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The survey of 10-century-old illuminations showed that the gold-like areas were made with the use of brass powder. Since this layer has been showing significant damage, it is vital to identify the degradation mechanisms to prevent the priceless manuscript from further deterioration. Degradation of the pseudo-gilded areas, such as darkening of the metal phase and disintegration of the binder, are well visible on the illuminations. The aim of the study was to compare the corrosivity of brass induced by binders using artificial aging tests modelling the conditions for the deposition of illuminated documents in the archives. Egg white, gum Arabic, isinglass and parchment glue were applied throughout the experiments. The samples on brass coupons and electrical resistance probes (ER-probes) were subjected to artificial aging at a high relative humidity and in the air containing acetic acid vapour and the effect of an increased relative humidity on the corrosion behaviour of brass was evaluated. Corrosion depth of the ER-probes versus time was evaluated as well. The results show that the presence of the binder layer on brass increases the corrosion rate of brass at an elevated relative humidity of ambient air. Protein-based binders resulted in a higher corrosion rate of brass probes compared to that of polysaccharide-based binder - gum Arabic. [ABSTRACT FROM AUTHOR]

Despite availability of multiple FDA approved therapies, many children with juvenile idiopathic arthritis (JIA) suffer pain and disability due to uncontrolled disease. The term JIA includes a heterogeneous set of conditions unified by chronic inflammatory arthritis, collectively affecting 1:1,000 children. When reviewing treatment options with families the rheumatologist currently refers to the experience of the average patient in relatively small controlled clinical trials, to consensus-based treatment plans, or increasingly the choice is dictated by the formulary restrictions of insurance payers. The current paradigm for treatment selection does not incorporate real-world evidence of treatment effectiveness centered to the individual patients with whom decisions are to be made. Treatment decisions based on the evidence of the average patient are not optimized to reflect the unique clinical characteristics of an individual with JIA and their disease course, nor does it account for heterogeneous treatment effects. To guide treatment choices centered around each patient, we describe a novel concept of utilizing digital health technology to bring patient-centered information into shared decision-making discussions based on comparative effectiveness analysis of electronic health record or observational clinical registry data of patients with similar characteristics. The envisioned digital tool will organize and present data relevant to the individual patient and enable evidence-based individualized treatment decision making when used in a collaborative manner with the patient family and rheumatologist. Capabilities in digital health technology, data capturing, and analytical methodologies are ripe for this endeavor. This brings the concept of a learning health system directly to the point of care., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2024 Huang, Kouril, Chen, Daraiseh, Ferraro, Mannion, Brunner, Lovell and Morgan.)

We present an in silico approach for drug discovery, dubbed connectivity enhanced structure activity relationship (ceSAR). Building on the landmark LINCS library of transcriptional signatures of drug-like molecules and gene knockdowns, ceSAR combines cheminformatic techniques with signature concordance analysis to connect small molecules and their targets and further assess their biophysical compatibility using molecular docking. Candidate compounds are first ranked in a target structure-independent manner, using chemical similarity to LINCS analogs that exhibit transcriptomic concordance with a target gene knockdown. Top candidates are subsequently rescored using docking simulations and machine learning-based consensus of the two approaches. Using extensive benchmarking, we show that ceSAR greatly reduces false-positive rates, while cutting run times by multiple orders of magnitude and further democratizing drug discovery pipelines. We further demonstrate the utility of ceSAR by identifying and experimentally validating inhibitors of BCL2A1, an important antiapoptotic target in melanoma and preterm birth-associated inflammation.

Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables coupled surface protein and transcriptome profiling, thereby revealing genomic programs underlying progenitor states. To perform CITE-seq systematically on primary human bone marrow cells, we used titrations with 266 CITE-seq antibodies (antibody-derived tags) and machine learning to optimize a panel of 132 antibodies. Multimodal analysis resolved >80 stem, progenitor, immune, stromal and transitional cells defined by distinctive surface markers and transcriptomes. This dataset enables flow cytometry solutions for in silico-predicted cell states and identifies dozens of cell surface markers consistently detected across donors spanning race and sex. Finally, aligning annotations from this atlas, we nominate normal marrow equivalents for acute myeloid leukemia stem cell populations that differ in clinical response. This atlas serves as an advanced digital resource for hematopoietic progenitor analyses in human health and disease., (© 2024. The Author(s).)

An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts, we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multiomics data, and a diverse collection of image data that span mammalian lung development and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances, including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, and mouse) to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, reanalysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). As this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP, and external research efforts.

Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs., (© 2023. The Author(s).)

There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates mining and re-analysis of the large collection of omics datasets (>34,000), pre-computed signatures (>200,000), and their connections, as well as the analysis of user-submitted omics signatures of diseases and cellular perturbations. iLINCS analysis workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures. iLINCS user-friendly interfaces enable execution of sophisticated analyses of omics signatures, mechanism of action analysis, and signature-driven drug repositioning. We illustrate the utility of iLINCS with three use cases involving analysis of cancer proteogenomic signatures, COVID 19 transcriptomic signatures and mTOR signaling., (© 2022. The Author(s).)

Child sexual abuse (CSA) is associated with revictimization and sexual risk-taking behaviours. The Internet has increased the opportunities for teens to access sexually explicit imagery and has provided new avenues for victimization and exploitation. Online URL activity and offline psychosocial factors were assessed for 460 females aged 12-16 (CSA = 156; comparisons = 304) with sexual behaviours and Internet-initiated victimization assessed 2 years later. Females who experienced CSA did not use more pornography than comparisons but were at increased odds of being cyberbullied (odds ratio = 2.84, 95% confidence interval = 1.67-4.81). These females were also more likely to be represented in a high-risk latent profile characterized by heightened URL activity coupled with problematic psychosocial factors, which showed increased odds of being cyberbullied, receiving online sexual solicitations and heightened sexual activity. While Internet activity alone may not confer risk, results indicate a subset of teens who have experienced CSA for whom both online and offline factors contribute to problematic outcomes., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

The aim of this review is to summarize the possibilities of replacing graphite bipolar plates in fuel-cells. The review is mostly focused on metallic bipolar plates, which benefit from many properties required for fuel cells, viz. good mechanical properties, thermal and electrical conductivity, availability, and others. The main disadvantage of metals is that their corrosion resistance in the fuel-cell environment originates from the formation of a passive layer, which significantly increases interfacial contact resistance. Suitable coating systems prepared by a proper deposition method are eventually able to compensate for this disadvantage and make the replacement of graphite bipolar plates possible. This review compares coatings, materials, and deposition methods based on electrochemical measurements and contact resistance properties with respect to achieving appropriate parameters established by the DOE as objectives for 2020. An extraordinary number of studies have been performed, but only a minority of them provided promising results. One of these is the nanocrystalline β-Nb 2 N coating on AISI 430, prepared by the disproportionation reaction of Nb(IV) in molten salt, which satisfied the DOE 2020 objectives in terms of corrosion resistance and interfacial contact resistance. From other studies, TiN, CrN, NbC, TiC, or amorphous carbon-based coatings seem to be promising. This paper is novel in extracting important aspects for future studies and methods for testing the properties of metallic materials and factors affecting monitoring characteristics and parameters.

Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Frequently overridden alerts in the electronic health record can highlight alerts that may need revision. This method is a way of fine-tuning clinical decision support. We evaluated the feasibility of a complementary, yet different method that directly involved pediatric emergency department (PED) providers in identifying additional medication alerts that were potentially incorrect or intrusive. We then evaluated the effect subsequent resulting modifications had on alert salience., Methods: We performed a prospective, interventional study over 34 months (March 6, 2014, to December 31, 2016) in the PED. We implemented a passive alert feedback mechanism by enhancing the native electronic health record functionality on alert reviews. End-users flagged potentially incorrect/bothersome alerts for review by the study's team. The alerts were updated when clinically appropriate and trends of the impact were evaluated., Results: More than 200 alerts were reported from both inside and outside the PED, suggesting an intuitive approach. On average, we processed 4 reviews per week from the PED, with attending physicians as major contributors. The general trend of the impact of these changes seems favorable., Discussion: The implementation of the review mechanism for user-selected alerts was intuitive and sustainable and seems to be able to detect alerts that are bothersome to the end-users. The method should be run in parallel with the traditional data-driven approach to support capturing of inaccurate alerts., Conclusions: User-centered, context-specific alert feedback can be used for selecting suboptimal, interruptive medication alerts.

Objective: The study sought to create an online resource that informs the public of coronavirus disease 2019 (COVID-19) outbreaks in their area., Materials and Methods: This R Shiny application aggregates data from multiple resources that track COVID-19 and visualizes them through an interactive, online dashboard., Results: The Web resource, called the COVID-19 Watcher, can be accessed online (https://covid19watcher.research.cchmc.org/). It displays COVID-19 data from every county and 188 metropolitan areas in the United States. Features include rankings of the worst-affected areas and auto-generating plots that depict temporal changes in testing capacity, cases, and deaths., Discussion: The Centers for Disease Control and Prevention does not publish COVID-19 data for local municipalities, so it is critical that academic resources fill this void so the public can stay informed. The data used have limitations and likely underestimate the scale of the outbreak., Conclusions: The COVID-19 Watcher can provide the public with real-time updates of outbreaks in their area., (© The Author(s) 2020. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The implicit association test (IAT) is widely used in psychology. Unfortunately, the IAT cannot be run within online surveys, requiring researchers who conduct online surveys to rely on third-party tools. We introduce a novel method for constructing IATs using online survey software (Qualtrics); we then empirically assess its validity. Study 1 (student n = 239) revealed good psychometric properties, expected IAT effects, and expected correlations with explicit measures for survey-software IATs. Study 2 (MTurk n = 818) showed predicted IAT effects across four survey-software IATs (ds = 0.82 [Black-White IAT] to 2.13 [insect-flower IAT]). Study 3 (MTurk n = 270) compared survey-software IATs and IATs run via Inquisit, yielding nearly identical results and intercorrelations that would be expected for identical IATs. Survey-software IATs appear to be reliable and valid, offer numerous advantages, and make IATs accessible for researchers who use survey software to conduct online research. We present all the materials, links to tutorials, and an open-source tool that rapidly automates survey-software IAT construction and analysis.

The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for reusing these data, we have developed a web-application GREIN (GEO RNA-seq Experiments Interactive Navigator) which provides user-friendly interfaces to manipulate and analyze GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>6,500) of already processed datasets. The front-end user interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, and connectivity analysis with LINCS L1000 data. The combination of the massive amount of back-end data and front-end analytics options driven by user-friendly interfaces makes GREIN a unique open-source resource for re-using GEO RNA-seq data. GREIN is accessible at: https://shiny.ilincs.org/grein , the source code at: https://github.com/uc-bd2k/grein , and the Docker container at: https://hub.docker.com/r/ucbd2k/grein .

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Quantifying the response of cell lines to drugs or other perturbagens is the cornerstone of pre-clinical drug development and pharmacogenomics as well as a means to study factors that contribute to sensitivity and resistance. In dividing cells, traditional metrics derived from dose-response curves such as IC 50 , AUC, and E max , are confounded by the number of cell divisions taking place during the assay, which varies widely for biological and experimental reasons. Hafner et al. (Nat Meth 13:521-627, 2016) recently proposed an alternative way to quantify drug response, normalized growth rate (GR) inhibition, that is robust to such confounders. Adoption of the GR method is expected to improve the reproducibility of dose-response assays and the reliability of pharmacogenomic associations (Hafner et al. 500-502, 2017)., Results: We describe here an interactive website ( www.grcalculator.org ) for calculation, analysis, and visualization of dose-response data using the GR approach and for comparison of GR and traditional metrics. Data can be user-supplied or derived from published datasets. The web tools are implemented in the form of three integrated Shiny applications (grcalculator, grbrowser, and grtutorial) deployed through a Shiny server. Intuitive graphical user interfaces (GUIs) allow for interactive analysis and visualization of data. The Shiny applications make use of two R packages (shinyLi and GRmetrics) specifically developed for this purpose. The GRmetrics R package is also available via Bioconductor and can be used for offline data analysis and visualization. Source code for the Shiny applications and associated packages (shinyLi and GRmetrics) can be accessed at www.github.com/uc-bd2k/grcalculator and www.github.com/datarail/gr_metrics ., Conclusions: GRcalculator is a powerful, user-friendly, and free tool to facilitate analysis of dose-response data. It generates publication-ready figures and provides a unified platform for investigators to analyze dose-response data across diverse cell types and perturbagens (including drugs, biological ligands, RNAi, etc.). GRcalculator also provides access to data collected by the NIH LINCS Program ( http://www.lincsproject.org /) and other public domain datasets. The GRmetrics Bioconductor package provides computationally trained users with a platform for offline analysis of dose-response data and facilitates inclusion of GR metrics calculations within existing R analysis pipelines. These tools are therefore well suited to users in academia as well as industry.

Objective: More than 70% of hospitals in the United States have electronic health records (EHRs). Clinical decision support (CDS) presents clinicians with electronic alerts during the course of patient care; however, alert fatigue can influence a provider's response to any EHR alert. The primary goal was to evaluate the effects of alert burden on user response to the alerts., Methods: We performed a retrospective study of medication alerts over a 24-month period (1/2013-12/2014) in a large pediatric academic medical center. The institutional review board approved this study. The primary outcome measure was alert salience, a measure of whether or not the prescriber took any corrective action on the order that generated an alert. We estimated the ideal number of alerts to maximize salience. Salience rates were examined for providers at each training level, by day of week, and time of day through logistic regressions., Results: While salience never exceeded 38%, 49 alerts/day were associated with maximal salience in our dataset. The time of day an order was placed was associated with alert salience (maximal salience 2am). The day of the week was also associated with alert salience (maximal salience on Wednesday). Provider role did not have an impact on salience., Conclusion: Alert burden plays a role in influencing provider response to medication alerts. An increased number of alerts a provider saw during a one-day period did not directly lead to decreased response to alerts. Given the multiple factors influencing the response to alerts, efforts focused solely on burden are not likely to be effective.

Objectives: Electronic trigger detection tools hold promise to reduce Adverse drug event (ADEs) through efficiencies of scale and real-time reporting. We hypothesized that such a tool could automatically detect medication dosing errors as well as manage and evaluate dosing rule modifications., Materials and Methods: We created an order and alert analysis system that identified antibiotic medication orders and evaluated user response to dosing alerts. Orders associated with overridden alerts were examined for evidence of administration and the delivered dose was compared to pharmacy-derived dosing rules to confirm true overdoses. True overdose cases were reviewed for association with known ADEs., Results: Of 55 546 orders reviewed, 539 were true overdose orders, which lead to 1965 known overdose administrations. Documentation of loose stools and diarrhea was significantly increased following drug administration in the overdose group. Dosing rule thresholds were altered to reflect clinically accurate dosing. These rule changes decreased overall alert burden and improved the salience of alerts., Discussion: Electronic algorithm-based detection systems can identify antibiotic overdoses that are clinically relevant and are associated with known ADEs. The system also serves as a platform for evaluating the effects of modifying electronic dosing rules. These modifications lead to decreased alert burden and improvements in response to decision support alerts., Conclusion: The success of this test case suggests that gains are possible in reducing medication errors and improving patient safety with automated algorithm-based detection systems. Follow-up studies will determine if the positive effects of the system persist and if these changes lead to improved safety outcomes., (© The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com)

Objective: The current study aims to fill the gap in available healthcare de-identification resources by creating a new sharable dataset with realistic Protected Health Information (PHI) without reducing the value of the data for de-identification research. By releasing the annotated gold standard corpus with Data Use Agreement we would like to encourage other Computational Linguists to experiment with our data and develop new machine learning models for de-identification. This paper describes: (1) the modifications required by the Institutional Review Board before sharing the de-identification gold standard corpus; (2) our efforts to keep the PHI as realistic as possible; (3) and the tests to show the effectiveness of these efforts in preserving the value of the modified data set for machine learning model development., Materials and Methods: In a previous study we built an original de-identification gold standard corpus annotated with true Protected Health Information (PHI) from 3503 randomly selected clinical notes for the 22 most frequent clinical note types of our institution. In the current study we modified the original gold standard corpus to make it suitable for external sharing by replacing HIPAA-specified PHI with newly generated realistic PHI. Finally, we evaluated the research value of this new dataset by comparing the performance of an existing published in-house de-identification system, when trained on the new de-identification gold standard corpus, with the performance of the same system, when trained on the original corpus. We assessed the potential benefits of using the new de-identification gold standard corpus to identify PHI in the i2b2 and PhysioNet datasets that were released by other groups for de-identification research. We also measured the effectiveness of the i2b2 and PhysioNet de-identification gold standard corpora in identifying PHI in our original clinical notes., Results: Performance of the de-identification system using the new gold standard corpus as a training set was very close to training on the original corpus (92.56 vs. 93.48 overall F-measures). Best i2b2/PhysioNet/CCHMC cross-training performances were obtained when training on the new shared CCHMC gold standard corpus, although performances were still lower than corpus-specific trainings., Discussion and Conclusion: We successfully modified a de-identification dataset for external sharing while preserving the de-identification research value of the modified gold standard corpus with limited drop in machine learning de-identification performance., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Users of electronic health record (EHR) systems frequently prescribe doses outside recommended dose ranges, and tend to ignore the alerts that result. Since some of these dosing errors are the result of system design flaws, analysis of large overdoses can lead to the discovery of needed system changes., Objectives: To develop database techniques for detecting and extracting large overdose orders from our EHR. To identify and characterize users' responses to these large overdoses. To identify possible causes of large-overdose errors and to mitigate them., Methods: We constructed a data mart of medication-order and dosing-alert data from a quaternary pediatric hospital from June 2011 to May 2013. The data mart was used along with a test version of the EHR to explain how orders were processed and alerts were generated for large (>500%) and extreme (>10,000%) overdoses. User response was characterized by the dosing alert salience rate, which expresses the proportion of time users take corrective action., Results: We constructed an advanced analytic framework based on workflow analysis and order simulation, and evaluated all 5,402,504 medication orders placed within the 2 year timeframe as well as 2,232,492 dose alerts associated with some of the orders. 8% of orders generated a visible alert, with ¼ of these related to overdosing. Alerts presented to trainees had higher salience rates than those presented to senior colleagues. Salience rates were low, varying between 4-10%, and were lower with larger overdoses. Extreme overdoses fell into eight causal categories, each with a system design mitigation., Conclusions: Novel analytic systems are required to accurately understand prescriber behavior and interactions with medication-dosing CDS. We described a novel analytic system that can detect apparent large overdoses (≥500%) and explain the sociotechnical factors that drove the error. Some of these large overdoses can be mitigated by system changes. EHR design should prospectively mitigate these errors.

We present the construction of three annotated corpora to serve as gold standards for medical natural language processing (NLP) tasks. Clinical notes from the medical record, clinical trial announcements, and FDA drug labels are annotated. We report high inter-annotator agreements (overall F-measures between 0.8467 and 0.9176) for the annotation of Personal Health Information (PHI) elements for a de-identification task and of medications, diseases/disorders, and signs/symptoms for information extraction (IE) task. The annotated corpora of clinical trials and FDA labels will be publicly released and to facilitate translational NLP tasks that require cross-corpora interoperability (e.g. clinical trial eligibility screening) their annotation schemas are aligned with a large scale, NIH-funded clinical text annotation project.

Progress in functional genomics and structural studies on biological macromolecules are generating a growing number of potential targets for therapeutics, adding to the importance of computational approaches for small molecule docking and virtual screening of candidate compounds. In this review, recent improvements in several public domain packages that are widely used in the context of drug development, including DOCK, AutoDock, AutoDock Vina and Screening for Ligands by Induced-fit Docking Efficiently (SLIDE) are surveyed. The authors also survey methods for the analysis and visualisation of docking simulations, as an important step in the overall assessment of the results. In order to illustrate the performance and limitations of current docking programs, the authors used the National Center for Toxicological Research (NCTR) oestrogen receptor benchmark set of 232 oestrogenic compounds with experimentally measured strength of binding to oestrogen receptor alpha. The methods tested here yielded a correlation coefficient of up to 0.6 between the predicted and observed binding affinities for active compounds in this benchmark.