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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

The Impact of Grant Funding on the Publication Activity of Awarded Applicants: A Systematic Review of Comparative Studies and Meta-analytical Estimates

The connection between grant funding and research productivity has not been well established.\n\nObjectiveto examine the impact of grant funding on the publication activity of awarded applicants.\n\nMethodsa systematic review of results from comparative studies on the publication activity of applicants (awarded vs rejected) both prior to and after the award process. All pool estimates (weighted mean difference) were based on random-effects models.\n\nResultsrevealed 16 relevant publications (grant funding from 14 funds, 1980 to 2007 years), all with results from quasi-experimental studies. 45 paired values (ex ante - ex post) for the number of articles published by awarded and rejected applicants were used in the quantitative synthesis. The median average publication activity of awarded applicants before the award process was 2.4 (1.3; 3.4) and after the award process 3.1 (1.7; 4.3) publications per year, for rejected applicants was 1.8 (1.0; 2.9) and 2.4 (1.1; 3.8) respectively. The summation of the results from these studies using the difference-in-differences approach showed that awarded applicants published 0.14 articles per year (95% Cl 0.07 to 0.21) more than rejected applicants (adjusted for publication bias). A meta-regression analysis made it possible to tie together the revealed small difference with the difference-in-differences approach bias - the subsequent differences in the groups are determined by the scale of the initial differences in their publication activity.\n\nConclusionawarded applicants published slightly more often than their rejected opposites. However, this effect may be the result of a bias caused by the shortcomings of the difference-in-differences approach.

scientific communication and education↗

bioRxiv2018

Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey

The postdoctoral community is an essential component of the academic and scientific workforce. As economic and political pressures impacting these enterprises continue to change, the postdoc experience has evolved from short, focused periods of training into often multidisciplinary, extended positions with less clear outcomes. As efforts are underway to amend U.S. federally funded research policies, the paucity of postdoc data has made evaluating the impact of policy recommendations challenging. Here we present comprehensive survey results from over 7,600 postdocs based at 351 academic and non-academic U.S. institutions in 2016. In addition to demographic and salary information, we present multivariate analyses on the factors that influence postdoc career plans and mentorship satisfaction in this population. We further analyze gender dynamics and expose wage disparities and career choice differences. Academic research positions remain the predominant career choice of postdocs in the U.S., although unequally between postdocs based on gender and residency status. Receiving mentorship training during the postdoctoral period has a large, positive effect on postdoc mentorship satisfaction. Strikingly, the quality of and satisfaction with postdoc mentorship appears to also heavily influence career choice. The data presented here are the most comprehensive data on the U.S. postdoc population to date. These results provide an evidence basis for informing government and institutional policies, and establish a critical cornerstone for quantifying the effects of future legislation aimed at the academic and scientific workforce.

scientific communication and education↗

bioRxiv2018

A comparison of asymmetric before-after control impact (aBACI) and staircase experimental designs for testing the effectiveness of stream restoration

Before-after-control-impact (BACI) experimental designs are commonly used in large-scale experiments to test for environmental impacts. However, high natural variability of environmental conditions and populations, and low replication in both treatment and control areas in time and space hampers detection of responses. We compare the power of two asymmetric BACI (aBACI) designs to two staircase designs for detecting changes in juvenile steelhead (Oncorhynchus mykiss) abundance associated with a watershed-scale stream restoration experiment. We performed a simulation study to estimate the effect of a 25% increase in steelhead abundance using spatial and temporal estimates of variance from an ongoing study, and determined the power of each design. Experimental designs were then applied to three streams and each stream was composed of three 4 km long sections. We compared the power of a single treatment section in one stream (BACI-1), three simultaneous treatments of all sections in one stream (BACI-3), three sequential treatments in one stream (STAIRCASE-1), and three sequential treatments in one section in each stream (STAIRCASE-3). All designs had [≥] 94% power to detect a 25% increase in abundance assuming average variance. Under worst-case variance (i.e., upper 95% confidence limits of historical variance estimates), the STAIRCASE-3 design outperformed the BACI-1, BACI-3, and STAIRCASE-1 designs (i.e., 77%, 41%, 8%, and 33% power respectively). All the designs estimated the effect of the simulated 25% abundance increase, but the length of the confidence interval was much shorter for the STAIRCASE-3 design compared to the other designs, which had confidence intervals 58-596% longer. The STAIRCASE-3 design continued to have high power (88%) to detect a 10% change in abundance, but the power of the other designs was much lower (range 34-56%). Our study demonstrates that staircase designs can have significant advantages over BACI designs and therefore should be more widely used for testing environmental impacts.

scientific communication and education↗

bioRxiv2018

Illuminating women’s hidden contribution to the foundation of theoretical population genetics

Plentiful evidence shows an historic and continuing gender gap in participation and success in scientific research. However, less attention has been directed at clarifying obscured contributions of women to science. The lack of visible women role models (particularly in computational fields) contributes to a reduced sense of belonging and retention among women. We seek to counteract this cycle by illuminating the contribution of women programmers to the foundation of our own fields--population and evolutionary genetics. We consider past acknowledged programmers (APs), who developed, ran, and sometimes analyzed the results of early computer programs. Due to authorship norms at the time, these programmers were credited in the acknowledgments sections of manuscripts, rather than being recognized as authors. For example, one acknowledgement reads \"I thanks Mrs. M. Wu for help with the numerical work, and in particular for computing table I.\". We identified APs in Theoretical Population Biology articles published between 1970 and 1990. While only 7% of authors were women, 43% of APs were women. This significant difference (p = 4.0x10-10) demonstrates a substantial proportion of womens contribution to foundational computational population genetics has been unrecognized. The proportion of women APs, as well as number of APs decreased over time. These observations correspond to the masculinization of computer programming, and the shifting of programming responsibilities to individuals credited as authors (likely graduate students). Finally, we note recurrent APs who contributed to several highly-cited manuscripts. We conclude that, while previously overlooked, historically, women have made substantial contributions to computational biology.

scientific communication and education↗

bioRxiv2018

The Big Five, Self-efficacy, and Self-control in Boxers

Inviting 210 boxers of national athletes in China as participants, this study applied the NEO Five-Factor Inventory and self-control and self-efficacy scales for athletes to examine the relationship between personality traits and self-control, as well as any effect of self-efficacy as a mediator between the two variables. The data analysis indicated that, firstly, the boxers overall level of self-control is high, and the higher the competitive level, the higher the level of self-control. Secondly, there were significant correlations among the Big Five, self-control, and self-efficacy. Thirdly, the mediation model showed that self-efficacy has a significant mediating effect between the Big Five and self-control. These results suggest that formulating training and intervention programs based on the personality traits of boxers and focusing on training their self-efficacy (1) to help them enhance their self-control ability, thereby improving athletic performance and promoting physical and mental health, and (2) to support the inclusion of personality traits, self-efficacy, and self-control among psychological indicators to be assessed in boxers.

scientific communication and education↗

bioRxiv2018

Help-seeking behavior for problematic substance uses in Bahir Dar town, North-West Ethiopia

BackgroundMental, neurological and substance use disorders are common, but 76% to 85% of people with those disorders in low and middle-income countries did not receive treatment.\n\nObjectiveOur objective was to assess the level of help seeking behavior and associated factors among residents with problematic substance uses (alcohol, khat, tobacco and hashish).\n\nMethodsCommunity based cross sectional study was conducted in Bahir Dar town among total of 548 participants with problematic substance users. We had interviewed for help seeking behavior by pre-tested modified General Help Seeking Questionnaire. Logistic regression was done and p-value < 0.05 was used for declaration of significant level. Adjusted odds ratios (AOR) and 95% confidence intervals (CI) have been used.\n\nResultsAmong five hundred and forty-eight participants with problematic substance users, only one hundred and sixty-eight (30.7%) sought help for their substance related problems. Participants age above 35 years [AOR = .47 95% CI (.25, .90)], positively screened for common mental disorders [AOR = 4.12, 95% CI (2.7, 6.3)], comorbid medical [AOR = 3.0, 95% CI (1.7, 5.3)], and grand-families history of substance user [AOR = 2.18, 95% CI (1.4, 3.4)] found significantly associated with help seeking.\n\nConclusionThere was low proportion of help seeking behavior among participants with problematic substance users. Advanced age was a barrier to seek help while medical illnesses, common mental disorders and history of substance use in grand families were found to enforce to seek help.

scientific communication and education↗

bioRxiv2018

High cost of bias: Diminishing marginal returns on NIH grant funding to institutions

Scientific output is not a linear function of amounts of federal grant support to individual investigators. As funding per investigator increases beyond a certain point, productivity decreases. This study reports that such diminishing marginal returns also apply for National Institutes of Health (NIH) research project grant funding to institutions. Analyses of data (2006-2015) for a representative cross-section of institutions, whose amounts of funding ranged from $3 million to $440 million per year, revealed robust inverse correlations between funding (per institution, per award, per investigator) and scientific output (publication productivity and citation impact productivity). Interestingly, prestigious institutions had on average 65% higher grant application success rates and 50% larger award sizes, whereas less-prestigious institutions produced 65% more publications and had a 35% higher citation impact per dollar of funding. These findings suggest that implicit biases and social prestige mechanisms (e.g., the Matthew effect) have a powerful impact on where NIH grant dollars go and the net return on taxpayers investments. They support evidence-based changes in funding policy geared towards a more equitable, more diverse and more productive distribution of federal support for scientific research. Success rate/productivity metrics developed for this study provide an impartial, empirically based mechanism to do so.

scientific communication and education↗

bioRxiv2018

Datamining a medieval medical text reveals patterns in ingredient choice that reflect biological activity against the causative agents of specified infections

The pharmacopeia used by physicians and lay people in medieval Europe has largely been dismissed as placebo or superstition. While we now recognise that some of the materia medica used by medieval physicians could have had useful biological properties, research in this area is limited by the labour-intensive process of searching and interpreting historical medical texts. Here, we demonstrate the potential power of turning medieval medical texts into contextualised electronic databases amenable to exploration by algorithm. We use established methodologies from network science to reveal statistically significant patterns in ingredient selection and usage in a key text, the fifteenth-century Lylye of Medicynes, focusing on remedies to treat symptoms of microbial infection. We discuss the potential that these patterns reflect rational medical decisions. In providing a worked example of data-driven textual analysis, we demonstrate the potential of this approach to encourage interdisciplinary collaboration and to shine a new light on the ethnopharmacology of historical medical texts.

scientific communication and education↗

bioRxiv2018

Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course

Intensive postgraduate courses provide an opportunity for junior and senior level scientists to learn concepts and techniques that will advance their training and research programs. It is commonly assumed that short intensive courses have positive impacts within fields of research; however, these assumptions are rarely tested. Here we describe the framework of a long running postgraduate summer course at Cold Spring Harbor and attempt to quantify the impact made over its history. For over three decades, the Drosophila Neurobiology: Genes, Circuits & Behavior Summer Course at Cold Spring Harbor Laboratories (CSHL) has provided participants with intense instruction on a wide variety of topics and techniques in integrative neuroscience using Drosophila as a model organism. Students are introduced to the latest approaches for studying nervous system development, activity and connectivity, as well as complex behaviors and diseases. The course has a long history of successful alumni, many of whom describe participation in the course as foundational to their training. Student surveys of recent participants indicate a high level of satisfaction, improved career outcomes, and direct impact on publications. Analysis of student success reveals that over 64% of participants obtain independent faculty positions. Further, we describe ongoing efforts to enhance diversity and encourage access to scientific research at undergraduate-focused institutions. Together, our findings suggest that laboratory-intensive postgraduate courses provide a highly effective mechanism for scientific training that has lasting positive impacts on trainees.

scientific communication and education↗

bioRxiv2018

A randomised controlled trial of an Intervention to Improve Compliance with the ARRIVE guidelines (IICARus)

The ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines. In a randomised controlled trial, manuscripts reporting in vivo animal research submitted to PLOS ONE (March-June 2015) were allocated to either requested completion of an ARRIVE checklist or current standard practice. We measured the change in proportion of manuscripts meeting all ARRIVE guideline checklist items between groups. We randomised 1,689 manuscripts, 1,269 were sent for peer review and 762 accepted for publication. The request to complete an ARRIVE checklist had no effect on full compliance with the ARRIVE guidelines. Details of animal husbandry (ARRIVE sub-item 9a) was the only item to show improved reporting, from 52.1% to 74.1% (X2=34.0, df=1, p=2.1x10-7). These results suggest that other approaches are required to secure greater implementation of the ARRIVE guidelines.\n\nBackgroundThere are widespread failures across in vivo animal research to adequately describe and report research methods, including critical measures to reduce the risk of experimental bias (Kilkenny et al., 2009, Macleod et al., 2015). Such omissions have been shown to be associated with overestimation of effect sizes (Macleod et al., 2015, Hirst et al., 2014) and are likely to contribute, in part, to translational failure. In an effort to improve reporting standards, an expert working group coordinated by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) developed the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines (Kilkenny et al., 2010), published in 2010.\n\nSince the ARRIVE guidelines were first published, they have been endorsed by many journals in their instructions to authors, but this has not been accompanied by substantial improvements in reporting (Baker et al., 2014, McGrath and Lilley, 2015, Gulin et al., 2015a, Avey et al., 2016). Simply endorsing the guidelines does not appear to be sufficient to encourage compliance. Recent findings suggest that following the introduction of mandated completion of a distinct reporting checklist at ten Nature Journals at the stage of first revision significantly improved the quality in reporting versus that of comparator journals (Han et al., 2017, Macleod and The NPQIP Collaborative Group, 2017)\n\nPLOS ONE is an open access online only journal which at the time this study began published around 32,000 research articles per year. Of these, some 5,000 described in vivo research. At present, PLOS ONE instructions to authors encourage compliance with the ARRIVE guidelines, but do not mandate checklist completion. Journals have an important role to play in ensuring that the quality of reporting in the research they publish is robust, yet the most effective mechanism by which they can achieve this remains unclear.\n\nOur aim was to test the impact on the quality of published reports of an intervention which would request, at the time of manuscript submission, that authors complete a checklist detailing where in the manuscript the various components of the ARRIVE checklist were met. This study, to our knowledge, is the first randomised controlled trial of requested ARRIVE guideline completion.

scientific communication and education↗

bioRxiv2018

Making headlines: An analysis of US government-funded cancer research mentioned in online media

BackgroundConsiderable resources are devoted to producing knowledge about cancer, which in turn is disseminated to policymakers, practitioners, and the public. Online media are a key dissemination channel for cancer research. Yet which cancer research receives media attention is not well understood. Understanding the characteristics of journal articles that receive media attention is crucial to optimize research dissemination.\n\nMethodsThis cross-sectional study examines journal articles on cancer funded by the US government published in 2016, using data from PubMed and Altmetric to determine whether an article received online media attention. Frequencies and proportions were calculated to describe the cancer types and continuum stages covered in journal articles.\n\nResults16.8% of articles published on US government-funded research were covered in the media. Published journal articles addressed all common cancers. Roughly one-fourth to one-fifth of journal articles within each cancer category received online media attention. Media mentions were disproportionate to actual burden of each cancer type (ie, incidence and mortality), with breast cancer articles receiving the most media mentions. Cancer prevention and control articles received less online media attention than diagnosis or therapy articles.\n\nConclusionFindings revealed a mismatch between prevalent cancers and cancers highlighted in the media. Further, journal articles on cancer control and prevention received less media attention than other cancer continuum stages. Media mentions were not proportional to actual public cancer burden nor volume of scientific publications in each cancer category. Results highlight a need for continued research on the role of media, especially online media, in research dissemination.

scientific communication and education↗

bioRxiv2018

ERNIE: A Data Platform for Research Assessment

Data mining coupled to network analysis has been successfully used to study relationships between basic discovery and translational applications such as drug development; and to document research collaborations and knowledge flows. Assembling relevant data for such studies in a form that supports analysis presents challenges. We have developed Enhanced Research Network Information Environment (ERNIE), an open source, scalable cloud-based platform that (i) integrates data drawn from public and commercial sources (ii) provides users with analytical workflows that incorporate expert input at critical stages. A modular design enables the addition, deletion, or substitution of data sources. To demonstrate the capabilities of ERNIE, we have conducted case studies that span drug development and pharmacogenetics. In these studies, we analyze data from regulatory documents, bibliographic and patent databases, research grant records, and clinical trials, to document collaborations and identify influential research accomplishments.

scientific communication and education↗

bioRxiv2018

The GRE Over the Entire Range of Scores Lacks Predictive Ability for PhD Outcomes in the Biomedical Sciences

The association between GRE scores and academic success in graduate programs is currently of national interest. GRE scores are often assumed to be predictive of student success in graduate school. However, we found no such association in admission data from Vanderbilts Initiative for Maximizing Student Diversity (IMSD), which recruited historically underrepresented students for graduate study in the biomedical sciences at Vanderbilt University spanning a wide range of GRE scores. This study avoids the typical biases of most GRE investigations of performance where only high-achievers on the GRE were admitted. GRE scores, while collected at admission, were not used or consulted for admission decisions and comprise the full range of percentiles, from 1% to 91%. We report on the 29 students recruited to the Vanderbilt IMSD from 2007-2011 who have completed the program at this date. While the data set is not large, the predictive trends between GRE and long-term graduate outcomes (publications, first author publications, time to degree, predoctoral fellowship awards, and faculty evaluations) are remarkably null and there is sufficient precision to rule out even mild relationships between GRE and these outcomes. Career outcomes are encouraging; many students are in postdocs, and the rest are in stage-appropriate career environments for such a cohort, including tenure track faculty, biotech and entrepreneurship careers.

scientific communication and education↗

bioRxiv2018

Opposing effects of impulsivity and mindset on sources of science self-efficacy and STEM interest in adolescents

Impulsivity has been linked to academic performance in the context of Attention Deficit Hyperactivity Disorder, though its influence on a wider spectrum of students remains largely unexplored, particularly in the context of STEM learning (i.e. science, technology, engineering, and math). STEM learning was hypothesized to be more challenging for impulsive students, since it requires the practice and repetition of tasks as well as concerted attention to task performance. Impulsivity was assessed in a cross-sectional sample of 2,476 students in grades 6-12. Results show impulsivity affects a larger population of students, not limited to students with learning disabilities. Impulsivity was associated with lower sources of science self-efficacy (SSSE) scores, interest in all STEM domains (particularly math), and self-reported STEM skills. The large negative effect observed for impulsivity was opposed by \"growth\" mindset, which describes a students belief in the importance of effort when learning is difficult. Mindset had a large positive effect, which was associated with greater SSSE, STEM interest, and STEM skills. When modeled together, results suggest that mindset interventions may benefit impulsive students who struggle with STEM. Together, these data suggest important interconnected roles for impulsivity and mindset that can influence secondary students STEM trajectories.

scientific communication and education↗

bioRxiv2018

How do citizens perceive farm animal welfare conditions in Brazil?

The aim of this study is to understand the perceptions of Brazilian citizens about the actual conditions of farm animal welfare in the poultry, beef, and dairy supply chains. To reach this aim, an online survey was conducted. The analysis was based on descriptive statistics and three logistic regressions models. Results of descriptive statistics showed that citizens in Brazil had mostly negative perceptions about the actual conditions of animal welfare in the poultry, beef, and dairy supply chains. Results of the logistic regression models showed that in the poultry and dairy supply chains, citizens with background in agricultural/veterinary sciences, and citizens who reported a higher level of knowledge about these supply chains, were more likely to perceive as bad the actual conditions of farm animal welfare. In the poultry supply chain, citizens who reported previous contact with poultry farms were also more likely to perceive as bad the actual condition of farm animal welfare. In addition, the perception that farmers are mainly focused on the economic aspect of farming and less on animal welfare, the perception that animals do not have a good quality of life while housed on farms, and the perception that animals are not adequately transported and slaughtered, negatively impact on perceptions about the actual conditions of farm animal welfare in the three supply chains. We concluded that a protocol aimed to improve citizens perceptions about the actual conditions of farm animal welfare should focus in all phases of the supply chains.

scientific communication and education↗

bioRxiv2018

Climate Resilience Index as a tool to explore households’ resilience to climate change-induced shocks in Dinki watershed, central highlands of Ethiopia Households’ resilience to climate change impacts

This study assessed households resilience to climate change-induced shocks in Dinki watershed, northcentral highlands of Ethiopia. The data were collected through cross-sectional survey conducted on 288 households, six focus group discussions and 15 key informant interviews. The Climate Resilience Index (CRI) and the Livelihood Resilience Index (LRI) based on the three-resilience capacities (3Ds) frame, using absorptive, adaptive and transformative, were used to measure households resilience to climate change-induced shocks on agro-ecological unit of analysis. Findings indicate that the CRI and the resilience capacities based on the indexed scores of major components clearly differentiated the study communities in terms of their agro-ecological zones. Specifically, the LRI score showed that absorptive capacity (0.495) was the leading contributing factor to resilience followed by adaptive (0.449) and transformative (0.387) capacities. Likewise, the midland was relatively more resilient with a mean index value of 0.461. The study showed that access to and use of livelihood resources, such as farmlands and livestock holdings, diversity of income sources, infrastructure and social capital were determinants of households resilience. In general, it might be due to their exposure to recurrent shocks coupled with limited adaptive capacities including underdeveloped public services, poor livelihood diversification practices, among others, the study communities showed minimal resilience capacity with a mean score of 0.44. Thus, in addition to short-term buffering strategies, intervention priority focusing on both adaptive and transformative capacities, particularly focusing on most vulnerable localities and constrained livelihood strategies, would contribute to ensure long-term resilience in the study communities.

scientific communication and education↗

bioRxiv2018

Cancer In The News: Bias And Quality In Media Reporting Of Cancer Research.

Cancer research in the news is often associated with sensationalising and inaccurate reporting, giving rise to false hopes and expectations. The role of study selection for cancer-related news stories is an important but less commonly acknowledged issue, as the outcomes of primary research are generally less reliable than those of meta-analyses and systematic reviews. Few studies have investigated the quality of research that makes the news and no previous analyses of the proportions of primary and secondary research in the news have been found in the literature. The main aim of this study was to investigate the nature and quality of cancer research covered in online news reports by four major news sources from USA, UK and Australia. We measured significant variation in reporting quality, and observed biases in many aspects of cancer research reporting, including the types of study selected for coverage, and in the spectrum of cancer types, gender of scientists, and geographical source of research represented. We discuss the implications of these finding for guiding accurate, contextual reporting of cancer research, which is critical in helping the public understand complex science and appreciate the outcomes of publicly funded research, avoid undermining trust in science, and assist informed decision-making.

scientific communication and education↗

bioRxiv2018

Measuring researcher independence using bibliometric data: A proposal for a new performance indicator

Bibliometric indicators are increasingly used at the individual level - as is exemplified by the popularity of the H-index and many other publication and citation based indicators used in evaluation. The issue isnt whether these indicators can be considered useful, as they do provide a description of a researchers oeuvre. However, at the same time, they are not enough to assess the quality of a researcher and his/her oeuvre: Quality has more dimensions than productivity and impact alone. In this paper, we argue that independence is an equally important characteristic that however lacks validated indicators for measuring it at the individual level. We propose two indicators to measure different dimensions of independence: one assessing whether a researcher has developed an own collaboration network, and another assessing the level of thematic independence. We illustrate how these indicators distinguish between researchers that are equally productive and have similar impact. The independence indicator is a step forward in evaluating individual scholarly quality: in cases where citations and publications do not distinguish, the indicators for independence may do.

scientific communication and education↗