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Results for “Scientific Communication and Education”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 415 records · Page 23Linked to original sources

bioRxiv2015

Why clinical trials are terminated

BackgroundEvidence-based clinical practice relies on unbiased reporting of negative results. Meta-analysis of drug safety and efficacy across many clinical trials is difficult given the unconstrained nature of reasons that are provided to ClinicalTrials.gov to explain clinical trial terminations.\n\nMethods and FindingsWe scanned all trials in ClinicalTrials.gov marked with the \"terminated\" status (N=3122), meaning the trial had been stopped before the scheduled end date. Under the current reporting framework, any number of reasons may be given for termination, and these need not conform to a controlled vocabulary. Here we develop a controlled vocabulary for trial termination, and map each terminated trial to as many as three vocabulary terms. Mapping to this \"ontology of termination\" allows further analysis and conclusions. First, we identify the subset of terminated trials that ended citing safety concerns (6.2%) or failure to establish efficacy (10.8%), and were further able to stratify these rates across trials of different phases. Second, we examine termination reasons where a stricter data model could have preserved more evidentiary value, either because the data model was misused (7.6%) or because the given reason left unclear whether the decision to terminate was based on analysis of the data (74.9%, with 20.4% mentioning a decision-maker that may have had access to the data). Third, we show that imposing a controlled vocabulary of reasons for termination would avoid ambiguity and improve the evidentiary value of clinical trials.\n\nConclusionsWe encourage wider use of an \"ontology of termination\" and propose four questions that should be posed on trial termination. These simple steps would promote transparency and enable ready access to negative trial results for meta-analysis.

Scientific Communication and Education↗

bioRxiv2015

Publishing descriptions of non-public clinical datasets: guidance for researchers, repositories, editors and funding organisations

Sharing of experimental clinical research data usually happens between individuals or research groups rather than via public repositories, in part due to the need to protect research participant privacy. This approach to data sharing makes it difficult to connect journal articles with their underlying datasets and is often insufficient for ensuring access to data in the long term. Voluntary data sharing services such as the Yale Open Data Access (YODA) and Clinical Study Data Request (CSDR) projects have increased accessibility to clinical datasets for secondary uses while protecting patient privacy and the legitimacy of secondary analyses but these resources are generally disconnected from journal articles - where researchers typically search for reliable information to inform future research. New scholarly journal and article types dedicated to increasing accessibility of research data have emerged in recent years and, in general, journals are developing stronger links with data repositories. There is a need for increased collaboration between journals, data repositories, researchers, funders, and voluntary data sharing services to increase the visibility and reliability of clinical research. We propose changes to the format and peer-review process for journal articles to more robustly link them to data that are only available on request. We also propose additional features for data repositories to better accommodate non-public clinical datasets, including Data Use Agreements (DUAs).

Scientific Communication and Education↗

bioRxiv2015

Accelerating Scientific Publication in Biology

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. Considerably more experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for the life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and scientific community.

Scientific Communication and Education↗

bioRxiv2015

Classifying Aging as a Disease in the context of ICD-11

Aging is a complex continuous multifactorial process leading to loss of function and crystalizing into the many age-related diseases. Here, we explore the arguments for classifying aging as a disease in the context of the upcoming World Health Organizations 11th International Statistical Classification of Diseases and Related Health Problems (ICD-11), expected to be finalized in 2018. We hypothesize that classifying aging as a disease will result in new approaches and business models for addressing aging as a treatable condition, which will lead to both economic and healthcare benefits for all stakeholders. Classification of aging as a disease may lead to more efficient allocation of resources by enabling funding bodies and other stakeholders to use quality-adjusted life years (QALYs) and healthy-years equivalent (HYE) as metrics when evaluating both research and clinical programs. We propose forming a Task Force to interface the WHO in order to develop a multidisciplinary framework for classifying aging as a disease.

Scientific Communication and Education↗

bioRxiv2015

Relative Citation Ratio (RCR): A new metric that uses citation rates to measure influence at the article level

Despite their recognized limitations, bibliometric assessments of scientific productivity have been widely adopted. We describe here an improved method that makes novel use of the co-citation network of each article to field-normalize the number of citations it has received. The resulting Relative Citation Ratio is article-level and field-independent, and provides an alternative to the invalid practice of using Journal Impact Factors to identify influential papers. To illustrate one application of our method, we analyzed 88,835 articles published between 2003 and 2010, and found that the National Institutes of Health awardees who authored those papers occupy relatively stable positions of influence across all disciplines. We demonstrate that the values generated by this method strongly correlate with the opinions of subject matter experts in biomedical research, and suggest that the same approach should be generally applicable to articles published in all areas of science. A beta version of iCite, our web tool for calculating Relative Citation Ratios of articles listed in PubMed, is available at https://icite.od.nih.gov.

Scientific Communication and Education↗

bioRxiv2015

Evolving cohesion metrics of a research network on rare diseases: a longitudinal study over 14 years

Research collaboration is necessary, rewarding, and beneficial. Cohesion between team members is related to their collective efficiency. To assess collaboration processes and their eventual outcomes, agencies need innovative methods - and social network approaches are emerging as a useful analytical tool. We identified the research output and citation data of a network of 61 research groups formally engaged in publishing rare disease research between 2000 and 2013. We drew the collaboration networks for each year and computed the global and local measures throughout the period, relating connectivity with the normalized impact. Although global network measures remained steady over the whole period, the local and subgroup metrics revealed a growing cohesion between the teams. Transitivity and density showed little or no variation throughout the period. In contrast the following points indicated an evolution towards greater network cohesion: the emergence of a giant component (which grew from just 30% to reach 85% of groups); the decreasing number of communities (following a tripling in the average number of members); the growing number of fully connected subgroups; and increasing average strength. Normalized citation measures, although ranking the member groups as above average impact for Spanish biomedical output, do not support correlation between collaboration and citation impact. The Spanish research network on rare diseases has evolved towards a growing cohesion - as revealed by local and subgroup metrics following social network analysis. This greater cohesion does not translate into a greater impact, as measured by the citation analysis of the papers.

Scientific Communication and Education↗

bioRxiv2015

Sequential Multiple Assignment Randomized Trials: An Opportunity for Improved Design of Stroke Reperfusion Trials

Background: Modern clinical trials in stroke reperfusion fall into two categories: alternative systemic pharmacological regimens to alteplase and \"rescue\" endovascular approaches using targeted thrombectomy devices and/or medications delivered directly for persistently vessel occlusions. Clinical trials in stroke have not evaluated how initial pharmacological thrombolytic management might influence subsequent rescue strategy. A sequential multiple assignment randomized trial (SMART) is a novel trial design that can test these dynamic treatment regimens and lead to treatment guidelines which more closely mimic practice.\n\nAim: To characterize a SMART design in comparison to traditional approaches for stroke reperfusion trials.\n\nMethods: We conducted a numerical simulation study that evaluated the performance of contrasting acute stroke clinical trial designs of both initial reperfusion and rescue therapy. We compare a SMART design where the same patients are followed through initial reperfusion and rescue therapy within one trial to a standard phase III design comparing two reperfusion treatments and a separate phase II futility design of rescue therapy in terms of sample size, power, and ability to address particular research questions.\n\nResults: Traditional trial designs can be well powered and have optimal design characteristics for independent treatment effects. When treatments, such as the reperfusion and rescue therapies, may interact, commonly used designs fail to detect this. A SMART design, with similar sample size to standard designs, can detect treatment interactions.\n\nConclusions: The use of SMART designs to investigate effective and realistic dynamic treatment regimens is a promising way to accelerate the discovery of new, effective treatments for stroke.

Scientific Communication and Education↗

bioRxiv2016

Comparing the Citation Performance of PNAS Papers by Submission Track

Purpose: To determine whether papers contributed by National Academy of Sciences (NAS) members perform differently than direct submissions.\n\nData/Methods: 55,889 original papers published in PNAS from 1997 through 2014. Regression analysis measuring total citations, controlling for editorial track (Contributed, Direct, Communicated), date of publication, and paper topic.\n\nMain findings: Contributed papers consistently underperformed against Direct submissions, receiving 9% fewer citations, ceteris paribus. The effect was greatest for Social Sciences papers (12% fewer citations). Nonetheless, the main effect has attenuated over the past decade, from 13.6% fewer citations in 2005 to just 2.2% fewer citations in 2014.\n\nSignificance: Successive editorial policies placing limits, restrictions, and other qualifications on the publication privileges of NAS members may be responsible for the submission of better performing Contributed papers.

Scientific Communication and Education↗

bioRxiv2016

Two Similarity Metrics for Medical Subject Headings (MeSH): An Aid to Biomedical Text Mining and Author Name Disambiguation

In the present paper, we have created and characterized several similarity metrics for relating any two Medical Subject Headings (MeSH terms) to each other. The article-based metric measures the tendency of two MeSH terms to appear in the MEDLINE record of the same article. The author-based metric measures the tendency of two MeSH terms to appear in the body of articles written by the same individual (using the 2009 Author-ity author name disambiguation dataset as a gold standard). The two metrics are only modestly correlated with each other (r = 0.50), indicating that they capture different aspects of term usage. The article-based metric provides a measure of semantic relatedness, and MeSH term pairs that co-occur more often than expected by chance may reflect relations between the two terms. In contrast, the author metric is indicative of how individuals practice science, and may have value for author name disambiguation and studies of scientific discovery. We have calculated article metrics for all MeSH terms appearing in at least 25 articles in MEDLINE (as of 2014) and author metrics for MeSH terms published as of 2009. The dataset is freely available for download and can be queried at http://arrowsmith.psych.uic.edu/arrowsmith_uic/mesh_pair_metrics.html.

Scientific Communication and Education↗

bioRxiv2016

Evaluation of Techniques for Performing Cellular Isolation and Preservation during Microgravity Conditions

Genomic and epigenomic studies require the precise transfer of small volumes from one container to another. Epigenomic and transcriptional analysis require separation of purified cell types, and long term preservation of cells requires their isolation and transfer into appropriate freezing media. There are currently no protocols for these procedures on the ISS. Currently samples are either frozen as mixed cell populations, with poor yield, or returned under ambient conditions, requiring timing with Soyuz missions. Here, we evaluate the feasibility of translating terrestrial cell purification techniques to the ISS. Our evaluations were performed in microgravity conditions during parabolic atmospheric flight. The pipetting of open liquids in microgravity was evaluated using analog blood fluids and several types of pipette hardware. The best performing pipettes were used to evaluate the pipetting steps required for peripheral blood mononuclear cell (PBMC) isolation via density gradient centrifugation (DGC). Evaluation of actual blood products was performed for both the overlay of diluted blood, and the extraction of isolated PBMCs. We also validated magnetic purification of cells. We found that positive displacement pipettes avoided air bubbles, and the tips allowed the strong surface tension of water, glycerol and blood to maintain a patent meniscus and withstand robust pipetting in microgravity. These procedures will greatly increase the breadth of research that can be performed onboard the ISS, and allow improvised experimentation on extraterrestrial missions.

Scientific Communication and Education↗

bioRxiv2016

Advancing insect vector biology research: a community survey for future directions, research applications and infrastructure requirements

BackgroundVector-borne pathogens impact public health and economies worldwide. It has long been recognized that research on arthropod vectors such as mosquitoes, ticks, sandflies and midges which transmit parasites and arboviruses to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is an increasing issue. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies. This has increased interest in vector biology and genetics as well as vector-pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructures will benefit from community input.\n\nMethodology/Principal FindingsA survey initiated by the European Horizon2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key issues that should be addressed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such work to be carried out.\n\nConclusions/SignificanceWe summarize the key findings of the survey which in particular reflect priorities in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations.\n\nAuthor SummaryResearch on arthropod vectors that transmit so-called arboviruses or parasites, such as mosquitoes, ticks, sandflies and midges is important for the development of control measures that target transmission of these pathogens. Important developments in this research area, for example vector genome sequencing, genome manipulation and use of transmission-blocking endosymbionts such as Wolbachia have increased interest in vector biology. As such, strategic decisions on research directions as well as research infrastructures will benefit from community input. A survey initiated by the European Horizon2020 INFRAVEC-2 consortium set out to investigate priorities in the vector biology research community as well as key issues that impact on research, and access to the structures and services that allow such studies to be carried out. Here we summarize the key findings of this survey, which in particular reflect priorities in European countries. The survey data will be of use to decision makers such as governments and research organizations, but also researchers and others in the field.

Scientific Communication and Education↗

bioRxiv2016

Zika Virus Disease: A Simple Model Approach to Rapid Impact Assessment

There has been substantial media attention regarding Zika infection as a threat to pregnancy, prompted by WHOs declaration of a Public Health Event of International Concern (PHEIC). Here we present a simple risk assessment model for two states within the continental United States at-risk for autochthonous transmission of Zika virus, Texas and Florida. Our simple impact assessment model is partially validating at this early interval in the crisis.

Scientific Communication and Education↗

bioRxiv2016

Has the time come for preprints in biology?

Preprints, non-peer reviewed drafts of manuscripts available on the internet, have been used in conjunction with peer review and publication in journals in the physical sciences for almost 25 years. Recently, more scientists have been discussing whether preprints can play a similar role in biological and biomedical research. Here, I discuss my excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences.

Scientific Communication and Education↗

bioRxiv2016

Discrimination between Onchocerca volvulus and O. ochengi filarial larvae in Simulium damnosum (s.l.) and their distribution throughout central Ghana using a versatile high-resolution speciation assay

BackgroundGenetic surveillance of the human filarial parasite, Onchocerca volvulus, from onchocerciasis endemic regions will ideally focus on genotyping individual infective larval stages collected from their intermediate host, Simuliid blackflies. However, blackflies also transmit other Onchocerca species, including the cattle parasite O. ochengi, which are difficult to distinguish from the human parasite based on morphological characteristics alone. This study describes a versatile approach to discriminate between O. volvulus and O. ochengi that is demonstrated using parasite infective larvae dissected from blackflies.\n\nResultsA speciation assay was designed based on genetic differentiation between O. volvulus and O. ochengi mitochondrial genome sequences that can be performed in highthroughput high-resolution melt (HRM)- or lower throughput conventional restriction fragment length polymorphism (RFLP) analyses. This assay was validated on 185 Onchocerca larvae dissected from blackflies captured from 14 communities in Ghana throughout 2011-13. The frequency of O. ochengi was approximately 67 % of all larvae analysed, which is significantly higher than previously reported in this region. Furthermore, the species distribution was not uniform throughout the study region, with 25 %, 47 % and 93 % of O. volvulus being found in the western-most (Black Volta, Tain and Tombe), the central (Pru) and eastern-most (Daka) river basins, respectively.\n\nConclusionsThis tool provides a simple and cost-effective approach to determine the identity and distribution of two Onchocerca species, and will be valuable for future genetic studies that focus on parasites collected from blackflies. The results presented highlight the need to discriminate Onchocerca species in transmission studies, as the frequency of each species varied significantly between the communities studied.

Scientific Communication and Education↗

bioRxiv2016

The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications

Inaccurate data in scientific papers can result from honest error or intentional falsification. This study attempted to determine the percentage of published papers containing inappropriate image duplication, a specific type of inaccurate data. The images from a total of 20,621 papers in 40 scientific journals from 1995-2014 were visually screened. Overall, 3.8% of published papers contained problematic figures, with at least half exhibiting features suggestive of deliberate manipulation. The prevalence of papers with problematic images rose markedly during the past decade. Additional papers written by authors of papers with problematic images had an increased likelihood of containing problematic images as well. As this analysis focused only on one type of data, it is likely that the actual prevalence of inaccurate data in the published literature is higher. The marked variation in the frequency of problematic images among journals suggest that journal practices, such as pre-publication image screening, influence the quality of the scientific literature.

Scientific Communication and Education↗

bioRxiv2016

Is most published research really false?

There has been an increasing concern that most published medical findings are false. But what does it mean to be false? Here we describe the range of definitions of false discoveries in the scientific literature. We summarize the philosophical, statistical, and experimental evidence for each type of false discovery. We discuss common underpinning problems with the scientific and data analytic practices and point to tools and behaviors that can be implemented to reduce the problems with published scientific results.

Scientific Communication and Education↗

bioRxiv2016

search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any website to be integrated with articles from preprint servers. The bioPreprint search engine is publicly available at http://www.hsls.pitt.edu/resources/preprint.

Scientific Communication and Education↗

bioRxiv2016

Building a Web of Linked Data Resources to Advance Neuroscience Research

The fundamental goal of neuroscience is to understand the nervous system at all levels of description, from molecular components to behavior. The complexity of achieving this goal in neuroscience, and biomedicine in general, poses many technical and sociological challenges. Among these are the need to organize neuroscientific data, information, and knowledge to facilitate new scientific endeavors, provide credibility and visibility of research findings, and increase the efficiency of data reuse. Linked Data is a set of principles based on Web technology that can aid this process as it organizes data as an interconnected network of information. This review examines the history, practical impact, potential, and challenges of applying Linked Data principles to neuroscience.

Scientific Communication and Education↗