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Discover the most talked about and latest scientific content & concepts.

Concept: Peer-to-peer

173

Weight-based stigma compromises the social networks of overweight children. To date, research on the position of overweight children in their peer network has focused only on friendship relations, and not on negative relationship dimensions. This study examined how overweight was associated with relations of friendship and dislike (antipathies) in the peer group. Exponential random graph models (ERGM) were used to examine friendship and antipathy relations among overweight children and their classmates, using a sub-sample from the TRacking Adolescents' Individual Lives Survey (N = 504, M age 11.4). Findings showed that overweight children were less likely to receive friendship nominations, and were more likely to receive dislike nominations. Overweight children were also more likely than their non-overweight peers to nominate classmates that they disliked. Together, the results indicate that positive and negative peer relations are impacted by children’s weight status, and are relevant to addressing the social marginalization of overweight children.

Concepts: Sociology, Adolescence, Graph theory, Peer group, Friendship, Peer-to-peer, Network theory, Random graph

173

BACKGROUND: For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications with known masses. Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed. RESULTS: We present a sequence database search engine that is specifically designed to run efficiently on the Hadoop MapReduce distributed computing framework. The search engine implements the K-score algorithm, generating comparable output for the same input files as the original implementation. The scalability of the system is shown, and the architecture required for the development of such distributed processing is discussed. CONCLUSION: The software is scalable in its ability to handle a large peptide database, numerous modifications and large numbers of spectra. Performance scales with the number of processors in the cluster, allowing throughput to expand with the available resources.

Concepts: Mass spectrometry, Phosphorylation, Search engine optimization, Computer science, Matrix-assisted laser desorption/ionization, Peer-to-peer, Hadoop, Distributed computing

170

BACKGROUND: The clinical course of Cystic Fibrosis (CF) is usually measured using the percent predicted FEV1 and BMI Z-score referenced against a healthy population, since achieving normality is the ultimate goal of CF care. Referencing against age and sex matched CF peers may provide valuable information for patients and for comparison between CF centers or populations. Here, we used a large database of European CF patients to compute CF specific reference equations for FEV1 and BMI, derived CF-specific percentile charts and compared these European data to their nearest international equivalents. METHODS: 34859 FEV1 and 40947 BMI observations were used to compute European CF specific percentiles. Quantile regression was applied to raw measurements as a function of sex, age and height. Results were compared with the North American equivalent for FEV1 and with the WHO 2007 normative values for BMI. RESULTS: FEV1 and BMI percentiles illustrated the large variability between CF patients receiving the best current care. The European CF specific percentiles for FEV1 were significantly different from those in the USA from an earlier era, with higher lung function in Europe. The CF specific percentiles for BMI declined relative to the WHO standard in older children. Lung function and BMI were similar in the two largest contributing European Countries (France and Germany). CONCLUSION: The CF specific percentile approach applied to FEV1 and BMI allows referencing patients with respect to their peers. These data allow peer to peer and population comparisons in CF patients.

Concepts: Median, Quantile, Cystic fibrosis, Peer-to-peer, Quartile, Reference, Percentile rank, File sharing

92

US and UK suicide prevention strategies suggest that bereavement by the suicide of a relative or friend is a risk factor for suicide. However, evidence is lacking that the risk exceeds that of any sudden bereavement, is specific to suicide, or applies to peer suicide. We conducted the first controlled UK-wide study to test the hypothesis that young adults bereaved by suicide have an increased risk of suicidal ideation and suicide attempt compared with young adults bereaved by other sudden deaths.

Concepts: Death, Sociology, Bipolar disorder, Suicide, Parasuicide, Peer-to-peer, American Foundation for Suicide Prevention, Suicidal ideation

32

All editorial decisions at eLife are taken by working scientists in a process that emphasizes fairness, speed and transparency.

Concepts: Review, Peer-to-peer, File sharing

31

The benefits of physical activity are well documented, but scalable programs to promote activity are needed. Interventions that assign tailored and dynamically adjusting goals could effect significant increases in physical activity but have not yet been implemented at scale.

Concepts: Clinical trial, Randomized controlled trial, Effectiveness, Pharmaceutical industry, Clinical research, Efficacy, Program, Peer-to-peer

27

Objectives To determine whether the outcome of drug studies influenced submission and/or acceptance rates for publication in peer reviewed medical journals.Design A six year retrospective review of publication status by study outcome for all human drug research studies conducted by a single industry sponsor (GlaxoSmithKline) that completed from 1 January 2009 to 30 June 2014 and were therefore due for manuscript submission (per the sponsor’s policy) to peer reviewed journals within 18 months of study completion-that is, 31 December 2015. In addition, manuscripts from studies completing after 30 June 2014 were included irrespective of outcome if they were submitted before 31 December 2015.Setting Studies conducted by a single industry sponsor (GlaxoSmithKline)Studies reviewed 1064 human drug research studies.Main outcome measures All studies were assigned a publication status at 26 February 2016 including (as applicable): study completion date, date of first primary manuscript submission, number of submissions, journal decision(s), and publication date. All studies were also classified with assessors blinded to publication status as “positive” (perceived favorable outcome for the drug under study), “negative” (perceived unfavorable outcome for the drug under study), mixed, or non-comparative based on the presence and outcome of the primary outcome measure(s) for each study. “Negative” studies included safety studies in which the primary outcome was achieved but was adverse for the drug under study. For the total cohort and each of the four study outcomes, measures included descriptive statistics for study phase, time from study completion to submission and publication, and number and outcome (accepted/rejected) of publication submissions.Results Of the 1064 studies (phase I-IV, interventional and non-interventional) included, 321 had study outcomes classified as positive, 155 as negative, 52 as mixed, and 536 as non-comparative. At the time of publication cut-off date (26 February 2016), 904 (85%) studies had been submitted for publication as full manuscripts and 751 (71%) had been successfully published or accepted, with 100 (9%) still under journal review. An additional 77 (7%) studies were conference abstracts and were not included in submission or publication rates. Submission rates by study outcome were 79% for the 321 studies with positive outcomes, 92% for the 155 with negative outcomes, 94% for the 52 with mixed outcomes, and 85% for the 536 non-comparative studies; while rates of publication at the cut-off date were 66%, 77%, 77%, and 71%, respectively. Median time from study completion to submission was 537 days (interquartile range 396-638 days) and 823 days (650-1063 days) from completion to publication, with similar times observed across study outcomes. First time acceptance rates were 56% for studies with positive outcomes and 48% for studies with negative outcomes. Over 10% of studies across all categories required three or more submissions to achieve successful publication. At the time of analysis, 83 studies had not been submitted for publication, including 49 bioequivalence studies with positive outcomes and 33 non-comparative studies. Most studies (98%, 1041/1064) had results posted to one or more public registers, including all studies subject to FDAAA (Food and Drug Administration Amendments Act) requirements for posting to www.clinicaltrials.govConclusions Over the period studied, there was no evidence of submission or publication bias: 92% of studies with negative outcomes were submitted for publication by the cut-off date versus 79% of those with positive outcomes. Publication rates were slightly higher for studies with a negative (that is, unfavorable) outcome compared with a positive outcome, despite a slightly lower rate of acceptance at first submission. Many studies required multiple submission attempts before they were accepted for publication. Analyses focusing solely on publication rates do not take into account unsuccessful efforts to publish. Sponsors and journal editors should share similar information to contribute to better understanding of issues and barriers to full transparency.

Concepts: Academic publishing, Peer review, Cultural studies, Outcome, Peer-to-peer, Mixed martial arts, 2016, 2015

18

Journals are exploring new approaches to peer review in order to reduce bias, increase transparency and respond to author preferences. Funders are also getting involved.

Concepts: Review, Peer-to-peer, File sharing

9

Five years after eLife published its first papers, we reflect on our consultative approach to peer review, the challenges of reproducibility, and the need to reform how published research is assessed.

Concepts: Scientific method, Academic publishing, Peer review, Peer-to-peer

9

This editorial introduces a series of tutorials by experts, who provide tips and advice for junior reviewers on how to conduct peer review based on specific study designs. The aim of these articles is to provide an easy-to-use, quick reference for those who are seeking more guidance on how to peer review biomedical research papers. Unlike previous tips and guides on peer review, this series is the first to provide advice from experts for those in their specific fields.

Concepts: Academic publishing, Medical research, Peer review, Field, Peer-to-peer