "content": "[\"ImageNet\", \"CIFAR-10\"]", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: For example, patients with [high blood pressure] or diabetes have worse outcomes with COVID-19\n\nResearch Abstract:\nThe effects of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) on the risk of COVID-19 infection and disease progression are yet to be investigated.\nThe relationship between ACEI/ARB use and COVID-19 infection was systematically reviewed.\nTo identify relevant studies that met predetermined inclusion criteria, unrestricted searches of the PubMed, Embase, and Cochrane Library databases were conducted.\nThe search strategy included clinical date published until May 9, 2020.\nTwelve articles involving more than 19,000 COVID-19 cases were included.\nTo estimate overall risk, random-effects models were adopted.\nOur results showed that ACEI/ARB exposure was not associated with a higher risk of COVID-19 infection (OR = 0.99; 95 % CI, 0-1.04; P = 0.672).\nAmong those with COVID-19 infection, ACEI/ARB exposure was also not associated with a higher risk of having severe infection (OR = 0.98; 95 % CI, 0.87-1.09; P = 0.69) or mortality (OR = 0.73, 95 %CI, 0.5-1.07; P = 0.111).\nHowever, ACEI/ARB exposure was associated with a lower risk of mortality compared to those on non-ACEI/ARB antihypertensive drugs (OR = 0.48, 95 % CI, 0.29-0.81; P = 0.006).\nIn conclusion, current evidence did not confirm the concern that ACEI/ARB exposure is harmful in patientswith COVID-19 infection.\nThis study supports the current guidelines that discourage discontinuation of ACEIs or ARBs in COVID-19 patients and the setting of the COVID-19 pandemic.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: Some people with certain medical conditions, such as kidney problems, cannot safely take vitamin D.\n\nResearch Abstract:\nOBJECTIVE Coronavirus disease 2019 (COVID-19) is a fatal and fast-spreading viral infection.\nTo date, the number of COVID-19 patients worldwide has crossed over six million with over three hundred and seventy thousand deaths (according to the data from World Health Organization; updated on 2 June 2020).\nAlthough COVID-19 can be rapidly diagnosed, efficient clinical treatment of COVID-19 remains unavailable, resulting in high fatality.\nSome clinical trials have identified vitamin C (VC) as a potent compound pneumonia management.\nIn addition, glycyrrhizic acid (GA) is clinically as an anti-inflammatory medicine against pneumonia-induced inflammatory stress.\nWe hypothesized that the combination of VC and GA is a potential option for treating COVID-19.\nMETHODS The aim of this study was to determine pharmacological targets and molecular mechanisms of VC + GA treatment for COVID-19, using bioinformational network pharmacology.\nRESULTS We uncovered optimal targets, biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of VC + GA against COVID-19.\nOur findings suggested that combinatorial VC and GA treatment for COVID-19 was associated with elevation of immunity and suppression of inflammatory stress, including activation of the T cell receptor signaling pathway, regulation of Fc gamma R-mediated phagocytosis, ErbB signaling pathway and vascular endothelial growth factor signaling pathway.\nWe also identified 17 core targets of VC + GA, which suggest as antimicrobial function.\nCONCLUSIONS For the first time, our study uncovered the pharmacological mechanism underlying combined VC and GA treatment for COVID-19.\nThese results should benefit efforts to address the most pressing problem currently facing the world.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Craft a concise summary for a chemistry research paper using the provided title and selected text segments.\n\nHeading:\nRoles of Lewis Acid Catalysts in Diels‐Alder Reactions between Cyclopentadiene and Methyl Acrylate\n\nContent Extracts:\n\n<p>The Lewis acid catalyzed Diels-Alder reaction is a powerful tool for synthetic organic chemistry. [1] In the catalytic cycloaddition between dienes and dienophiles, Lewis acid catalysts have been shown to accelerate the reactions and make the reaction highly stereo-and/or regio-selective. [1,2] Houk and co-worker ascribed the reason why the Lewis acid facilitates the reaction with normal electron demand to the energy lowering of the LUMO in the dienophile part in the presence of Lewis acids. [3] Electron delocalization from the diene part to the dienophile part is thus strengthened by the attachment of a Lewis acid to the dienophile. This idea has widely been accepted until now. [4,5] Our previous study of the Diels-Alder reaction catalyzed by the Lewis acid activated oxazaborolidine, showed, however, that the weakening of the overlap repulsion between the occupied orbitals of diene and those of dienophile is another important outcome of attaching the catalyst. [6] Here, we examine in detail the mechanism of activation of the endo-cycloaddition by a Lewis acid catalyst, AlCl 3 , in the reaction between cyclopentadiene and methyl acrylate (Scheme 1), in which the endo/exo selectivity has been shown experimentally to be improved by adding the catalyst. [7] We investigated first the cycloaddition in the absence of Lewis acid by using M06-2X level DFT calculations. [8,9] Six transition state structures were obtained at the M06-2X/6-311(d,p) level of theory as shown in Figure 1. [10,11] Among the three transition states leading to the endo addition, called here TS endo-1 , TS endo-2 and TS endo-3 , TS endo-1 was calculated to be the lowest in energy. Calculations at the other levels of theory also show the same trend, though the barrier height obtained changes to some extent depending on the level of calculations as seen in Table 1. The most preferred transition state giving the exo addition, TS exo-1 , is located only 0.4 kcal/ mol above TS endo-1 . The energy difference is very small and, therefore, it is suggested that the stereoselectivity would not be high (cal. endo : exo = 0.69 : 0.31 at 273 K), [12] fairly in agreement with the experimental results. [7] The AlCl 3 -catalyzed reaction system gives also the six transition-state structures shown in Figure 2. [13] Among the three transition-state structures giving the endo product, TS' endo-1 , TS' endo-2 , and TS' endo-3 , the first has the lowest energy . In contrast to the non-catalyzed case, TS' exo-1 and TS' exo-3 are shown to be very similar in energy among the three exo transition-state structures with an attached AlCl 3 . The difference in energy between TS' endo-1 and TS' exo-3 is 2.8 kcal/mol, which is considerably larger than that between TS endo-1 and TS exo-1 . The attachment of AlCl 3 is shown to lead to a larger energy difference between the endo and exo transition states and, therefore, to a higher stereoselectivity (calc. endo : exo = 0.99 : 0.01 at 273 K) also in good agreement with the experimental observations. [12] Calculations at the other levels of theory show the same trend except for the PCM calculations (Table 2). The three endo transition-state structures are shown to be located more closely in energy and the three exo transition-state structures are so in dichloromethane, as compared with the results in vacuo. The energy difference between the endo and exo transition states remains similar to those obtained without the effect of solvent.</p><p>The relative Gibbs free energy diagram is shown in Figure 3. The energy of TS endo-1 relative to the two reactant molecules in an isolated state which corresponds to the activation energy is calculated here to be 22.9 kcal/mol. On the other hand, the energy difference between the reactant molecules (cyclopentadiene + AlCl 3 -attached methyl acrylate) and the transition state TS' endo-1 is 13.1 kcal/mol. The activation energy for AlCl 3 -catalyzed reaction is much lower than that for the non-catalyzed reaction. The calculations demonstrate not only that the endo selectivity is enhanced but also that the reaction is accelerated by an attachment of AlCl 3 .</p><p>For the transition state TS' endo-1 , IRC calculations were performed. [14] The calculations show clearly that the formation of the two CÀ C bonds is highly asynchronous in the presence of AlCl 3 , as illustrated in Figure 4(a). The C 2 À C 6 bond, which is located farther from the methoxycarbonyl group, is formed much faster than the other bond, C 3 À C 7 . The C 2 À C 6 bond is 2.01 angstrom at the transition state, but the C 3 À C 7 bond reaches the same bond length at a much later stage of the reaction, s ~4.0 amu 1/2 bohr. The fragment charge profile based on NPA charges, presented in Figure 4(b), demonstrates that electronic charge is shifted from the diene fragment to the dienophile fragment at an early stage of the reaction involving the transition state, and the net electronic charges on the fragments begin to be reduced at the later stage, after passing the point, s ~1.8 amu 1/2 bohr. This signifies that the C 2 À C 6 bond formation is brought about primarily by electron delocalization from the diene part to the dienophile part, while the C 3 À C 7 bond formation is associated mainly with electron delocalization in an opposite direction. In this point, the Lewis-acid catalyzed Diels-Alder cycloaddition studied here makes a clear contrast to the well-established concept of symmetry-allowed [4 + 2] cycloadditions. [15] The attached AlCl 3 part is seen to retain almost the same amount of negative charge throughout the reaction coordinate in this case.</p><p>Houk and co-worker proposed that the attached Lewis acid lowers the energy of LUMO of dienophile and, hence, accelerates the Diels-Alder reaction of normal electron demand. [3] One should note now that the dienophile molecule is polarized by the attachment of the Lewis acid molecule, as to reduce the π-type electron population on the terminal carbon, C 6 , and increase the π-type electron population on the other carbon, C 7 , of the C=C bond. This change in electron population is reflected in the electron-accepting orbital of the dienophile that shows a considerably larger amplitude on C 6 and in the electron-donating orbital that shows a larger amplitude on C 7 , in comparison with the dienophile without the catalyst (see, Figures S2 and S3 in Supporting Information). [16] The unoccupied and occupied interaction orbitals are lowered in energy by 2.05 eV and 1.79 eV, respectively, by attaching AlCl 3 . Electron delocalization from the diene to the dienophile, dominantly onto C 6 , is thus strengthened, whereas that from the dienophile part to the diene part, dominantly from C 7 , is not enhanced. In addition, the increase in electron population on C 7 leads to the strengthening of repulsion with C 3 of the diene that arises from the overlap between the occupied orbitals of the diene and those of the dienophile. On the other hand, the overlap repulsion between C 6 and C 2 is lightened. As a result, asynchronous formation of new CÀ C bonds should become marked in the catalyzed case. This view of bond formation is fully supported by a partitioning of overlap population of the C 2 À C 6 and C 3 À C 7 bonds into the repulsive and attractive orbital interactions (see, Tables S2 and S3 in Supporting Information).</p><p>In the Diels-Alder reactions, the endo transition state is placed generally under a stronger overlap repulsion between the occupied orbitals of the diene part and those of the dienophile part, but the repulsion is reduced by introducing electron-withdrawing groups into the dienophile part, as we have already seen in the cycloaddition between cyclopentadiene and maleic anhydride. [17] There the electrostatic attraction and delocalization-polarization are shown to be strong enough to cover the overlap repulsion that have been suppressed considerably by the electron deficiency in the dienophile ring. The \"normal electron demand\" in the reaction and the high endo selectivity are connected to each other at this point. [17,18] Introduction of electron-releasing groups into the diene part in place of introducing electron-withdrawing groups into the dienophile part is not a way to achieve high endo selectivity, as the path will suffer from an intense overlap repulsion. Though the barrier height obtained in this study depends slightly on the level of DFT calculations, the difference in the activation Gibbs free energy between TS endo-1 and TS exo-1 remains in a narrow range, 0.4-1.2 kcal/ mol (see Table 1), and that between TS' endo-1 and TS' exo-1 does so in the range of 2.2-3.5 kcal/mol (see Table 2), indicating that the endo transition state is preferred at all the levels of calculation. The RHF/6-311G(d,p) level calculation also gives similar results, as it did in the calculations on the cycloaddition between cyclopentadiene and maleic anhydride previously studied. [17] To see next the reason why the endo-path is preferred in this highly asynchronous process, let us compare the reacting system with AlCl 3 and the system without AlCl 3 that are produced by removing the AlCl 3 part from TS' endo-1 and TS' exo-1, respectively, freezing the geometry of other atoms as they were in those structures. A simple partitioning analysis of the interaction energy at the RHF/6-311G(d,p) level [19] and an analysis of the M06-2X/6-311G(d,p) level DFT interaction energy by a scheme proposed by Su and Li [20] indicate that the difference in energy between TS' endo-1 and TS' exo-1, comes not from the orbital interaction terms but mainly from the electrostatic attraction. [21] The sum of the repulsive and attractive orbital interaction terms, i. e., exchange and overlap repulsive interactions and electron delocalization between the diene and the dienophile with the associated polarization within the two parts, is very similar in magnitude in the endo-and exo-paths (see, Tables S4 and S5, and Figure S4 in Supporting Information). The electrostatic attraction between the diene part and the dienophile part is stronger in the endo structure than in the exo structure, the attraction between the positive charge on C 8 in the dienophile and the negative charges on C 4 and C 5 atoms in the diene part being added in the endo structure. Thus, the endo-addition is preferred even in the absence of AlCl 3 . The difference in electrostatic attraction between the two transition states becomes more significant, because the positive charges on C 8 gets larger in the dienophile polarized by attached AlCl 3 (the electrostatic potential maps and atomic charges of the reactants are shown in Figures S8 and S9, respectively, in Supporting Information). The energy difference between TS' endo-3 and TS' exo-3 can also be interpreted in this manner (Tables S6 and S7, and Figure S5 in Supporting Information). [22] In conclusion, electron delocalization strengthened in the presence of the Lewis acid lowers the barrier height of the cycloaddition to accelerate the reaction both in the endo-and exo-paths, while the electrostatic attraction favors the endo-path.</p><p>In summary, the reactivity and stereoselectivity in the Diels-Alder reaction between cyclopentadiene and methyl acrylate catalyzed by a Lewis acid are controlled by a combination of several interaction terms. An AlCl 3 molecule attached to the carbonyl oxygen atom of methyl acrylate lowers the energy of orbitals in acrylate and also polarizes the molecule. [23] The unoccupied interaction orbital of the dienophile that plays the dominant role in electron delocalization from the diene is lowered in energy and shows a larger amplitude on of the two reaction sites, C 6 , which is placed farther from the carbonyl group. Thus, the electronaccepting ability of the terminal carbon is enhanced. In contrast, the occupied interaction orbital tends to show a larger amplitude on the other reaction site, C 7 , but the orbital is also lowered considerably in energy by the presence of AlCl 3 . The electron-donating ability of that carbon is weakened. The electron redistribution caused by the attached Lewis acid reduces overlap repulsion in the C 2 À C 6 bond region and strengthens the repulsion in the C 3 À C 7 bond region. As a consequence, the formation of new CÀ C bonds is highly asynchronous in the Lewis-acid catalyzed Diels-Alder reaction between cyclopentadiene and methyl acrylate, the formation of the C 2 À C 6 bond preceding the formation of the C 3 À C 7 bond. Lower barrier heights are provided both for the endo-path and for the exo-path than those in the reaction without AlCl 3 . Here again the electrostatic interaction is shown to play an important role in bringing the high endo selectivity to this cycloaddition, as we have seen previously in the Diels-Alder reactions in which the formation of two CÀ C bonds take place in a synchronous manner. [17,24]</p>", "role": "user" }, { "content": "The Diels-Alder reaction of cyclopentadiene with methyl acrylate catalyzed by AlCl 3 has been theoretically investigated. M06-2X level DFT calculations have shown that the formation of two CÀ C bonds is asynchronous in the cycloaddition both in the endo path and in the exo path, thus making a good contrast to the well-known concept of [4 + 2] reactions based on the orbital symmetry arguments. It was found that the catalyst facilitates the cycloaddition and brings a higher endo selectivity in the highly asynchronous process, as compared with the reaction of the diene and the dienophile without the catalyst.", "role": "assistant" } ]

[ { "content": "Transform the following sections from a biomedical study into a simple summary for the general public. Focus on making the information accessible and easy to understand.\n\nResearch Heading: Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation\nContent:\nAbstract:\nAmino acid covariation, where the identities of amino acids at different sequence positions are correlated, is a hallmark of naturally occurring proteins. This covariation can arise from multiple factors, including selective pressures for maintaining protein structure, requirements imposed by a specific function, or from phylogenetic sampling bias. Here we employed flexible backbone computational protein design to quantify the extent to which protein structure has constrained amino acid covariation for 40 diverse protein domains. We find significant similarities between the amino acid covariation in alignments of natural protein sequences and sequences optimized for their structures by computational protein design methods. These results indicate that the structural constraints imposed by protein architecture play a dominant role in shaping amino acid covariation and that computational protein design methods can capture these effects. We also find that the similarity between natural and designed covariation is sensitive to the magnitude and mechanism of backbone flexibility used in computational protein design. Our results thus highlight the necessity of including backbone flexibility to correctly model precise details of correlated amino acid changes and give insights into the pressures underlying these correlations.\nIntroduction:\nEvolutionary selective pressures on protein structure and function have shaped the sequences of today's naturally occurring proteins[1]–[3]. As a result of these pressures, sequences of natural proteins are close to optimal for their structures[4]. Natural protein sequences therefore provide an excellent test for computational protein design methods, where the goal is to predict protein sequences that are optimal for a desired protein structure and function[5]. It is often assumed that given a natural polypeptide backbone conformation, an accurate protein design algorithm should be able to predict sequences that are similar to the natural protein sequence. This test is commonly referred to as native sequence recovery[4] and it has been used extensively to evaluate various protein design sampling methods and energy functions[6]–[8]. Beyond simply recovering the native sequence, a further challenge in computational protein design is to predict the set of tolerated sequences that are compatible with a given protein fold and function[9]–[13]. Predicting sequence tolerance is important for applications such as characterizing mutational robustness[14],[15], predicting the specificity of molecular interactions[16]–[20], and designing libraries of proteins with altered functions[21],[22]. Recent methods developed for this goal involve generating an ensemble of backbone structures similar to the native structure and then designing low energy sequences for the different structures in the ensemble[9],[16],[19],[23]–[25]. These flexible backbone design methods can produce sequences that are highly divergent from the native sequence but may still fold into the desired structure, which makes simple native sequence recovery a poor indicator for the accuracy of these methods. A more useful computational test of these approaches involves comparing designed sequences with a set of reference sequences, either naturally occurring or experimentally derived, that share the desired protein fold. This comparison can be based on sequence profile similarity, which involves quantifying the difference between the frequencies of observing each amino acid at corresponding positions in the designed and reference sequences[16],[17],[19]. While high similarity between designed and reference sequence profiles can be informative to gauge the accuracy of a protein design method, it does not guarantee that the method will predict sequences that fold into the desired structure. This is because sequence profile comparisons evaluate amino acid positions independently from each other and therefore ignore the details of amino acid interactions that are critical for protein structure and function. Naturally occurring protein structures are formed cooperatively and each amino acid can physically interact with multiple neighboring amino acids. Evolutionary selective pressures have acted upon these interactions, resulting in the patterns of amino acid covariation that can be observed within today's naturally occurring protein families. Accordingly, previous studies have used information theoretic methods to detect amino acid covariation in multiple sequence alignments of many different protein families[26]–[28] and have used contact prediction based on covariation to dramatically improve the accuracy of protein structure modeling[29]. Despite the clear occurrence of amino acid covariation in natural protein sequences, the extent to which different selective pressures have shaped amino acid covariation in diverse protein families is unknown. Additionally, it is difficult to dissect to what extent phylogenetic bias has influenced the observations of amino acid covariation. Previous work has indicated that networks of covarying amino acids play a role in allosterically linking distant functional sites, suggesting that amino acid covariation is driven by protein functional constraints[30],[31]. However, other studies have shown in two test cases that computational protein design can recapitulate naturally occurring covariation in the cores of SH3 domains[4],[13],[32] and for two-component signaling systems[33]. These results indicate that constraints imposed by protein structure have played a role in producing the covariation in the studied examples, but it has not yet been shown that these observations are general. In this paper, we use computational protein design to measure the extent to which protein structure has shaped amino acid covariation in a diverse set of 40 protein domains. Since computational protein design predicts sequences that are energetically optimal based on protein structure alone, we expect that pairs of amino acids that highly covary in both designed and natural sequences to have likely covaried to maintain protein structure. We find significant overlap in the sets of highly covarying amino acid pairs between designed and natural sequences for all 40 domains examined, suggesting that maintenance of protein structure is a dominant selective pressure that constrains the evolution of amino acid interactions in proteins. Our analysis furthermore quantifies the extent to which different types of interactions explain the observed covariation. Finally, we demonstrate the utility of amino acid covariation recapitulation as a sensitive test for evaluating different protein design methods. We find that flexible backbone design significantly improves covariation recapitulation relative to fixed backbone design and that recapitulation of amino acid covariation is exquisitely sensitive to both the magnitude and mechanism of backbone flexibility. Taken together, these results provide fundamental insights into the physical nature of amino acid co-evolution and, more practically, provide a new benchmark that may help improve the accuracy of computational protein design methods.\nDiscussion:\nOur study tested the hypothesis that the structural constraints imposed by protein architecture are a major determinant of amino acid covariation in naturally occurring proteins. If true, we reasoned that computational design methods that design sequences based on protein structure alone should be able to recapitulate amino acid covariation, provided that design predictions are sufficiently accurate. Confirming these ideas, we found a significant overlap between amino acid covariation in natural and designed protein sequences across a set of 40 diverse protein domains. These results quantify the influential role of the selective pressures for maintaining protein structure on shaping amino acid covariation. Therefore, even though correlated changes are undoubtedly important to evolve new activities and regulatory mechanisms[30],[31] the presence of covariation alone may not necessarily indicate a functional role. Our study also illustrates how recapitulation of amino acid covariation serves as a stringent test for the ability of computational protein design methods to capture precise details of interactions between amino acids. We demonstrate that modeling backbone flexibility significantly increases the similarity between natural and designed covariation, and that this similarity is exquisitely sensitive to the mechanism used to model backbone changes. These findings indicate that protein backbone motions are required for allowing precise adjustments in amino acid interactions that enable covariation. Moreover, simulations that perform local backbone movements( Backrub and KIC) result in sequences with more natural-like covariation than simulations that perform non-local backbone movements( AbRelax, Relax, Small). Proteins may have undergone local motions similar to Backrub and KIC moves to accommodate new mutations and amino acid interactions during evolution[24],[35],[36],[41]. Such motions could have provided proteins with a mechanism to allow subtle, incremental changes to their structures without adversely affecting protein structure or protein function. While local motions may be a common mechanism for proteins to accommodate point mutations, larger structural adjustments may be necessary for dealing with insertions or deletions. In this study, we found that a moderate degree of backbone flexibility best recapitulated natural amino acid covariation, however, the magnitude of structural variation produced by this degree of backbone flexibility was less than the structural variation among naturally occurring protein families. This discrepancy is likely due to the assumption in the design method that the protein remains a fixed length. This is not true in naturally occurring sequences; in fact, all 40 domains in our benchmark include loop regions that have varying lengths. Mutations that change the length of a flexible loop could allow for secondary structure elements to re-orient themselves and slightly alter the tertiary structure. The accumulation of mutations in loop regions can produce significant structural diversity that cannot be modeled using a protein design method that keeps the number of amino acids in a protein constant. Future protein design methods, particularly those involving loop regions such as protein-protein interaction design or enzyme specificity design, could potentially benefit from incorporating moves that both change the conformation and length of the protein backbone. In addition to observing significant similarity between the sets of natural and designed highly covarying amino acid pairs, we observed a high correlation in the amino acid propensities of these covarying pairs and showed that the structural mechanisms underlying covariation are similar for both natural and designed sequences. Differences between natural and designed covarying pairs highlight areas for improvement in the energy function used for protein design. For instance, cation-pi interactions, which are not explicitly accounted for in the energy function used in this study, have high propensities among naturally covarying pairs but not in designed covarying pairs. Similarly, polar amino acid pairs are more frequent in the cores of designed proteins than in naturally occurring proteins. Interestingly, we found differences in the pair propensities between nature-specific pairs and pairs that highly covary in both natural and design sequences. We also observed that nature-specific pairs tend to be more distant in three-dimensional structure. These results have implications for the field of contact prediction, as combining amino acid covariation with amino acid pair propensity information could improve the prediction of three-dimensional contacts in protein structures compared to using amino acid covariation alone. Improving methods of contact prediction would increase the accuracy of recent protein structure prediction algorithms that use amino acid covariation[29]. Unlike nature-specific pairs, design-specific pairs have amino acid propensities that are highly correlated with the amino acid propensities of pairs that covary in both natural and designed sequences. These design-specific pairs represent candidate positions for engineering amino acid interactions that have not been sampled by natural protein evolution. A practical application of this is the re-wiring of protein interaction specificity to design orthogonal protein-protein interactions for use in synthetic biology. Natural intermolecular covariation has previously been exploited to alter specificity in two component signaling systems[42]. Future work could exploit designed intermolecular covariation to re-engineer protein interactions with novel specificities that are orthogonal from naturally occurring protein-protein interactions[43] and therefore useful for synthetic applications.", "role": "user" }, { "content": "Proteins generally fold into specific three-dimensional structures to perform their cellular functions , and the presence of misfolded proteins is often deleterious for cellular and organismal fitness . For these reasons , maintenance of protein structure is thought to be one of the major fitness pressures acting on proteins . Consequently , the sequences of today's naturally occurring proteins contain signatures reflecting the constraints imposed by protein structure . Here we test the ability of computational protein design methods to recapitulate and explain these signatures . We focus on the physical basis of evolutionary pressures that act on interactions between amino acids in folded proteins , which are critical in determining protein structure and function . Such pressures can be observed from the appearance of amino acid covariation , where the amino acids at certain positions in protein sequences are correlated with each other . We find similar patterns of amino acid covariation in natural sequences and sequences optimized for their structures using computational protein design , demonstrating the importance of structural constraints in protein molecular evolution and providing insights into the structural mechanisms leading to covariation . In addition , these results characterize the ability of computational methods to model the precise details of correlated amino acid changes , which is critical for engineering new proteins with useful functions beyond those seen in nature .", "role": "assistant" } ]

[ { "content": "Examine the abstracts provided from a main scientific article and its cited works. Craft a narrative that synthesizes the key insights and contributions, emphasizing their interconnections. Employ numerical citations such as [1], [2], etc., to reference the cited works.\n\nMain Article Summary:\nIn the software development industry, technical debt is regarded as a critical issue in term of the negative consequences such as increased software development cost, low product quality, decreased maintainability, and slowed progress to the long-term success of developing software. However, despite the vast research contributions in technical debt management for software engineering, the idea of technical debt fails to provide a holistic consideration to include both IT and business aspects. Further, implementing an enterprise architecture (EA) project might not always be a success due to uncertainty and unavailability of resources. Therefore, we relate the consequences of EA implementation failure with a new metaphor --Enterprise Architecture Debt (EA Debt). We anticipate that the accumulation of EA Debt will negatively influence EA quality, also expose the business into risk.\n\nCited Works Summary:\n[1]: The metaphor of technical debt in software development was introduced two decades ago to explain to nontechnical stakeholders the need for what we call now \"refactoring.\" As the term is being used to describe a wide range of phenomena, this paper proposes an organization of the technical debt landscape, and introduces the papers on technical debt contained in the issue.", "role": "user" }, { "content": "According to [1] Technical Debt refers to invisible elements, because visible elements for improving, like new features for evolution or repairing defects for maintainability issues, should not be considered as debt. Technical debt should rather serve as a retrospect reflecting change of the environment, rapid success, or technological advancements as a possible cause for debt. However, the debt might actually be a good investment, but it's imperative to remain aware of this debt and the increased friction it will impose on the development team'' [1] . Hence, tools are required to increase the awareness to identify debt and its causes, and to manage debt-related tasks. Finally, the debt should not be treated in isolation from the visible elements of evolving and maintaining. Consequently, debt is the invisible result of past decisions about software that negatively affect its future'' [1] .", "role": "assistant" } ]

[ { "content": "Explore the following research question and associated terms. Identify the most suitable dataset from the list provided. Use the dataset descriptions to guide your choice.\n\nInquiry: We propose a semi-supervised method to improve heading direction estimation performance. The proposed algorithm is\n\nKeywords: aerial filming video\n\nDataset Information:\nFriedman1: The friedman1 data set is commonly used to test semi-supervised regression methods.\nUCF101: UCF101 dataset is an extension of UCF50 and consists of 13,320 video clips, which are classified into 101 categories. These 101 categories can be classified into 5 types (Body motion, Human-human interactions, Human-object interactions, Playing musical instruments and Sports).\nSuperGLUE: SuperGLUE is a benchmark dataset designed to pose a more rigorous test of language understanding than GLUE. SuperGLUE has the same high-level motivation as GLUE: to provide a simple, hard-to-game measure of progress toward general-purpose language understanding technologies for English.\nVOT2018: VOT2018 is a dataset for visual object tracking. It consists of 60 challenging videos collected from real-life datasets.\n\nAvailable Datasets: A: Friedman1 B: UCF101 C: SuperGLUE D: VOT2018", "role": "user" }, { "content": "UCF101", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\nspasticity is a common neurological complication following central nervous system injuries such as traumatic or acquired brain and spinal cord injury .\nindications for the treatment of spasticity include pain , function limitations , contracture prevention , and positioning assistance .\nnon - pharmacological modalities include proper positioning of the affected body region , range of motion / stretching exercises , splinting , or casting .\nhowever , the use of medications can be limited by cognitive and sedative side effects .\nthus , the use of botulinum toxin ( bont ) type a and b injections has been preferred for localized spasticity .\nit binds presynaptic peripheral cholinergic nerve endings , acting intracellularly to cleave polypeptides involved in acetylcholine and norepinephrine exocytosis.1,2 in multiple systematic reviews and clinical trials , bont used for various muscle tone disorders has proven to reduce spasticity , increase range of motion , improve positioning , and decrease pain.36 bont is also approved for the treatment of blepharospasm , overactive bladder , chronic migraine , axillary hyperhidrosis , and strabismus.7 as with any pharmacological therapies for spasticity , onabotulinumtoxin a ( botox ) is also associated with adverse effects such as nausea , fatigue , bronchitis , muscular weakness , and pain.7,8 in cases of detrusor overactivity , there have been reports of hematuria associated with bont injections.9 although this may be a result of mucosal trauma from the injection itself , studies have demonstrated a greater incidence of hematuria in bont groups compared with placebo and also with higher drug concentrations.10,11 however , there are few to no reports of hematuria when it is used for spasticity in the upper limb .\nthis case documents the unusual side effect of hematuria following bont injection for upper limb spasticity .\na 29-year - old male with a history of hemophilia a presented to an outpatient specialty clinic for right upper limb spasticity secondary to traumatic brain injury .\nthe institutional review board of university of california , irvine , orange , ca , usa approved collection of patient data with written consent .\nthe patient reported dull pain localized to his right wrist radiating up to the shoulder ( rated 68/10 on a numeric rating scale ) and associated paresthesias of the second to fifth digits .\nthe pain improved with massage , but was exacerbated with writing and long distance stick shift driving involving finger flexion with repetitive elbow and shoulder joint motions .\nthis condition was previously treated with 140 units of bont , resulting in limited improvement of his pain .\nexamination of his right upper limb revealed increased tone ( rated 1 on the modified ashworth scale ) with shoulder internal rotation and adduction , elbow flexion , and wrist flexion .\nhe had no atrophy of the right thenar eminence , but had decreased strength of the right finger and thumb .\nthe previous diagnosis of pain due to right upper limb spasticity was confirmed , and was further treated with a total of 500 units of onabotulinumtoxin a ( 100 units for right anterior deltoid , 50 units for pectoralis , 100 units for biceps , 75 units for brachioradialis , 50 units for brachialis , 75 units for extensor carpi radialis , 25 units for extensor carpi ulnaris , and 25 units for flexor digitorum superficialis ) . after a month , his pain decreased to 45/10 on the numeric rating scale .\nhowever , a day after leaving the clinic , the patient reported developing hematuria , which lasted 45 days and resolved upon self - infusion of factor viii as recommended by his hematologist . of note\n, he had not had hematuria in the past and does not require regular infusions .\ngiven his history of bladder stones , he was further evaluated in the emergency room , where the workup did not show evidence of cystoliths or urinary tract infection .\nbont preferentially binds and penetrates peripheral cholinergic nerve endings , acting intracellularly on metalloendoprotease to cleave polypeptides involved in acetylcholine exocytosis.1 by preventing acetylcholine release from the presynaptic membrane , bont blocks nerve impulses involved in muscle contractions , which induces chemodenervation resulting in decreased muscle tone.12 bont also causes muscle fiber atrophy and reduces the potential size of motor units , leading to weakness in muscle strength .\nstudies have demonstrated the clinical effect of bont in patients with upper limb spasticity from traumatic brain injury and stroke resulting in improved range of motion as well as in modified ashworth scale rating and muscle tone.13,14 various side effects , including pain , fatigue , muscle weakness , bronchitis , and upper respiratory tract infections have been reported with bont injection for upper limb spasticity , but little is known of bont - associated hematuria when used for spasticity in the upper limb .\nthis report illustrates hematuria that resolved after self - infusion of factor viii . as such\n, bont may play a role in the intrinsic coagulation cascade , resulting in or exacerbating spontaneous hemorrhage in those with underlying hematological deficiencies .\nacetylcholine is suggested to be involved in the activation of antifibrinolytic compounds.15 another study has reported similar mechanisms , implying that acetylcholine results in increased thrombin release and prothrombin gene expression.16 additionally , higher concentrations of the toxin are able to block norepinephrine exocytosis from other nerve endings.2 a report has shown norepinephrine increases thrombin and fibrin formation via 2-adrenergic receptors.17 another study demonstrated similar findings when norepinephrine was infused into patients with traumatic brain injury , resulting in a reduction in platelets possibly due to thrombus formation.18 as such , by blocking norepinephrine release , higher levels of bont may indirectly prevent clot formation , resulting in spontaneous hemorrhage . therefore , it is hypothesized that by reducing the release of acetylcholine and norepinephrine , bont causes spontaneous hemorrhage through an anticoagulation effect .\nfurthermore , our patient had a history of factor viii deficiency , which imposes a greater risk for spontaneous bleeding .\nhemophilia is an inherited x - linked disorder associated with a defect of clotting factor viii or ix .\nspontaneous hematuria is relatively common in patients with hemophilia , and theorized to be due to tubular damage caused by immune complexes.19 this , in sequence with the negative effect of bont on coagulation , suggests that its use may convert what typically occurs as clinically insignificant microhematuria into gross hematuria by destabilizing clot formation that is used to heal the damage that occurs at baseline in patients with hemophilia .\nalthough it is difficult to explain systemic reactions caused by localized bont injection , some studies have shown subclinical effects of the toxin distant from the injection site .\npost - marketing surveillance reports have illustrated toxin spread in adults treated for spasticity , such as dysphagia and breathing difficulties after treatment of cervical dystonia.7 likewise , a double - blind , placebo - controlled trial reported an increased incidence of dry mouth in patients treated with bont for upper limb spasticity.20 additional findings were seen in a study that demonstrated an increased average jitter value on single fiber electromyography of the extensor digitorum after patients with craniocervical dystonia and hemifacial spasms received twice the dose of bont injections.21 a similar dose - related response was seen in our case as the patient was able to tolerate lower doses of the toxin without complication , but developed hematuria with increased doses .\nfurthermore , dose - dependent responses have been observed in clinical accounts involving generalized weakness after upper limb injection , and detrusor weakness in patients with detrusor hyperreflexia.22,23 these studies suggest that despite localization , bont may enter the systemic circulation , resulting in generalized effects in a dose - dependent manner .\nclinically , it is critical to consider the potential systemic effects with localized bont injections .\nit can be hypothesized that bont has a negative effect on the coagulation cascade , given the effects of acetylcholine and norepinephrine on thrombin and fibrin .\ntherefore , it is crucial that clinicians are aware of the bleeding risk with a dosage increase , especially in patients with pre - existing hematological disorders .\nadditional studies should be undertaken to further elucidate the effect of bont in the coagulation pathway as well as to determine optimal doses and techniques that may avoid these complications .", "role": "user" }, { "content": "hematuria is a documented side effect of botulinum toxin injection and has only been reported when it is used for overactive bladder . \n here we report a rare case of hematuria following onabotulinumtoxin a ( botox ) injection for upper limb spasticity in a 29-year - old male with a history of traumatic brain injury and hemophilia . \n hematuria resolved without further complication after self - injection of factor viii as recommended by his hematologist . \n botulinum toxin binds peripheral cholinergic nerve endings to prevent acetylcholine and norepinephrine exocytosis . \n studies have shown that both of these compounds are involved in antifibrinolytic activation , suggesting botulinum toxin may play a role in the coagulation cascade by preventing formation of fibrin . \n this is further supported by resolution of hematuria in our patient after self - injection of factor viii . \n as such , botulinum toxin injection may result in mild spontaneous hemorrhage in patients with underlying hematological deficiencies . \n further studies are needed to elucidate its effects in coagulation .", "role": "assistant" } ]

[ { "content": "Consider the following research inquiry and associated key terms. Review the dataset summaries provided and determine which datasets are suitable for addressing the research question. Base your decision on your understanding of machine learning datasets.\nProvide your answer as a JSON list. For example, for the inquiry \"Semi supervised image classification\", a possible response could be: [\"CIFAR-10\", \"CIFAR-100\"]. Ensure the response contains only the dataset names in JSON format.\n\nResearch Inquiry: I want to solve the problem of class-distinct and\n\nKey Terms: class-distinct class-mutual image generation images\n\nDataset Summaries:\nLS3D-W: A 3D facial landmark dataset of around 230,000 images.\nCelebA: CelebFaces Attributes dataset contains 202,599 face images of the size 178×218 from 10,177 celebrities, each annotated with 40 binary labels indicating facial attributes like hair color, gender and age.\nMathQA: MathQA significantly enhances the AQuA dataset with fully-specified operational programs.\nCIFAR-10: The CIFAR-10 dataset (Canadian Institute for Advanced Research, 10 classes) is a subset of the Tiny Images dataset and consists of 60000 32x32 color images. The images are labelled with one of 10 mutually exclusive classes: airplane, automobile (but not truck or pickup truck), bird, cat, deer, dog, frog, horse, ship, and truck (but not pickup truck).\nSNIPS: The SNIPS Natural Language Understanding benchmark is a dataset of over 16,000 crowdsourced queries distributed among 7 user intents of various complexity: SearchCreativeWork (e.g. Find me the I, Robot television show), GetWeather (e.g.\nRAVEN: RAVEN consists of 1,120,000 images and 70,000 RPM (Raven's Progressive Matrices) problems, equally distributed in 7 distinct figure configurations.\n\nDataset Options: A: LS3D-W B: CelebA C: MathQA D: CIFAR-10 E: SNIPS F: RAVEN", "role": "user" }, { "content": "[\"CelebA\", \"CIFAR-10\"]", "role": "assistant" } ]

[ { "content": "Examine the given text from a research paper in the field of NLP. Your task is to identify the role of the citation within the context provided. Focus on understanding the intent behind the citation and classify it accordingly.\n\nSection Title:\nNone\n\nText Before Citation:\nThe last years have seen considerable advances in the field of anaphora resolution, but a number of outstanding issues either remain unsolved or need more attention and, as a consequence, represent major challenges to the further development of the field (Mitkov 2001a). Instead of defining a total preference ordering, Kibble argues that a partial ordering emerges from the interaction among cohesion (maintaining the same center), salience (realizing the center as subject), and cheapness (realizing the anticipated center of a following utterance as subject). Finally, in his squib Kibble discusses a reformulation of the centering transitions (Continue, Retain, and Shift), which specify the center movement across sentences.\n\nCitation Text:\nThe last years have seen considerable advances in the field of anaphora resolution , but a number of outstanding issues either remain unsolved or need more attention and , as a consequence , represent major challenges to the further development of the field ( Mitkov 2001a ) .\n\nText After Citation:\nA fundamental question that needs further investigation is how far the performance of anaphora resolution algorithms can go and what the limitations of knowledge-poor methods are. In particular, more research should be carried out on the factors influencing the performance of these algorithms. One of the impediments to the evaluation or fuller utilization of machine learning techniques is the lack of widely available corpora annotated for anaphoric or coreferential links. More work toward the proposal of consistent and comprehensive evaluation is necessary; so too is work in multilingual contexts.", "role": "user" }, { "content": "FutureWork", "role": "assistant" } ]

[ { "content": "Analyze the given paragraph from COVID-19 research. Determine the relevant topics discussed in the text. Your response should be a JSON array containing the identified topics. Ensure the output is a valid JSON array with no additional commentary.\n\nText:\n\nThe Italian College of Breast Radiologists by the Italian Society of Medical Radiology (SIRM) provides recommendations for breast care provision and procedural prioritization during COVID-19 pandemic, being aware that medical decisions must be currently taken balancing patient's individual and community safety: (1) patients having a scheduled or to-be-scheduled appointment for in-depth diagnostic breast imaging or needle biopsy should confirm the appointment or obtain a new one; (2) patients who have suspicious symptoms of breast cancer (in particular: new onset palpable nodule; skin or nipple retraction; orange peel skin; unilateral secretion from the nipple) should request non-deferrable tests at radiology services; (3) asymptomatic women performing annual mammographic follow-up after breast cancer treatment should preferably schedule the appointment within 1 year and 3 months from the previous check, compatibly with the local organizational conditions; (4) asymptomatic women who have not responded to the invitation for screening mammography after the onset of the pandemic or have been informed of the suspension of the screening activity should schedule the check preferably within 3 months from the date of the not performed check, compatibly with local organizational conditions. The Italian College of Breast Radiologists by SIRM recommends precautions to protect both patients and healthcare workers (radiologists, radiographers, nurses, and reception staff) from infection or disease spread on the occasion of breast imaging procedures, particularly mammography, breast ultrasound, breast magnetic resonance imaging, and breast intervention procedures.", "role": "user" }, { "content": "[\"Prevention\"]", "role": "assistant" } ]

[ { "content": "Analyze the given text to identify specific entities. Focus on extracting relevant data.\n\nProvide your findings in JSON format. Each category should list the entities found.\n\nText:\n\nDynamics and structural changes of small water clusters on ionization. Despite utmost importance in understanding water ionization process, reliable theoretical results of structural changes and molecular dynamics (MD) of water clusters on ionization have hardly been reported yet. Here, we investigate the water cations [(H2 O)n = 2-6 (+) ] with density functional theory (DFT), Möller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The complete basis set limits of interaction energies at the CCSD(T) level are reported, and the geometrical structures, electronic properties, and infrared spectra are investigated. The characteristics of structures and spectra of the water cluster cations reflect the formation of the hydronium cation moiety (H3 O(+) ) and the hydroxyl radical. Although most density functionals fail to predict reasonable energetics of the water cations, some functionals are found to be reliable, in reasonable agreement with high-level ab initio results. To understand the ionization process of water clusters, DFT- and MP2-based Born-Oppenheimer MD (BOMD) simulations are performed on ionization. On ionization, the water clusters tend to have an Eigen-like form with the hydronium cation instead of a Zundel-like form, based on reliable BOMD simulations. For the vertically ionized water hexamer, the relatively stable (H2 O)5 (+) (5sL4A) cluster tends to form with a detached water molecule (H2 O). © 2013 Wiley Periodicals, Inc.", "role": "user" }, { "content": "{\"Chemical\": [\"(H2 O)5 (+)\", \"hydronium\", \"(H2 O)n\", \"hydroxyl\", \"H2 O\", \"H3 O(+)\"]}", "role": "assistant" } ]

[ { "content": "Read the provided biomedical research paper and create a concise abstract. Ensure the abstract captures the main points of the paper.\n\nFull Paper:\nthe anorectum plays an important role in regulation of defecation and in the maintenance of continence.1 the most widely used test for anorectal function is anorectal manometry . a comprehensive assessment of anorectal function consists of measuring at a minimum each of the following parameters : ( 1 ) anal sphincter function , ( 2 ) rectoanal reflex activity , ( 3 ) rectal sensation , ( 4 ) changes in anal and rectal pressures during attempted defecation , ( 5 ) rectal compliance and ( 6 ) performance of a balloon expulsion test.2\nanal sphincter function is assessed by measurement of resting sphincter pressure , squeeze sphincter pressure , and the functional length of the anal canal .\nmaximum resting anal canal tone predominantly reflects internal anal sphincter function , while voluntary anal squeeze pressure reflects external anal sphincter ( eas ) function .\nfunctional anal canal length is defined as the length of the anal canal over which resting pressure exceeds that of the rectum by greater than 5 mmhg or , alternatively , as the length of the anal canal over which pressures are greater than half of the maximal pressure at rest ( fig .\nmaximal resting anal pressure is defined as the difference between intrarectal pressure and the highest recorded anal sphincter pressure at rest , and is generally recorded 1 - 2 cm from the anal verge .\nmaximum squeeze pressure is defined as the difference between the intrarectal pressure and the highest pressure that is recorded at any level within the anal canal during the squeeze maneuver ( fig .\nrapid distention of the rectum induces a transient increase in rectal pressure , followed by a transient increase in anal pressure associated with eas contraction ( the rectoanal contractile reflex ) , and in turn , a more prolonged reduction in anal pressure due to relaxation of the internal anal sphincter ( the rectoanal inhibitory reflex , fig .\nthe rectoanal contractile reflex is a compensatory guarding mechanism that allows a positive anorectal pressure gradient to be maintained during transient increases in intra - abdominal pressure ( such as coughing ) , which is essential for preserving continence . in fecal incontinence patients , anal sphincter pressure\nthe lowest volume of air that evokes sensation and a desire to defecate , and the maximum tolerable volume are recorded.4 assessment of rectal sensation is useful in patients with fecal incontinence or rectal hyposensitivity .\nwhen an individual is requested to ' bear down , ' as if attempting to defecate , the normal response consists of an increase in rectal pressure that is coordinated with a relaxation of the eas ( fig .\ninability to perform this coordinated maneuver suggests a diagnosis of dyssynergic or obstructive defecation , a common cause of constipation.5 this response can be quantified using the defecation index = maximum rectal pressure during attempted defecation / minimum anal residual pressure during attempted defecation .\na normal defecation index is > 1.5.5 three types of dyssynergic defecation are recognized.6 most patients show paradoxical increase in anal sphincter pressure during attempted defecation with normal adequate pushing force ( type 1 , fig .\nsome patients are unable to generate an adequate pushing force , and exhibit a paradoxical anal contraction ( type 2 ) . in type 3 , the patient can generate an adequate pushing force , but has absent or incomplete ( < 20% ) sphincter relaxation .\nrectal compliance is calculated by plotting the relationship between balloon volume ( dv ) and steady state intrarectal pressure ( dp ) .\nthe balloon expulsion test is used to assess rectoanal co - ordination during defecatory maneuvers.7 the test evaluates a patient 's ability to expel a filled balloon from the rectum , providing a simple and more physiologic assessment of defecation dynamics .\nmost normal subjects can expel the balloon within 1 minute.5 if the patient is unable to expel the balloon within 3 minutes , dyssynergic defecation should be suspected .", "role": "user" }, { "content": "anorectal manometry is the most well established and widely available tool for investigating anorectal function . \n anal sphincter tone can be quantified by anorectal manometry . the anorectal sensory response , \n anorectal reflexes , rectal compliance , and defecatory function are also assessed by anorectal manometry . \n this report will focus on defining parameters for measurement and interpretation of anorectal manometry tests .", "role": "assistant" } ]

[ { "content": "Given the full text of a scientific research paper, write an abstract section for the paper. Your response should contain only the abstract without any other text.\n\nArticle text:\nvortices in magnetic field concentrations in the simulated upper solar photosphere , first identified by @xcite , have recently attracted a lot of interest .\nthese structures have been suggested as a primary candidate mechanism for energy transport from the solar interior to the outer layers of the solar atmosphere @xcite .\nrecently , @xcite demonstrated that the major contributor to vertical vorticity in these photospheric magnetic field concentrations is magnetic tension in the low plasma @xmath0 regions .\ninitial analysis of velocity fields in magnetic photospheric vortices demonstrated a complex multi - layered structure of oppositely rotating surfaces with nearly constant vorticity that are parallel to the magnetic field lines @xcite .\n@xcite found a similar behaviour of the velocity field in the solar photospheric simulations carried out with co5bold @xcite .\npoynting flux emerging from the simulated solar photosphere was linked to the horizontal plasma motions in the photospheric magnetic field @xcite .\n@xcite showed that vortex motions in the simulated photosphere are able to dissipate their energy and produce additional local heating of the solar chromosphere .\n@xcite suggested that small - scale solar atmospheric eruptions , such as spicules , are linked to horizontal vortex - like motions in photospheric magnetic flux tubes .\n@xcite observationally demonstrated excitation of incompressible waves in the solar chromosphere by photospheric vortex motions . using multi - wavelength observations\n, it was recently demonstrated that these essentially magnetic structures extend from the lower photosphere to the corona , and are connected to the observed swirls in the solar chromosphere @xcite and lower coronal regions @xcite . in this letter , using a time series of magnetised photospheric models produced by the muram code @xcite , we further analyse the character of plasma motions in intergranular magnetic field concentrations . we demonstrate that , if dependence of the local velocity field on time is taken into account , the apparent swirling motions in the strong magnetic field disappear , and swirls do not exist in photospheric magnetic flux tubes . instead , a wave - like behaviour is observed for horizontal motions of test particles following the time - dependent velocity field . the restoring force of magnetic tension acts as a conduit of oscillatory vorticity upward from deeper photospheric layers , where it is generated by convective motions .\nusing vertical - component - of - vorticity time - distance diagrams taken along a vertical axis we show that the vorticity perturbations propagate upward along the nearly - vertical field lines of photospheric magnetic field concentrations with time - dependent local alfvn speed , and thus can be identified as torsional alfvn waves .\nthis result also explains quasiperiodic oscillations and the short lifetimes of photospheric magnetic vortices , as noted by @xcite and @xcite .\nthis letter is structured as follows . in section 2\nwe describe the simulation setup and the data we use for our analysis of photospheric vortices .\nthe time - distance analysis of plasma motions in the upper - photospheric magnetic field concentrations is described in section 3 .\nsection 4 concludes our findings .\nthe muram radiative mhd code @xcite has been used to carry out simulations of the magnetised solar photosphere .\nthe code is well - tested , has demonstrated similar performance to other radiative mhd codes available in the community@xcite , and has been widely used to provide an insight into the physical processes behind various solar observational phenomena , such as , for example , sunspots @xcite , magnetic flux emergence @xcite , and photospheric bright points @xcite .\nthe code reproduces thermal and radiative properties of the solar photosphere well , as demonstrated by comparison of simulated photospheric spectral lines with observations @xcite . for the analysis presented in this letter we use the code setup described in detail by @xcite .\nthe physical domain size is @xmath1 in the horizontal directions and @xmath2 in the vertical direction , and the resolution is @xmath3 and @xmath4 , respectively . to generate the photospheric data\n, we introduce a uniform 200 g vertical magnetic field into a well - developed non - magnetic photospheric convection model , and , after the initial transient phase ( about 40 minutes of physical time ) , we record 240 snapshots of photospheric model data with a mean cadence of 2.41 seconds .\nthis short time step is required to capture processes at alfvnic time scales in strongly magnetised regions of the solar photosphere where the characteristic speed can reach 50100 @xmath5 . during the initial simulation phase\n, the magnetic field is advected into the intergranular lanes by convective motions , and photospheric magnetic flux concentrations with the strength of about 1.7 kg at the continuum formation height and of about 800 g in the upper photosphere are formed .\nsimultaneously , magnetic vortex structures appear in the low plasma @xmath0 regions of the simulated solar atmosphere .\nfigure [ fig1 ] displays the dependences of absolute values of magnetic ( black curve ) and hydrodynamic ( blue curve ) sources in the vertical component of vorticity according to equation ( 4 ) of @xcite , as well as the modulus of the vertical component of vorticity itself ( pink curve ) , all averaged horizontally over the numerical domain .\nthe figure shows that in the lower photosphere ( below 0.2 mm ) the main source of vorticity is compressible fluid motion .\nconversely , in the strongly magnetised upper photosphere ( above 0.2 mm ) , magnetic sources dominate over purely hydrodynamic vorticity sources .\nthis clearly indicates that magnetic field effects are responsible for a strong increase in vertical vorticity above 0.3 mm in the photosphere .\n@xcite demonstrated that the vorticity source term , which contains magnetic tension , is responsible for this effect .\nto visualise the three - dimensional velocity field in as simple and clear a manner as possible , we use a small number of seed particles that are randomly magnetic field - weight distributed around a magnetic field concentration over a horizontal plane close to the top boundary of the domain .\nthis biases them toward the strong - field regions near the tube axis .\nwe first plot probe particle tracks under the action of the velocity field obtained from the first snapshot of the data series .\nan example of probe particle tracks under the action of this velocity field is shown in fig .\nthese are streamlines .\nas is evident from the figure , a vortex - like structure is present in the upper part of the simulated photosphere .\nhowever , if the probe particles with the same initial coordinates are let to evolve in the time - dependent velocity field from the whole time series of the simulation , the upper - photospheric vortex completely disappears and is replaced by nearly random , quasi - oscillatory particle tracks ( see fig .\n[ fig3 ] ) .\nthese are pathlines .\nstreamlines and pathlines coincide only in steady flows .\ntheir disparity clearly demonstrates that three - dimensional flow in upper - photospheric vortices in regions of strong magnetic field is far from steady .\n@xcite recently pointed out that the low twist of the magnetic field lines in their modelling indicates a non - stationary character of the flow .\nindeed , the time scale for flow change is similar to the flow time scale itself .\nthus , processes in the upper - photospheric magnetic vortices can not be physically related to those in sinks or tornadoes in earth s atmosphere , where steady velocity fields are present .\nvortical flow in a low - beta atmosphere can not be sustained over many alfvn crossing times unless it is an essentially solid - body rotation induced by rotational flows or flux tube unwindings in the high - beta layers below , since dominant magnetic tension will resist it .\nin the following section , we confirm this finding with more detailed analysis of propagation of the vorticity perturbation through the solar atmosphere .\nbasic analysis of the probe particle motions given in the previous section shows an absence of steady vortex flows in photospheric magnetic field concentrations .\nthe presence of both vorticity signs , earlier reported by @xcite and @xcite , manifests both clockwise and anti - clockwise torsional motions within the same magnetic structure .\nthis fact suggests wave - like motions of the plasma in photospheric magnetic field concentrations . to study these waves and to identify their types we perform time - distance analysis of the vorticity perturbation along the magnetic field lines in the simulated domain .\nconstruction of time - dependent three - dimensional magnetic surfaces is a computationally difficult task , so we choose points where the magnetic field is nearly vertical in the neighbourhood of the upper boundary of the domain .\nfigure [ fig4 ] shows a map of the vertical ( @xmath6-)component of vorticity measured at about 500 km above the average continuum formation level ( left panel ) , and four examples of time - distance diagrams of vertical propagation of the vertical component of vorticity . in choosing the examples , we restricted the selection to waves that propagate upwards only , though both upward and downward directions of wave propagation are observed .\nas is evident from the plots , all examples show oscillatory patterns of fast - propagating perturbations along the vertical direction .\nwe were able to identify the wave type by overplotting the path for a test particle , which moves with the local , time - dependent alfvn speed , according to the equation @xmath7 in _ cgs _ units , where @xmath8 is local time - dependent vertical flow speed .\nthe test particle tracks are plotted over the time - distance diagrams and clearly coincide with the oscillatory pattern of the vertical component of the vorticity .\nnotably , the mean vertical flow speed averaged over the time series never exceeds @xmath9 , and the maximum vertical flow speed is about @xmath10 .\ntherefore , motions of the test particles with speed about @xmath11 can not be explained by vertical plasma flows , as is evident from fig .\nthis finding demonstrates that the propagation speed for the vorticity perturbation is equal to the alfvn speed . in the plots shown in the right part of fig .\n[ fig4 ] , the maximum magnetic field inclination angle in the time - distance region where a clear wave propagation pattern is observed is less than @xmath12 .\ntherefore , the assumption about equivalence of propagation along the magnetic field line and along the vertical direction is well - justified . summarising the findings ,\nthe perturbation in the vertical component of the vorticity , that propagates vertically along magnetic field lines , is a horizontal torsional velocity perturbation , and thus it can be identified as a torsional alfvn wave .\nin fact , nearly all vertical columns in the regions of strong magnetic field in the simulation domain show propagation of a perturbation with speed close to the alfvn speed .\nabundance of these patterns in the domain and nearly perfect agreement between the perturbation phase speed and the alfvn speed also rule out a possibility of advection of pre - existing vorticity patterns by horizontal bulk flows .\nthus , it can be concluded that torsional alfvn waves originating in the higher photosphere are abundant in plage regions of the solar photosphere .\nin this letter , we analysed apparent photospheric magnetic vortex structures in a dynamic realistic simulation of solar photospheric magnetoconvection .\nwe identified that no long - lived vortex structures in photospheric magnetic field concentrations exist .\ninstead , the time - dependent velocity field obtained from the simulations shows oscillatory behaviour in the strong intergranular magnetic field regions . using time - distance analysis of the vertical component of vorticity we found that the perturbations propagate vertically along the magnetic field lines with speeds equal to the local alfvn speed .\nthus we identified the perturbations as torsional alfvn waves in intergranular magnetic flux concentrations . in the structures shown in our simulations the velocity pattern changes within approximately 50 seconds to the opposite direction .\nthis timescale is considerably shorter than the lifetime of the inter granular magnetic field concentrations which continue to exist throughout this process .\nas our study shows , we must exercise caution when visualising three - dimensional motions in the turbulent and magnetised solar atmosphere .\nsteady velocity fields can not be used for analysis , since the speed with which the velocity pattern changes is of the same order as the actual velocity , while studies of time - dependent velocity fields impose additional requirements on the simulated data series , such as spatial resolution and cadence , as well as on the computational resources needed to perform the computations .\nthe vorticity perturbations we observe in the simulations , unlike pure alfvn waves , cause perturbations in thermodynamic parameters of the solar plasma .\nthese perturbations are possibly caused by some unavoidable amount of artificial diffusivity and resistivity included in the code for numerical stability .\nanother reason for these perturbations may be that other , magneto - acoustic oscillatory modes are present in the simulated magnetic field concentrations .\nit also should be mentioned that , apparently , photospheric magnetic bright point motions , which originate at the base of the photosphere , do not represent good candidates for this type of wave observation , since they are formed deeper in photospheric layers @xcite .\ntheir measured paths @xcite suggest a hydrodynamic , non - oscillatory type of photospheric horizontal motion .\nprevious observational and theoretical reports on alfvn waves in the solar chromosphere ( e.g. * ? ? ?\n* ) and in sunspots @xcite clearly suggest that alfvn waves are a common phenomenon in strong solar magnetic fields .\ninterestingly , recent high - cadence observations of prominences show that their tornado - like appearance is `` an illusion due to projection effects '' @xcite , suggesting a general presence of alfvn - type motions in the solar atmosphere and corona .\nobservational confirmation of the result given in this letter is currently rather difficult since it requires spectroscopic and spectropolarimetric observations with both very high resolution of the order of 2050 km and extremely high cadence of about 2 seconds .\nthese may become possible with upcoming high - aperture instruments , such as atst .\nfurther investigation of the reaction of spectral line profiles to photospheric alfvn waves will be needed before such an observational attempt .\nanother interesting problem is detailed identification of the lower - photospheric sources of upper - photospheric torsional waves . among the possibilities are hydrodynamic vortices in the deep photosphere , small - scale granular motions and short - lived turbulent eddies .\nfurther theoretical and computational work is needed to fully determine the sources of alfvn waves observed in the upper photosphere .\nthis research was undertaken with the assistance of resources provided at the nci national facility systems at the australian national university through the national computational merit allocation scheme supported by the australian government , and at the multi - modal australian sciences imaging and visualisation environment ( massive ) ( www.massive.org.au ) .\nthe authors also thank centre for astrophysics & supercomputing of swinburne university of technology ( australia ) for the computational resources provided .\ndr shelyag is the recipient of an australian research council s future fellowship ( project number ft120100057 ) .", "role": "user" }, { "content": "using advanced numerical magneto - hydrodynamic simulations of the magnetised solar photosphere , including non - grey radiative transport and a non - ideal equation of state , we analyse plasma motions in photospheric magnetic vortices . \n we demonstrate that apparent vortex - like motions in photospheric magnetic field concentrations do not exhibit `` tornado''-like behaviour or a `` bath - tub '' effect . while at each time instance the velocity field lines in the upper layers of the solar photosphere show swirls , the test particles moving with the time - dependent velocity field do not demonstrate such structures . \n instead , they move in a wave - like fashion with rapidly changing and oscillating velocity field , determined mainly by magnetic tension in the magnetised intergranular downflows . using time - distance diagrams , we identify horizontal motions in the magnetic flux tubes as torsional alfvn perturbations propagating along the nearly vertical magnetic field lines with local alfvn speed .", "role": "assistant" } ]

[ { "content": "Examine the following abstract and identify distinct entities. Focus on extracting entities related to participants, interventions, and outcomes.\n\nPresent your findings in a JSON format like: {\"Participant\": [\"example entity\", ...], \"Intervention\": [\"example entity\", ...], \"Outcome\": [\"example entity\", ...]}. If no entities are found for a category, use an empty list.\n\nAbstract Content:\n\nMyocardial extracellular volume by cardiac magnetic resonance imaging in patients treated with anthracycline-based chemotherapy . We aimed to determine whether the myocardial extracellular volume ( ECV ) , measured using T1 measurements obtained during cardiac magnetic resonance imaging were increased in patients treated with anthracyclines . We performed cardiac magnetic resonance imaging and echocardiography and measured the ECV in 42 patients treated with anthracyclines . The data from the cardiac magnetic resonance study were compared to those from healthy volunteers . The anthracycline-treated cohort consisted of 21 men and 21 women with a mean age of 55 ± 17 years , who presented a median of 84 months after chemotherapy with a cumulative anthracycline exposure of 282 ± 65 mg/m ( 2 ) and a mean left ventricular ejection fraction of 52 ± 12 % . The ECV was elevated in the anthracycline-treated patients compared to the age- and gender-matched controls ( 0.36 ± 0.03 vs 0.28 ± 0.02 , p < 0.001 ) . A positive association was found between the ECV and left atrial volume ( ECV vs indexed left atrial volume , r = 0.65 , p < 0.001 ) , and negative association was found between the ECV and diastolic function ( E ' lateral , r = -0.64 , p < 0.001 ) . In conclusion , the myocardial ECV is elevated in patients with previous anthracycline treatment and is associated with the diastolic function and increased atrial volumes .", "role": "user" }, { "content": "{\"Intervention\": [\"anthracyclines .\", \"anthracyclines\", \"cardiac magnetic resonance imaging and echocardiography and measured the ECV\"], \"Outcome\": [\"T1 measurements\", \"myocardial extracellular volume ( ECV )\", \"ECV\"], \"Participant\": [\"21\", \"men\", \"women\", \"age of 55 \\u00b1 17 years\", \"treated with anthracyclines\", \"a mean left ventricular ejection fraction of 52\", \"patients treated with anthracyclines\", \"who presented a median of 84 months after chemotherapy with a cumulative anthracycline exposure of 282 \\u00b1 65 mg/m ( 2 )\", \"elevated in patients with previous anthracycline treatment\", \"patients treated with anthracycline-based chemotherapy\", \"healthy volunteers\", \"42 patients\"]}", "role": "assistant" } ]

[ { "content": "Craft a cohesive chapter for a literature review using the abstracts provided. Focus on the chapter's theme, weaving together insights and findings from the abstracts. Highlight key points and note any research gaps.\nLiterature Review Title: Popularity-Based Video Caching Techniques for Cache-Enabled Networks: A Survey \nChapter Title: B. IMPORTANCE OF POPULARITY PREDICTION FOR VIDEOS CACHING \n1. Abstract of Cited Paper (BIB001): Streaming video algorithms dynamically select between different versions of a video to deliver the highest quality version that can be viewed without buffering over the client's connection. To improve the quality for viewers, the backing video service can generate more and/or better versions, but at a significant computational overhead. Processing all videos uploaded to Facebook in the most intensive way would require a prohibitively large cluster. Facebook's video popularity distribution is highly skewed, however, with analysis on sampled videos showing 1% of them accounting for 83% of the total watch time by users. Thus, if we can predict the future popularity of videos, we can focus the intensive processing on those videos that improve the quality of the most watch time. ::: ::: To address this challenge, we designed Chess, the first popularity prediction algorithm that is both scalable and accurate. Chess is scalable because, unlike the state-of-the-art approaches, it requires only constant space per video, enabling it to handle Facebook's video workload. Chess is accurate because it delivers superior predictions using a combination of historical access patterns with social signals in a unified online learning framework. We have built a video prediction service, ChessVPS, using our new algorithm that can handle Facebook's workload with only four machines. We find that re-encoding popular videos predicted by ChessVPS enables a higher percentage of total user watch time to benefit from intensive encoding, with less overhead than a recent production heuristic, e.g., 80% of watch time with one-third as much overhead.\n\nReview Chapter:", "role": "user" }, { "content": "The vast majority of today's network traffic produced by streaming video. According to a recent study by Cisco, the mobile traffic generated by videos is expected to reach 75% of the total generated traffic by 2020. BIB001 Videos consume much more cache space than images, documents or emails. Furthermore, the number of videos is increasing because video creation is no longer monopolized by TV channels and companies: most videos now comprise user-generated videos. It is therefore necessary to select popular videos for caching, and popularity prediction can select anticipated on-demand BIB001 http://tubularinsights.com/2020-mobile-video-traffic/ FIGURE 2. Content delivery procedures in small caching-enabled network in case of a) content is not store in the local cache b) content store in the local cache. videos in order to reduce traffic and better manage caching resources. Nowadays, users not only care about watching videos but also streaming them with high bit rates and ultra highresolution , . To ensure a great watching experience for viewers, the video must be viewed without stopping or buffing during the video session. Therefore, technologies such as adaptive bitrate streaming (ABR) and dynamic adaptive streaming over HTTP (DASH) are used. These select the best quality based on each user's device and bandwidth, and then dynamically modulate the video quality to maintain a steady playing experience. But, multiple encoded versions need to be created and stored which requires additional processing. Popularity prediction can reduce the additional processing by only focusing on selected, highly-popular videos BIB002 .", "role": "assistant" } ]

[ { "content": "Examine the provided biomedical abstract. Identify and list entities based on the specified categories: [\"Brand\", \"Drug\", \"DrugGroup\", \"UnapprovedDrug\"].\n\nFormat your findings as a JSON object: {\"Brand\": [\"Aspirin\", ...], \"DrugGroup\": [\"Salicylate\", ...], \"Drug\": [\"Phenobarbital\", ...], \"UnapprovedDrug\": [\"Heroin\", ...]}. Each key represents an entity type, and the corresponding value is a list of entities. If no entities are found for a type, use an empty list [].\n\nFocus solely on producing the JSON object.\n\nSource Text:\n\nAprepitant is a substrate, a moderate inhibitor, and an inducer of CYP3A4. Aprepitant is also an inducer of CYP2C9. Effect of aprepitant on the pharmacokinetics of other agents As a moderate inhibitor of CYP3A4, aprepitant can increase plasma concentrations of coadministered medicinal products that are metabolized through CYP3A4. Aprepitant has been shown to induce the metabolism of S(-) warfarin and tolbutamide, which are metabolized through CYP2C9. Coadministration of Aprepitant with these drugs or other drugs that are known to be metabolized by CYP2C9, such as phenytoin, may result in lower plasma concentrations of these drugs. Aprepitant is unlikely to interact with drugs that are substrates for the P-glycoprotein transporter, as demonstrated by the lack of interaction of Aprepitant with digoxin in a clinical drug interaction study. 5-HT3 antagonists: In clinical drug interaction studies, aprepitant did not have clinically important effects on the pharmacokinetics of ondansetron or granisetron. No clinical or drug interaction study was conducted with dolasetron. Corticosteroids: Dexamethasone: Aprepitant, when given as a regimen of 125mg with dexamethasone coadministered orally as 20 mg on Day 1, and Aprepitant when given as 80 mg/day with dexamethasone coadministered orally as 8 mg on Days 2 through 5, increased the AUC of dexamethasone, a CYP3A4 substrate by 2.2-fold, on Days 1 and 5. The oral dexamethasone doses should be reduced by approximately 50% when coadministered with Aprepitant, to achieve exposures of dexamethasone similar to those obtained when it is given without Aprepitant. The daily dose of dexamethasone administered in clinical studies with Aprepitant reflects an approximate 50% reduction of the dose of dexamethasone. Methylprednisolone Aprepitant, when given as a regimen of 125 mg on Day 1 and 80 mg/day on Days 2 and 3, increased the AUC of methylprednisolone, a CYP3A4 substrate, by 1.34-fold on Day 1 and by 2.5-fold on Day 3, when methylprednisolone was coadministered intravenously as 125 mg on Day 1 and orally as 40 mg on Days 2 and 3. The IV methylprednisolone dose should be reduced by approximately 25%, and the oral methylprednisolone dose should be reduced by approximately 50% when coadministered with Aprepitant to achieve exposures of methylprednisolone similar to those obtained when it is given without Aprepitant. Warfarin: A single 125-mg dose of Aprepitant was administered on Day 1 and 80 mg/day on Days 2 and 3 to healthy subjects who were stabilized on chronic warfarin therapy. Although there was no effect of Aprepitant on the plasma AUC of R(+) or S(-) warfarin determined on Day 3, there was a 34% decrease in S(-)warfarin (a CYP2C9 substrate) trough concentration accompanied by a 14% decrease in the prothrombin time (reported as International Normalized Ratio or INR) 5 days after completion of dosing with Aprepitant. In patients on chronic warfarin therapy, the prothrombin time (INR) should be closely monitored in the 2-week period, particularly at 7 to 10 days, following initiation of the 3-day regimen of Aprepitant with each chemotherapy cycle. Tolbutamide: Aprepitant, when given as 125 mg on Day 1 and 80 mg/day on Days 2 and 3, decreased the AUC of tolbutamide (a CYP2C9 substrate) by 23% on Day 4, 28% on Day 8, and 15% on Day 15, when a single dose of tolbutamide 500 mg was admini,stered orally prior to the administration of the 3-day regimen of Aprepitant and on Days 4,8, and 15. Oral contraceptives: Aprepitant, when given once daily for 14 days as a 100-mg capsule with an oral contraceptive containing 35 mcg of ethinyl estradiol and 1 mg of norethindrone, decreased the AUC of ethinyl estradiol by 43%, and decreased the AUC of norethindrone by 8%; therefore, the efficacy of oral contraceptives during administration of Aprepitant may be reduced. Although a 3-day regimen of Aprepitant given concomitantly with oral contraceptives has not been studied, alternative or back-up methods of contraception should be used. Midazolam: Aprepitant increased the AUC of midazolam, a sensitive CYP3A4 substrate, by 2.3-fold on Day 1 and 3.3-fold on Day 5, when a single oral dose of midazolam 2 mg was coadministered on Day 1 and Day 5 of a regimen of Aprepitant 125 mg on Day 1 and 80 mg/day on Days 2 through 5. The potential effects of increased plasma concentrations of midazolam or other benzodiazepines metabolized via CYP3A4 (alprazolam, triazolam) should be considered when coadministering these agents with Aprepitant. In another study with intravenous administration of midazolam, Aprepitant was given as 125 mg on Day 1 and 80 mg/day on Days 2 and 3, and midazolam 2 mg IV was given prior to the administration of the 3-day regimen of Aprepitant and on Days 4, 8, and 15. Aprepitant increased the AUC of midazolam by 25% on Day 4 and decreased the AUC of midazolam by 19% on Day 8 relative to the dosing of Aprepitant on Days 1 through 3. These effects were not considered clinically important. The AUC of midazolam on Day 15 was similar to that observed at baseline. Effect of other agents on the pharmacokinefics of aprepitant Aprepitant is a substrate for CYP3A4; therefore, coadministration of Aprepitant with drugs that inhibit CYP3A4 activity may result in increased plasma concentrations of aprepitant. Consequently, concomitant administration of Aprepitant with strong CYP3A4 inhibitors (e.g., ketoconazole, itraconazole, nefazodone, troleandomycin, clarithromycin, ritonavir, nelfinavir) should be approached with caution. Because moderate CYP3A4 inhibitors (e.g., diltiazem) result in 2-fold increase in plasma concentrations of aprepitant, concomitant administration should also be approached with caution. Aprepitant is a substrate for CYP3A4; therefore, coadministration of Aprepitant with drugs that strongly induce CYP3A4 activity (e.g., rifampin, carbamazepine, phenytoin) may result in reduced plasma concentrations of aprepitant that may result in decreased efficacy of Aprepitant. Ketoconazole: When a single 125-mg dose of Aprepitant was administered on Day5 of a Ketoconazole: When a single 125-mg dose of Aprepitant was administered on Day5 of a 10-day regimen of 400 mg/day of ketoconazole, a strong CYP3A4 inhibitor, the AUC of aprepitant increased approximately 5-fold and the mean terminal half-life of aprepitant increased approximately 3-fold. Concomitant administration of Aprepitant with strong CYP3A4 inhibitors should be approached cautiously. Rifampin: When a single 375-mg dose of Aprepitant was administered on Day9 of a 14-day regimen of 600 mg/day of rifampin, a strong CYP3A4 inducer, the AUC of aprepitant decreased approximately 11-fold and the mean terminal half-life decreased approximately 3-fold. Coadministration of Aprepitant with drugs that induce CYP3A4 activity may result in reduced plasma concentrations and decreased efficacy of Aprepitant. Additional interactions Diltiazem: In patients with mild to moderate hypertension, administration of aprepitant once daily, as a tablet formulation comparable to 230 mg of the capsule formulation, with diltiazem 120 mg 3 times daily for 5 days, resulted in a 2-fold increase of aprepitant AUC and a simultaneous 1.7-fold increase of diltiazem AUC. These pharmacokinetic effects did not result in clinically meaningful changes in ECG, heart rate or blood pressure beyond those changes induced by diltiazem alone. Paroxetine: Coadministration of once daily doses of aprepitant, as a tablet formulation comparable to 85 mg or 170 mg of the capsule formulation, with paroxetine 20 mg once daily, resulted in a decrease in AUC by approximately 25% and Cmax, by approximately 20% of both aprepitant and paroxetine.", "role": "user" }, { "content": "{\"Brand\": [], \"Drug\": [\"Rifampin\", \"alprazolam\", \"ritonavir\", \"Aprepitant\", \"troleandomycin\", \"Midazolam\", \"Ketoconazole\", \"tolbutamide\", \"diltiazem\", \"Warfarin\", \"norethindrone\", \"methylprednisolone\", \"Tolbutamide\", \"dexamethasone\", \"itraconazole\", \"Diltiazem\", \"ethinyl estradiol\", \"midazolam\", \"Paroxetine\", \"carbamazepine\", \"R(+) warfarin\", \"Dexamethasone\", \"triazolam\", \"S(-)warfarin\", \"clarithromycin\", \"S(-) warfarin\", \"ondansetron\", \"granisetron\", \"Methylprednisolone\", \"nelfinavir\", \"paroxetine\", \"nefazodone\", \"dolasetron\", \"rifampin\", \"aprepitant\", \"warfarin\", \"digoxin\", \"ketoconazole\", \"phenytoin\"], \"DrugGroup\": [\"contraceptives\", \"benzodiazepines\", \"contraceptive\", \"5-HT3 antagonists\", \"Corticosteroids\"], \"UnapprovedDrug\": []}", "role": "assistant" } ]

[ { "content": "Examine the following abstract and identify distinct entities. Focus on extracting entities related to participants, interventions, and outcomes.\n\nPresent your findings in a JSON format like: {\"Participant\": [\"example entity\", ...], \"Intervention\": [\"example entity\", ...], \"Outcome\": [\"example entity\", ...]}. If no entities are found for a category, use an empty list.\n\nAbstract Content:\n\nFifteen-year results of a randomized prospective trial of hyperfractionated chest wall irradiation versus once-daily chest wall irradiation after chemotherapy and mastectomy for patients with locally advanced noninflammatory breast cancer . PURPOSE To analyze the results of a Phase III clinical trial that investigated whether a hyperfractionated radiotherapy ( RT ) schedule could reduce the risk of locoregional recurrence in patients with locally advanced breast cancer treated with chemotherapy and mastectomy . METHODS AND MATERIALS Between 1985 and 1989 , 200 patients with clinical Stage III noninflammatory breast cancer were enrolled in a prospective study investigating neoadjuvant and adjuvant chemotherapy . Of the 179 patients treated with mastectomy after neoadjuvant chemotherapy , 108 participated in a randomized component of the trial that compared a dose-escalated , hyperfractionated ( twice-daily , b.i.d . ) chest wall RT schedule ( 72 Gy in 1.2-Gy b.i.d . fractions ) with a once-daily ( q.d . ) schedule ( 60 Gy in 2-Gy q.d . fractions ) . In both arms of the study , the supraclavicular fossa and axillary apex were treated once daily to 50 Gy . The median follow-up period was 15 years . RESULTS The 15-year actuarial locoregional recurrence rate was 7 % for the q.d . arm and 12 % for the b.i.d . arm ( p=0.36 ) . The rates of severe acute toxicity were similar ( 4 % for q.d . vs. 5 % for b.i.d . ) , but moist desquamation developed in 42 % of patients in the b.i.d . arm compared with 28 % of the patients in the q.d . arm ( p=0.16 ) . The 15-year actuarial rate of severe late RT complications did not differ between the two arms ( 6 % for q.d . vs. 11 % for b.i.d. , p=0.54 ) . CONCLUSION Although the sample size of this study was small , we found no evidence that this hyperfractionation schedule of postmastectomy RT offered a clinical advantage . Therefore , we have concluded that it should not be further studied in this cohort of patients .", "role": "user" }, { "content": "{\"Intervention\": [\"once-daily chest wall irradiation after\", \"neoadjuvant chemotherapy\", \"b.i.d . arm\", \"hyperfractionated ( twice-daily , b.i.d . ) chest wall RT\", \"mastectomy after\", \"postmastectomy RT\", \"chemotherapy\", \"hyperfractionated chest wall irradiation\", \"hyperfractionated radiotherapy ( RT )\", \"q.d . arm\"], \"Outcome\": [\"rates of severe acute toxicity\", \"15-year actuarial locoregional recurrence rate\", \"15-year actuarial rate of severe late RT complications\"], \"Participant\": [\"108\", \"locally advanced noninflammatory breast cancer\", \"Stage III noninflammatory breast cancer\", \"179\", \"200\", \"locally advanced breast cancer\"]}", "role": "assistant" } ]

[ { "content": "Analyze the given paragraph from COVID-19 research. Determine the relevant topics discussed in the text. Your response should be a JSON array containing the identified topics. Ensure the output is a valid JSON array with no additional commentary.\n\nText:\n\nThe global sanitary crisis caused by the emergence of the respiratory virus SARS-CoV-2 and the COVID-19 outbreak has revealed the urgent need for rapid, accurate, and affordable diagnostic tests to broadly and massively monitor the population in order to properly manage and control the spread of the pandemic. Current diagnostic techniques essentially rely on polymerase chain reaction (PCR) tests, which provide the required sensitivity and specificity. However, its relatively long time-to-result, including sample transport to a specialized laboratory, delays massive detection. Rapid lateral flow tests (both antigen and serological tests) are a remarkable alternative for rapid point-of-care diagnostics, but they exhibit critical limitations as they do not always achieve the required sensitivity for reliable diagnostics and surveillance. Next-generation diagnostic tools capable of overcoming all the above limitations are in demand, and optical biosensors are an excellent option to surpass such critical issues. Label-free nanophotonic biosensors offer high sensitivity and operational robustness with an enormous potential for integration in compact autonomous devices to be delivered out-of-the-lab at the point-of-care (POC). Taking the current COVID-19 pandemic as a critical case scenario, we provide an overview of the diagnostic techniques for respiratory viruses and analyze how nanophotonic biosensors can contribute to improving such diagnostics. We review the ongoing published work using this biosensor technology for intact virus detection, nucleic acid detection or serological tests, and the key factors for bringing nanophotonic POC biosensors to accurate and effective COVID-19 diagnosis on the short term.", "role": "user" }, { "content": "[\"Diagnosis\"]", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: The dual-antibody treatment worked best on patients who did not mount an immune system response to the virus.\n\nResearch Abstract:\nSeveral related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1.\nSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic spread2,3.\nZoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population.\nUsing diverse assays for detection of antibodies reactive with the SARS-CoV-2 Spike (S) glycoprotein, we demonstrate the presence of pre-existing immunity in uninfected and unexposed humans to the new coronavirus.\nSARS-CoV-2 S-reactive antibodies, exclusively of the IgG class, were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals with recent HCoV infection and targeted the S2 subunit.\nIn contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, as well as concomitant IgM and IgA antibodies throughout the observation period of 6 weeks since symptoms onset.\nHCoV patient sera also variably reacted with SARS-CoV-2 S and nucleocapsid (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays.\nNotably, HCoV patient sera exhibited specific neutralising activity against SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera.\nDistinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for serology, seroprevalence and vaccine studies, as well as for our understanding of susceptibility to and natural course of SARS-CoV-2 infection.", "role": "user" }, { "content": "{\"verdict\": \"NEI\", \"evidence\": []}", "role": "assistant" } ]

[ { "content": "Explore the following research question and associated terms. Identify the most suitable dataset from the list provided. Use the dataset descriptions to guide your choice.\n\nInquiry: The paper presents an efficient FPGA architecture to implement a real-time high-definition\n\nKeywords: 3d video depth estimation\n\nDataset Information:\nMiddlebury: The Middlebury Stereo dataset consists of high-resolution stereo sequences with complex geometry and pixel-accurate ground-truth disparity data. The ground-truth disparities are acquired using a novel technique that employs structured lighting and does not require the calibration of the light projectors.\nCholec80: Cholec80 is an endoscopic video dataset containing 80 videos of cholecystectomy surgeries performed by 13 surgeons. The videos are captured at 25 fps and downsampled to 1 fps for processing.\nTHEODORE: Recent work about synthetic indoor datasets from perspective views has shown significant improvements of object detection results with Convolutional Neural Networks(CNNs). In this paper, we introduce THEODORE: a novel, large-scale indoor dataset containing 100,000 high- resolution diversified fisheye images with 14 classes.\nMSU-MFSD: The MSU-MFSD dataset contains 280 video recordings of genuine and attack faces. 35 individuals have participated in the development of this database with a total of 280 videos.\n\nAvailable Datasets: A: Middlebury B: Cholec80 C: THEODORE D: MSU-MFSD", "role": "user" }, { "content": "Middlebury", "role": "assistant" } ]

[ { "content": "Examine the provided text and determine the interactions between chemical entities and genes. Focus on identifying any connections present.\n\nPresent your findings in a structured JSON format. Each relationship should be represented as an array entry. If no interactions are detected, return an empty array.\n\nText Content:\n\nPolymethoxyflavones as agents that prevent formation of cataract: nobiletin congeners show potent growth inhibitory effects in human lens epithelial cells. Posterior capsular opacification (PCO) is the most frequent complication and the primary reason for visual decrease after extracapsular cataract surgery. The proliferation and migration of leftover lens epithelial cells (LECs) after surgery may contribute to the development of PCO. To prevent PCO, a rational approach would be to inhibit both the proliferation and the migration of LECs using nontoxic xenobiotics. Nobiletin, one of the most abundant polymethoxyflavones (PMFs) in citrus peel, and its synthetic congeners displayed a potent inhibition of LEC proliferation. Structural features which enhance anti-proliferative activity have also been discussed.", "role": "user" }, { "content": "[]", "role": "assistant" } ]

[ { "content": "Analyze the provided text excerpt from a scientific document. Identify and extract distinct entities based on predefined categories.\n\nDeliver the results as a JSON structure where each key represents an entity category, and the associated value is a list of identified entities. If no entities are found for a category, return an empty list.\n\nText Excerpt:\n\nChanges in triiodothyronine (T3) mononuclear leukocyte receptor kinetics after T3 administration and multiple cold-air exposures. Repeated cold-air exposures increase human triiodothyronine (T3) plasma clearance rates. To study the response of the nuclear T3 receptor (NT3R) in this condition, binding characteristics were analyzed in human mononuclear leukocytes (MNL). In addition, we supplemented one group of individuals with a daily oral replacement dose of T3 to isolate the influence of serum thyroxine (T4) and thyrotropin (TSH) levels on receptor kinetics. The subjects were exposed to cold air (4 degrees C) twice / d, 30 min / exposure, for a total of 80 exposures. The T3-subjects received placebo [ n = 8 ] and the T3 + subjects received T3 (30 micrograms / d) [ n = 8 ] in a double-blind fashion. Mononuclear leukocytes were isolated from peripheral blood before the cold exposure and drug regimen began, and then after every 20 exposures. The dissociation constant (Kd) and maximum binding capacity (MBC) of the NT3R values were log transformed to minimize between-subject variability. In the T3 + group, serum total thyroxine (TT4), free T4 (FT4), and TSH were approx 50% lower than both basal and T3-values. The log10Kd increased 0. 304 + /-0. 139 (p < 0. 04) and the log10MBC increased 0. 49 + /-0. 10 (p < 0. 001) in the T3 + subjects compared to baseline. This change in MBC represents a 311% increase in the MBC over baseline and a fivefold increase over placebo-treated subjects. The T3-group showed no change in MBC over the study. These results describe for the first time the rapid modulation of the NT3R in response to the combined influence of cold exposure and reduced circulating T4 and TSH.", "role": "user" }, { "content": "{\"CellLine\": [], \"CellType\": [\"MNL\", \"human mononuclear leukocytes\", \"Mononuclear leukocytes\"], \"DNA\": [], \"Protein\": [\"nuclear T3 receptor\", \"NT3R\"], \"RNA\": []}", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nof gene transfer into dicotyledonous plants is to use the Agrobacterium tumefaciens transformation mechanism (Gasser and Fraley 1989).", "role": "user" }, { "content": "Method", "role": "assistant" } ]

[ { "content": "Analyze the given research paper excerpts and address the question provided. Extract the necessary information directly from the text. Your answer should be formatted as a JSON object with the following structure:\n\n\"answer\": A list of text segments from the paper that directly respond to the question.\n\"evidence\": A list of text segments from the paper where the answer can be found.\n\nIf the question cannot be answered with the given text, return \"null\".\n\nDocument: An Open-World Extension to Knowledge Graph Completion Models\n\nWe present a novel extension to embedding-based knowledge graph completion models which enables them to perform open-world link prediction, i.e. to predict facts for entities unseen in training based on their textual description. Our model combines a regular link prediction model learned from a knowledge graph with word embeddings learned from a textual corpus. After training both independently, we learn a transformation to map the embeddings of an entity's name and description to the graph-based embedding space. In experiments on several datasets including FB20k, DBPedia50k and our new dataset FB15k-237-OWE, we demonstrate competitive results. Particularly, our approach exploits the full knowledge graph structure even when textual descriptions are scarce, does not require a joint training on graph and text, and can be applied to any embedding-based link prediction model, such as TransE, ComplEx and DistMult.\n\nApproach\nOur approach starts with a regular link prediction model (in the following also referred to as the graph-based model) as outlined in Section \"Related Work\" and visualised in Fig. 1 . The model scores triples $(h, r, t)$ : \n$$score(h,r,t) = \\phi ({u}_{h}, {u}_{r}, {u}_{t})$$ (Eq. 6) \nwhere ${u}_{x}$ denotes the embedding of entity/relation $x$ . Typically, ${u}_{x} \\in \\mathbb {R}^d$ , but other options are possible. For example, in ComplEx BIBREF6 , ${u}_{x}$ is complex-valued ( ${u}_{x} \\in \\mathbb {C}^d$ ). $\\phi $ is a scoring function that depends on the link prediction model and will be adressed in more detail in Section \"Link Prediction Models\" .\n\nLink Prediction Models\nSince our approach is independent of the specific link prediction model used, we test three commonly used models in this work:\nTransE: $\\phi ({u}_{h}, {u}_{r}, {u}_{t}) = -||{u}_{h} {+} {u}_{r} {-} {u}_{t}||_2$ $\\;\\;\\;$ \nDistMult: $\\phi ({u}_{h}, {u}_{r}, {u}_{t}) = \\langle {u}_{h},{u}_{r},{u}_{t}\\rangle $ $\\;\\;\\;\\;\\;\\;\\;\\;$ \nComplEx: $\\phi ({u}_{h}, {u}_{r}, {u}_{t}) = \\textrm {Re}({\\langle }{u}_{h}, {u}_{r}, {\\overline{u}}_{t}{\\rangle })$ $\\;$ \nNote that the first two use real-valued embeddings, while ComplEx uses complex-valued embeddings (where ${\\overline{u}} = \\textrm {Re}({u}) - i{\\cdot } \\textrm {Im}({u})$ denotes the complex conjugate of embedding ${u}$ ). All models are trained using their original loss functions and validated using closed-world validation data.\n\nDatasets\nClosed-world KGC tasks are commonly evaluated on WordNet and Freebase subsets, such as WN18, WN18RR, FB15k, and FB15k-237. For open-world KGC, the following datasets have been suggested: BIBREF10 introduced FB20k, which builds upon the FB15k dataset by adding test triples with unseen entities, which are selected to have long textual descriptions. BIBREF11 introduced DBPedia50k and DBPedia500k datasets for both open-world and closed-world KGC tasks.\nHowever, the above datasets display a bias towards long textual descriptions: DBpedia50k has an average description length of 454 words, FB20k of 147 words. Also, for neither of the datasets precautions have been taken to avoid redundant inverse relations, which allows models to exploit trivial patterns in the data BIBREF24 . To overcome these problems, we introduce a new dataset named FB15k-237-OWE. FB15k-237-OWE is based on the well-known FB15K-237 dataset, where redundant inverse relations have been removed. Also, we avoid a bias towards entities with longer textual descriptions: Test entities are uniformly sampled from FB15K-237, and only short Wikidata descriptions (5 words on average) are used.\nIn the following section, the sampling strategy for FB15k-237-OWE is briefly outlined: For tail prediction test set, we start with FB15K-237 and randomly pick heads (by uniform sampling over all head entities). Each picked head $x$ is removed from the training graph by moving all triples of the form $(x,?,t)$ to the test set and dropping all triples of the form $(?,?,x)$ if $t$ still remains in the training set after these operations. Similarly, a head prediction test set is prepared from the set of dropped triplets which satisfy the conditions to be in head prediction test set i.e. head must be represented in training set while tail must not be represented. The dataset also contains two validation sets: A closed-world one (with random triples picked from the training set) and an open-world one (with random triples picked from the test set).\nWe evaluate our approach on DBPedia50k, FB20k, and the new dataset FB15k-237-OWE. Statistics of the datasets are highlighted in Table 1 and Table 2 .\n\nExperimental Setup\nWe perform multiple runs using different KGC models, transformation types, training data, and embeddings used. For each run, both KGC model and transformation $\\Psi ^{map}$ are trained on the training set: the KGC model without using any textual information and the transformation using entity names and descriptions. We manually optimize all hyperparameters on the validation set. Due to the lack of an open-world validation set on FB20k, we randomly sampled 10% of the test triples as a validation set.\nPerformance figures are computed using tail prediction on the test sets: For each test triple $(h,r,t)$ with open-world head $h \\notin E$ , we rank all known entities $t^{\\prime } \\in E$ by their score $\\phi (h,r,t^{\\prime })$ . We then evaluate the ranks of the target entities $t$ with the commonly used mean rank (MR), mean reciprocal rank (MRR), as well as Hits@1, Hits@3, and Hits@10.\nNote that multiple triples with the same head and relation but different tails may occur in the dataset: $(h,r,t_1),...,(h,r,t_p)$ . Following BIBREF13 , when evaluating triple $(h,r,t_i)$ we remove all entities $t_1,...,t_{i-1},t_{i+1},...,t_p$ from the result list . All results (except MRR(raw)) are reported with this filtered approach. Note also that when computing the MRR, given a triple $(h,r,t_i)$ only the reciprocal rank of $t_i$ itself is evaluated (and not the best out of $t_1,...,t_{i},...,t_p$ , which would give better results). This is common when evaluating KGC models BIBREF13 but differs from ConMask's evaluation code, which is why one result in Table 3 differs from BIBREF11 (see the (*) mark).\nNote also that BIBREF11 add a second filtering method called target filtering: When evaluating a test triple $(h,r,t)$ , tails $t^{\\prime }$ are only included in the ranked result list if a triple of the form $(?,r,t^{\\prime })$ exists in the training data, otherwise it is skipped. We found this to improve quantitative results substantially, but it limits the predictive power of the model because tails can never be linked via new relations. Therefore, we use target filtering only when comparing with the ConMask and DKRL models from BIBREF11 (Table 3 ).\nFor training TransE and DistMult, we use the OpenKE framework which provides implementations of many common link prediction models. For closed-world graph embedding, we use both OpenKE and our own implementation after validating the equivalence of both.\nFor training the transformation $\\Psi ^{map}$ , we used the Adam optimizer with a learning rate of $10^{-3}$ and batch size of 128. For DBPedia50k we use a dropout of 0.5, while for FB20k and FB15k-237-OWE we use no dropout. The embedding used is the pretrained 300 dimensional Wikipedia2Vec embedding and the transformation used is affine unless stated otherwise.\n\nText Embeddings and Robustness To Missing Entity Metadata\nIn some cases, the knowledge graph may lack textual metadata (both the name and description) for some or all of its entities. Other models like ConMask and DKRL are dependant on textual descriptions, e.g. ConMask uses attention mechanisms to select relation-specific target words from long texts. Therefore, ConMask and DKRL would require completely dropping triples without metadata and be unable to learn about the link structure of such entities as they use joint training. However, in our approach, we have to drop such entities only during the phase where the transformation $\\Psi ^{map}$ is learned, while the link prediction model can still be learned on the full graph.\nTo demonstrate the robustness of our approach to missing entity meta-data, we re-evaluate accuracy when randomly dropping metadata for training entities. Fig. 2 outlines the performance for two scenarios:\nDropping descriptions: We remove only the textual descriptions for a varying percentage of randomly selected entities (between 20% to 100%). The names of these entities are not removed and therefore, we still train $\\Psi ^{map}$ on them.\nDropping all meta-data: We randomly select entities and remove both their descriptions and names, effectively removing these entities from the training set altogether when training $\\Psi ^{map}$ .\nWe also included a baseline experiment to simulate an unsuccessful learning of $\\Psi ^{map}$ . In this baseline, when evaluating a test triple, we replace its head by the embedding of another random head from the training data. Note that this baseline still gives some reasonable hits for triples where the relation is a strong indicator. For example, if we have a triplet $(X,time\\_zone,?)$ : Even if the head $X$ is unknown, a model can achieve reasonable accuracy by simply ”guessing” time zones as tails.\nOverall, Fig. 2 suggests that transformation learning is able to generalize well even with very limited training data. In Fig. 2 a only the descriptions of entities have been removed. For Wikipedia2Vec embeddings, this removal has virtually no effect on prediction accuracy. We believe that this is because Wikipedia2Vec embeddings are trained such that we can lookup strong entity embeddings by the name alone. Even when removing 100% of descriptions (i.e., only training on the entity names), accuracy is only 2-3% lower than training on the full graph. However, in case of Glove embeddings, the drop in performance is very significant, especially when the description is dropped for all the entities.\nIn Fig. 2 b, we remove not only descriptions but also entity names. Even in this case, learning is robust. If half of the $12,324$ training entities are removed, the drop in accuracy is less than 1%. Only when removing 90% of training data (leaving 123 training entities), performance starts to deteriorate significantly. This highlights the ability of our model to learn from a limited amount of training data, when it is important to be able to train the KGC model itself on all the entities.\n\nSelected Results\nFinally, we inspect sample prediction results for ComplEx-OWE-300 in Table 6 . Besides the final prediction, we also test whether our transformation from text-based to semantic space is successful: For each test triple, we represent the open-world head entity by its text-based embedding $v_{head}$ , match it to a graph-based embedding $\\Psi ^{map}(v_{head})$ , and estimate the nearest neighbor entities in this space. We use the Euclidean distance on the real part of the ComplEx embeddings, but found results to be similar for the imaginary part.\nIf the transformation works well, we expect these nearest neighbors to be semantically similar to the head entity. This is obviously the case: For Bram Stoker (the author of Dracula), the nearest neighbors are other authors of fantasy literature. For Parma, the neighbors are cities (predominantly in Italy). For Bachelor of Science, the model predicts appropriate entities (namely, Universities) but – even though we apply filtering – the predictions are not rewarded. This is because the corresponding triples, like (Bachelor of Science, /.../institution, Harward Law School), are missing in the knowledge graph.\n\nTable 1: Dataset statistics for closed-world link prediction.\n\nTable 2: Dataset statistics for open-world link prediction. Eopen is the set of novel entities not in the graph. Note that the corresponding closed-world training set is used for training the open-world models.\n\nTable 3: Comparison with other open-world KGC models on tail prediction. Note that we used the same evaluation protocol with target filtering as in ConMask. The asterisk (*) denotes that the result differs from the one published, because the MRR is calculated differently.\n\nTable 4: Open-world tail prediction by applying the transformation to different closed-world link prediction models on the FB15k-237-OWE dataset without target filtering.\n\nTable 5: Comparison of different transformation functions with ComplEx-OWE-300 on the FB15k-237-OWE dataset without target filtering.\n\nInquiry: what was the evaluation metrics studied in this work?", "role": "user" }, { "content": "{\"answer\": [\"mean rank (MR), mean reciprocal rank (MRR), as well as Hits@1, Hits@3, and Hits@10\"], \"evidence\": [\"Performance figures are computed using tail prediction on the test sets: For each test triple $(h,r,t)$ with open-world head $h \\\\notin E$ , we rank all known entities $t^{\\\\prime } \\\\in E$ by their score $\\\\phi (h,r,t^{\\\\prime })$ . We then evaluate the ranks of the target entities $t$ with the commonly used mean rank (MR), mean reciprocal rank (MRR), as well as Hits@1, Hits@3, and Hits@10.\"]}", "role": "assistant" } ]

[ { "content": "Evaluate the given public health statement using the provided research abstract. Your goal is to determine the relationship between the claim and the abstract content.\n\n- \"decision\": Indicate whether the abstract \"SUPPORTS\", \"CONTRADICTS\", or provides \"INSUFFICIENT\" information regarding the claim.\n- \"justification\": List sentences from the abstract that back your decision. If the decision is \"INSUFFICIENT\", leave this list empty.\n\nStatement: social distancing means keeping people far enough apart that they can't spread coronavirus\n\nResearch Abstract:\nBACKGROUND: The Australian and New Zealand governments both initiated strict social distancing measures in response to the COVID-19 pandemic in late March.\nIt remains difficult to quantify the impact this had in reducing the spread of the virus.\nMETHODS: Bayesian structural time series model provide a model to quantify the scenario in which these government-level interventions were not placed.\nOur models predict these strict social distancing measures caused a 79% and 61% reduction in the daily cases of COVID-19 across Australia and New Zealand respectively.\nCONCLUSION: This provides both evidence and impetus for governments considering similar measures in response to COVID-19 and other pandemics.", "role": "user" }, { "content": "{\"verdict\": \"SUPPORT\", \"evidence\": [\"Our models predict these strict social distancing measures caused a 79% and 61% reduction in the daily cases of COVID-19 across Australia and New Zealand respectively.\"]}", "role": "assistant" } ]

[ { "content": "Review the following segment from a research document in AI. Answer the subsequent query based solely on the provided information. Limit your response to the answer itself.\n\nResearch Segment: The vast majority of these studies model the representations by predicting the missing word only through the contexts. These works do not consider the prior knowledge in the sentence.For example, In the sentence ” Harry Potter is a series of fantasy novels written by J. K. Rowling”. Harry Potter is a novel name and J. K. Rowling is the writer. It is easy for the model to predict the missing word of the entity Harry Potter by word collocations inside this entity without the help of long contexts.The model cannot predict Harry Potter according to the relationship between Harry Potter and J. K. Rowling.It is intuitive that if the model learns more about prior knowledge, the model can obtain more reliable language representation.\n\nInquiry: How can author claim that language models perform better if they use prior knowledge as well as context?", "role": "user" }, { "content": "People share a lot of prior knowledge when they talk each other.\nAlso, they assume others also know the prior knowledge such as ”Harry Potter is a series of fantasy novels written by J. K. Rowling”.\nHence, to make language model similar to human dialogue, it is important to use prior knowledge as well as context.\nThe reason is that they metioned it is intuitive that if the model learns more about prior knowledge, with using the example of Harry Potter.", "role": "assistant" } ]

[ { "content": "Examine the citation provided below. Determine the primary purpose of this citation within the context of the research paper. \n\nCitation:\n\nAll speech was recorded using a head-mounted microphone while the participants were connected to a Finometer [4], a device that enables continuous monitoring of CV parameters in a non-intrusive manner, i.e., by using a finger-cuff.", "role": "user" }, { "content": "Method", "role": "assistant" } ]