Automatic question answering for multiple stakeholders, the epidemic question answering dataset.

One of the effects of COVID-19 pandemic is a rapidly growing and changing stream of publications to inform clinicians, researchers, policy makers, and patients about the health, socio-economic, and cultural consequences of the pandemic. Managing this information stream manually is not feasible. Automatic Question Answering can quickly bring the most salient points to the user's attention. Leveraging a collection of scientific articles, government websites, relevant news articles, curated social media posts, and questions asked by researchers, clinicians, and the general public, we developed a dataset to explore automatic Question Answering for multiple stakeholders. Analysis of questions asked by various stakeholders shows that while information needs of experts and the public may overlap, satisfactory answers to these questions often originate from different information sources or benefit from different approaches to answer generation. We believe that this dataset has the potential to support the development of question answering systems not only for epidemic questions, but for other domains with varying expertise such as legal or finance.

Validation of two clinical color measuring instruments for use in dental research.

OBJECTIVE: There are several shade matching instruments developed for clinical use, but the validity of their use in dental research has not been thoroughly investigated. The objective of this study is to evaluate the accuracy of using two clinical color measuring instruments, VitaEasyshade and Spectroshade, against a referent laboratory color measuring instrument (Spectroradiometer PR670). METHODS AND MATERIALS: The validity and repeatability of the referent laboratory color measuring instrument was assessed using standard color patches with certified CIE L*a*b* values. 10% of the 240 color patches were randomly selected and measured ten times in a random order to test for repeatability. 16 metal ceramic specimens, fabricated from base metal alloy veneered with porcelain of different Vita Classic shades, were measured for L*a*b* values using the PR670, Vita EasyShade and the Spectroshade. The CIE L*a*b* values obtained from the three color measuring instruments were compared using repeated measures ANOVA and post hoc using the Bonferroni test. The color difference, CIEDE2000 (∆E00), between the gold standard (PR670) and the two color measuring instruments were also determined and compared against the known perceptible color difference. RESULTS: L*a*b* values varied significantly between the three instruments. When comparing the mean ΔE00, the differences in values between PR670 and Spectroshade were not clinically significantly. However, the mean ΔE00 values between PR670 and Vita Easyshade were both clinically and statistically significant. CONCLUSION: The lack of clinical significance in values obtained from the SpectroShade when compared to those obtained by the PR670 suggests that the SpectroShade may be recommended for use in dental color research. CLINICAL SIGNIFICANCE: The SpectroShade instrument and PR670 spectroradiometer provided values that lacked clinical significance, suggesting that its use may be highly beneficial for clinical shade matching as well as color research.

Searching for scientific evidence in a pandemic: An overview of TREC-COVID.

We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging topics at that state of the still-emerging pandemic. This paper provides a comprehensive overview of the structure and results of TREC-COVID. Specifically, the paper provides details on the background, task structure, topic structure, corpus, participation, pooling, assessment, judgments, results, top-performing systems, lessons learned, and benchmark datasets.

Harnessing the Power of Smart and Connected Health to Tackle COVID-19: IoT, AI, Robotics, and Blockchain for a Better World.

As COVID-19 hounds the world, the common cause of finding a swift solution to manage the pandemic has brought together researchers, institutions, governments, and society at large. The Internet of Things (IoT), artificial intelligence (AI)-including machine learning (ML) and Big Data analytics-as well as Robotics and Blockchain, are the four decisive areas of technological innovation that have been ingenuity harnessed to fight this pandemic and future ones. While these highly interrelated smart and connected health technologies cannot resolve the pandemic overnight and may not be the only answer to the crisis, they can provide greater insight into the disease and support frontline efforts to prevent and control the pandemic. This article provides a blend of discussions on the contribution of these digital technologies, propose several complementary and multidisciplinary techniques to combat COVID-19, offer opportunities for more holistic studies, and accelerate knowledge acquisition and scientific discoveries in pandemic research. First, four areas, where IoT can contribute are discussed, namely: 1) tracking and tracing; 2) remote patient monitoring (RPM) by wearable IoT (WIoT); 3) personal digital twins (PDTs); and 4) real-life use case: ICT/IoT solution in South Korea. Second, the role and novel applications of AI are explained, namely: 1) diagnosis and prognosis; 2) risk prediction; 3) vaccine and drug development; 4) research data set; 5) early warnings and alerts; 6) social control and fake news detection; and 7) communication and chatbot. Third, the main uses of robotics and drone technology are analyzed, including: 1) crowd surveillance; 2) public announcements; 3) screening and diagnosis; and 4) essential supply delivery. Finally, we discuss how distributed ledger technologies (DLTs), of which blockchain is a common example, can be combined with other technologies for tackling COVID-19.

Text mining approaches for dealing with the rapidly expanding literature on COVID-19.

More than 50 000 papers have been published about COVID-19 since the beginning of 2020 and several hundred new papers continue to be published every day. This incredible rate of scientific productivity leads to information overload, making it difficult for researchers, clinicians and public health officials to keep up with the latest findings. Automated text mining techniques for searching, reading and summarizing papers are helpful for addressing information overload. In this review, we describe the many resources that have been introduced to support text mining applications over the COVID-19 literature; specifically, we discuss the corpora, modeling resources, systems and shared tasks that have been introduced for COVID-19. We compile a list of 39 systems that provide functionality such as search, discovery, visualization and summarization over the COVID-19 literature. For each system, we provide a qualitative description and assessment of the system's performance, unique data or user interface features and modeling decisions. Many systems focus on search and discovery, though several systems provide novel features, such as the ability to summarize findings over multiple documents or linking between scientific articles and clinical trials. We also describe the public corpora, models and shared tasks that have been introduced to help reduce repeated effort among community members; some of these resources (especially shared tasks) can provide a basis for comparing the performance of different systems. Finally, we summarize promising results and open challenges for text mining the COVID-19 literature.

Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach

SARS-CoV-2 neutralizing antibodies represent an important component of the ongoing search for effective treatment of and protection against COVID-19. We report here on the use of a naive phage display antibody library to identify a panel of fully human SARS-CoV-2 neutralizing antibodies. Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Both antibodies demonstrated potent protection against the pathogenic effects of the disease and a dose-dependent reduction of virus load in the lungs, reaching undetectable levels following a single dose of 500 micrograms of STI-2020. These data support continued development of these antibodies as therapeutics against COVID-19 and future use of this approach to address novel emerging pandemic disease threats.

CORD-19: The Covid-19 Open Research Dataset.

The Covid-19 Open Research Dataset (CORD-19) is a growing resource of scientific papers on Covid-19 and related historical coronavirus research. CORD-19 is designed to facilitate the development of text mining and information retrieval systems over its rich collection of metadata and structured full text papers. Since its release, CORD-19 has been downloaded over 200K times and has served as the basis of many Covid-19 text mining and discovery systems. In this article, we describe the mechanics of dataset construction, highlighting challenges and key design decisions, provide an overview of how CORD-19 has been used, and describe several shared tasks built around the dataset. We hope this resource will continue to bring together the computing community, biomedical experts, and policy makers in the search for effective treatments and management policies for Covid-19.

TREC-COVID: rationale and structure of an information retrieval shared task for COVID-19.

TREC-COVID is an information retrieval (IR) shared task initiated to support clinicians and clinical research during the COVID-19 pandemic. IR for pandemics breaks many normal assumptions, which can be seen by examining 9 important basic IR research questions related to pandemic situations. TREC-COVID differs from traditional IR shared task evaluations with special considerations for the expected users, IR modality considerations, topic development, participant requirements, assessment process, relevance criteria, evaluation metrics, iteration process, projected timeline, and the implications of data use as a post-task test collection. This article describes how all these were addressed for the particular requirements of developing IR systems under a pandemic situation. Finally, initial participation numbers are also provided, which demonstrate the tremendous interest the IR community has in this effort.

Effects of total parenteral nutrition on drug metabolism gene expression in mice

Parenteral nutrition-associated liver disease (PNALD) is a liver dysfunction caused by various risk factors presented in patients receiving total parenteral nutrition (TPN). Omega-6 rich Intralipid® and omega-3 rich Omegaven® are two intravenous lipid emulsions used in TPN. TPN could affect the hepatic expression of genes in anti-oxidative stress, but it's unknown whether TPN affects genes in drug metabolism. In this study, either Intralipid®- or Omegaven®-based TPN was administered to mice and the expression of a cohort of genes involved in anti-oxidative stress or drug metabolism was analyzed, glutathione (GSH) levels were measured, and protein levels for two key drug metabolism genes were determined. Overall, the expression of most genes was downregulated by Intralipid®-based TPN ( and ). Omegaven® showed similar results as Intralipid® except for preserving the expression of and and increasing . Total GSH levels were decreased by Intralipid®, but increased by Omegaven®. CYP3A11 protein levels were increased by Omegaven®. In conclusion, TPN reduced the expression of many genes involved in anti-oxidative stress and drug metabolism in mice. However, Omegaven® preserved expression of , suggesting another beneficial effect of Omegaven® in protecting liver functions.

Mitigating Biases in CORD-19 for Analyzing COVID-19 Literature.

On the behest of the Office of Science and Technology Policy in the White House, six institutions, including ours, have created an open research dataset called COVID-19 Research Dataset (CORD-19) to facilitate the development of question-answering systems that can assist researchers in finding relevant research on COVID-19. As of May 27, 2020, CORD-19 includes more than 100,000 open access publications from major publishers and PubMed as well as preprint articles deposited into medRxiv, bioRxiv, and arXiv. Recent years, however, have also seen question-answering and other machine learning systems exhibit harmful behaviors to humans due to biases in the training data. It is imperative and only ethical for modern scientists to be vigilant in inspecting and be prepared to mitigate the potential biases when working with any datasets. This article describes a framework to examine biases in scientific document collections like CORD-19 by comparing their properties with those derived from the citation behaviors of the entire scientific community. In total, three expanded sets are created for the analyses: 1) the enclosure set CORD-19E composed of CORD-19 articles and their references and citations, mirroring the methodology used in the renowned "A Century of Physics" analysis; 2) the full closure graph CORD-19C that recursively includes references starting with CORD-19; and 3) the inflection closure CORD-19I, that is, a much smaller subset of CORD-19C but already appropriate for statistical analysis based on the theory of the scale-free nature of the citation network. Taken together, all these expanded datasets show much smoother trends when used to analyze global COVID-19 research. The results suggest that while CORD-19 exhibits a strong tilt toward recent and topically focused articles, the knowledge being explored to attack the pandemic encompasses a much longer time span and is very interdisciplinary. A question-answering system with such expanded scope of knowledge may perform better in understanding the literature and answering related questions. However, while CORD-19 appears to have topical coverage biases compared to the expanded sets, the collaboration patterns, especially in terms of team sizes and geographical distributions, are captured very well already in CORD-19 as the raw statistics and trends agree with those from larger datasets.

Predicting instances of pathway ontology classes for pathway integration.

BACKGROUND: To improve the outcomes of biological pathway analysis, a better way of integrating pathway data is needed. Ontologies can be used to organize data from disparate sources, and we leverage the Pathway Ontology as a unifying ontology for organizing pathway data. We aim to associate pathway instances from different databases to the appropriate class in the Pathway Ontology. RESULTS: Using a supervised machine learning approach, we trained neural networks to predict mappings between Reactome pathways and Pathway Ontology (PW) classes. For 2222 Reactome classes, the neural network (NN) model generated 10,952 class recommendations. We compared against a baseline bag-of-words (BOW) model for predicting correct PW classes. A 5% subset of Reactome pathways (111 pathways) was randomly selected, and the corresponding class recommendations from both models were evaluated by two curators. The precision of the BOW model was higher (0.49 for BOW and 0.39 for NN), but the recall was lower (0.42 for BOW and 0.78 for NN). Around 78% of Reactome pathways received pertinent recommendations from the NN model. CONCLUSIONS: The neural predictive model produced meaningful class recommendations that assisted PW curators in selecting appropriate class mappings for Reactome pathways. Our methods can be used to reduce the manual effort associated with ontology curation, and more broadly, for augmenting the curators' ability to organize and integrate data from pathway databases using the Pathway Ontology.

Electrical impedance myography for monitoring motor neuron loss in the SOD1 G93A amyotrophic lateral sclerosis rat.

OBJECTIVE: Human studies have shown that electrical impedance myography (EIM), a technique based on the surface application of high-frequency, low-intensity electrical current to localized areas of muscle, is sensitive to muscle denervation. In this study, we examined the role of EIM as a potential biomarker for assessing ALS disease progression in the SOD1 transgenic rat by comparing it to motor unit number estimation (MUNE). METHODS: Multi-frequency EIM and MUNE were performed twice weekly in 16 rats from approximately 10 weeks of age onward. Four different EIM measures were evaluated, including the previously studied 50 kHz phase and three condensed multi-frequency parameters. RESULTS: The rate of deterioration in the multi-frequency phase data from 100-500 kHz had the strongest correlation to survival (ρ=0.79, p<0.001), surpassing that of MUNE (ρ=0.57, p=0.020). These two measures were also strongly correlated (ρ=-0.94, p<0.001) to one another. CONCLUSIONS: These findings support that EIM is an effective tool for assessing disease progression in the ALS rat. SIGNIFICANCE: Given its ease of application and ability to assess virtually any superficial muscle, EIM deserves further study as a biomarker in human ALS clinical therapeutic trials.