Enhancing access to the Bibliome: the TREC 2004 Genomics Track

BACKGROUND: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed. RESULTS: A total of 27 research groups submitted 47 different runs. The most effective runs, as measured by the primary evaluation measure of mean average precision (MAP), used a combination of domain-specific and general techniques. The best MAP obtained by any run was 0.4075. Techniques that expanded queries with gene name lists as well as words from related articles had the best efficacy. However, many runs performed more poorly than a simple baseline run, indicating that careful selection of system features is essential. CONCLUSION: Various approaches to ad hoc retrieval provide a diversity of efficacy. The TREC Genomics Track and its test collection resources provide tools that allow improvement in information retrieval systems

Audubon Data Project Final Report

The Audubon Data Project was initiated as a Clark University Capstone project. The project’s client, Mass Audubon’s Shaping the Future of Your Community program, had identified a need to improve their data management methods and make better use of their data. The Capstone team, composed of Clark University graduate students, met with the client regularly to review the current state of the data and potential improvements to be made. The process began with a data review. During the review we worked with the client to explicitly define the purposes and requirements of the data, the current process for updating and using the data, and the ways that different types of records were related to one another. After the review, we were able to identify the issues in the current system which we would seek to resolve. These included data integrity issues such as ensuring crucial items (such as a town name) were always included when entering data, and data structure issues such as having a relatively user-friendly way to express relationships and update records that were part of a relationship

Structure and Magnetic Fields in the Precessing Jet System SS 433 II. Intrinsic Brightness of the Jets

Deep Very Large Array imaging of the binary X-ray source SS 433, sometimes classified as a microquasar, has been used to study the intrinsic brightness distribution and evolution of its radio jets. The intrinsic brightness of the jets as a function of age at emission of the jet material tau is recovered by removal of the Doppler boosting and projection effects. We find that intrinsically the two jets are remarkably similar when compared for equal tau, and that they are best described by Doppler boosting of the form D^{2+alpha}, as expected for continuous jets. The intrinsic brightnesses of the jets as functions of age behave in complex ways. In the age range 60 < tau < 150 days, the jet decays are best represented by exponential functions of tau, but linear or power law functions are not statistically excluded. This is followed by a region out to tau ~ 250 days during which the intrinsic brightness is essentially constant. At later times the jet decay can be fit roughly as exponential or power law functions of tau.Comment: 30 Pages, 11 Figures, Submitted to Ap

Multi-isotope reconstruction of Late Pleistocene large-herbivore biogeography and mobility patterns in Central Europe

We thank H. Dietl, K. G\u00E4rtner, S. Kimmig-V\u00F6lkner, R. Mischker and E. Pawlak, State Museum of Prehistory, Halle, for providing access to the material. We thank C. Pasda, Friedrich Schiller University, Jena, for providing research support.Peer reviewe

Women's information needs, decision-making and experiences of membrane sweeping to promote spontaneous labour

© 2019 Objective: To explore and synthesise evidence of women's information needs, decision-making and experiences of membrane sweeping to promote spontaneous labour. Design: A systematic review following the Joanna Briggs Institute (JBI) meta-aggregative approach to qualitative evidence synthesis. Relevant databases were searched for literature published in English between 2000–19. Study quality was assessed using the JBI quality assessment tool for qualitative studies. Setting: Qualitative research conducted in OECD countries describing women's information needs, decision-making and/or experiences of membrane sweeping to promote spontaneous labour. Findings: One article met the criteria for inclusion. This article describes the experience of a membrane sweep given without consent. Key conclusions and Implications for practice: There is a lack of evidence around women's information needs, decision-making and experiences of membrane sweeping. This is concerning, especially in the context of rising rates of formal induction of labour. Further research is needed to investigate how women are being offered membrane sweeping and what information women need to make informed choices about membrane sweeping to promote spontaneous labour

BioCreative III interactive task: an overview

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707