SEARCH · Search bioRxiv

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

bioRxiv2018

Impact of Human Behavioral Papers at Journal of Neuroscience

A recent policy change at Journal of Neuroscience (JN) has significantly increased editorial \"desk rejections\", reducing the number of papers that are considered for publication. Survey results from 130 scientists suggested that the new policy may have had a particularly large impact on studies that focused on human behavioral techniques. To quantify the effects of the new policy, we gathered data on all papers ever published in JN (~35,000), as well as all papers that had cited the JN papers (~2.7 million papers). We found that the recent change in editorial policy had disproportionately affected rejection rates of human behavioral papers: since 2015, the number of human behavioral papers as a proportion of all papers published in JN has seen a 30% decline. While there has been a long-term declining trend in the journals impact factor, we found that this declining impact factor was shared by both human behavioral papers as well as other papers in the journal. This suggested that whatever may have been the source of the declining impact factor at JN, this source was affecting the various areas of research equally. That is, it was unlikely that papers in any one field were responsible for the declining impact factor number at JN. Indeed, when impact was measured over the long-term, we found that the average human behavioral paper at JN consistently outperformed other papers, generating a significantly higher number of citations per year at 5 and 10 years post publication.

scientific communication and education↗

bioRxiv2018

The Healthy Nevada Project: rapid recruitment for population health study

BackgroundNevada ranks in the bottom half of overall health rankings in the United States. The majority of residents of Northern Nevada live in Washoe County, which is confounded with high age-adjusted death rates for heart disease, cancer and chronic lower respiratory disease.\n\nMethodsSaliva as a source of DNA was collected from adults in Northern Nevada as the first phase of a much larger (100,000 participants) effort to contribute to comprehensive population health studies in Nevada. The personal genetics company 23andMe was used to genotype the first 10,250 participants and deliver their custom ancestry, traits, wellness, and carrier status reports.\n\nResultsThe study was announced by Governor Brian Sandoval on September 15, 2016 and within two days the registration of 9,700 volunteers for an appointment was complete. Processing of 9,344 participants was achieved in 3 months, with a no-show rate of just over 11%. The participant population was skewed to female and was less racially diverse than the population.\n\nConclusionDNA genotyping was administered free-of-charge and the patient population was representative of the socio-economic diversity in northern Nevada - indicating that free genetic testing is of interest to a broad swath of the population and a powerful motivator for comprehensive population health study research.

scientific communication and education↗

bioRxiv2018

Open access policies of high impact medical journals: a cross-sectional study

ObjectivesAcademic and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use. We set out to clarify the open access variants provided by leading medical journals for research in general and industry-funded research in particular, and record the availability of the CC BY licence for commercially funded research.\n\nMethodsWe identified medical journals with a 2015 impact factor of at least 15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journals open access policies from their websites and/or by email contact. We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.\n\nResultsThirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access with varying embargo periods of up to 12 months. Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (e.g. to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organizations and one offered this option to funders who required it.\n\nConclusionsMost leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material. The journals policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academic funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.\n\nStrengths and limitations of this studyO_LIThis manuscript includes a systematic analysis of open access policies of journals with a high impact factor, including society-owned journals, from multiple publishers.\nC_LIO_LIThe open access policies of all journals analysed were clarified, and confirmation of our findings was received by email from 97% of the contacted journals.\nC_LIO_LIOpen access policies of the journals and publishers analysed are subject to change, so the information presented here may not be current.\nC_LIO_LIBy selecting journals with a high impact factor, our analysis does not include prestigious journals from specialized therapy areas and regional or non-English language journals, which may have lower impact factors.\nC_LIO_LIAlthough our study covers only a small number of journals, extending such a manual analysis to a greater number of journals without loss of detail and verification of all results would be cumbersome and inefficient by relying on traditional analysis tools.\nC_LI

scientific communication and education↗

bioRxiv2018

A survey on information sources used by academic researchers to evaluate scientific instruments

Most scientific research is fueled by research equipment (instruments); typically hardware purchased to suit a particular research question. Examples range from 17th century microscopes to modern particle colliders and high-throughput sequencers. Here, we studied the information sources used by academic researchers to assess scientific instruments, and reveal evidence of a worrying confluence of incentives similar to those that drove the biopharmaceutical industry to adopt controversial practices such as ghostwriting and hidden sponsorship. Our findings suggest there are little understood incentives against disclosure in the peer-reviewed literature on scientific instruments; constituting an underappreciated threat to scientific standards of trustworthiness and transparency. We believe that a public debate and subsequent editorial policy action are urgently required.

scientific communication and education↗

bioRxiv2018

revtools: bibliographic data visualization for evidence synthesis in R

The field of evidence synthesis is growing rapidly, with a corresponding increase in the number of software tools and workflows to support the construction of systematic reviews, systematic maps, and meta-analyses. Despite much progress, however, a number of problems remain including slow integration of new statistical or methodological approaches into user-friendly software, low prevalence of open-source software, and poor integration among distinct software tools. These issues hinder the utility and transparency of new methods to the research community. Here I present revtools, an R package to support article screening during evidence synthesis projects. It provides tools for the import and de-duplication of bibliographic data, screening of articles by title or abstract, and visualization of article content using topic models. The software is entirely open-source and combines command-line scripting for experienced programmers with custom-built user interfaces for casual users, with further methods to support article screening to be added over time. Revtools provides free access to novel methods in an open-source environment, and represents a valuable step in expanding the capacity of R to support evidence synthesis projects.

scientific communication and education↗

bioRxiv2018

The impact on authors and editors of introducing Data Availability Statements at Nature journals

This paper describes the adoption of a standard policy for the inclusion of data availability statements in all research articles published at the Nature family of journals, and the subsequent research which assessed the impacts that these policies had on authors, editors, and the availability of datasets. The key findings of this research project include the determination of average and median times required to add a data availability statement to an article; and a correlation between the way researchers make their data available, and the time required to add a data availability statement. This paper will be presented at the International Digital Curation Conference 2018, and has been submitted to the International Journal of Digital curation.

scientific communication and education↗

bioRxiv2018

Building a local community of practice in scientific programming for Life Scientists

For most experimental biologists, handling the avalanche of data generated is similar to learning how to drive on your own. Although that might be doable, it is preferable and safer to learn programming and good practices together and preferably from experienced scientists. One way to achieve this is to build local communities of practice in scientific programming by bringing together life scientists that perform code-intensive research to spread know-how and good practices. The community will make sure that, for a given researcher working for an academic institution, their capacity to conduct data-intensive research will not be arbitrarily reliant on the presence of well-trained bioinformaticians in their vicinity.\n\nIn this paper, we propose a three-step field guide for building a local community of practice in scientific programming for life scientists. The first step is organizing a Carpentries programming workshop designed for researchers new to computational biology. However, while such workshops provide an immediate solution for learning, more regular long-term assistance is also needed. Researchers need persisting, local support to continue learning and solving programming issues that may hamper their research progress. The solution we describe here is to implement a Mozilla Study Group where researchers can meet-up and help each other in a \"safe-learning atmosphere\". We describe two real-life examples of building local communities of practice: one in the Netherlands at the Amsterdam Science Park and one in the United States at the University of Wisconsin-Madison. In order to help future researchers to build their own community of practice in scientific programming we discuss challenges and implemented solutions.\n\nWe believe that our local communities of practice will prove useful for other life scien-tists who want to set up similar support groups for researchers involved in scientific programming and data science.\n\nAuthor summaryIn this paper, we describe why and how to build a community of practice for life scientists that start to make more use of computers and programming in their research. A community of practice is a small group of scientists that meet regularly to help each other and promote good practices in scientific computing. While most life scientists are well-trained in the laboratory to conduct experiments, good practices with (big) datasets and their analysis are often missing. This paper proposes a field-guide on how to build such a community of practice at a local academic institution. Based on two real-life examples, challenges and related recommendations are provided. We believe that the current data deluge that life scientists will increasingly face can benefit from the implementation of these small communities. Good practices spread among experimental scientists will foster open, transparent, sound scientific results beneficial to society.

scientific communication and education↗

bioRxiv2018

Social licence through citizen science: A tool for marine conservation

1. Introduction 1. Introduction 2. Methods 3. Results Discussion 4. Conclusion References Meaningful public engagement with science and research is essential to improving knowledge about the environment and supporting sustainable use of ecosystems and natural resources. Transparent and culturally-appropriate natural resource management is imperative (Christie et al. 2017) and the publics role in decision-making and data collection is increasingly recognised (Hecker et al. 2018), supported by a rise in the number of citizen science projects in recent years (Chandler et al. 2017;Pocock et al. 2017), including marine-based projects (Cigliano and Ballard 2017). In parallel, social licence has become an important theme for development, pa ...

scientific communication and education↗

bioRxiv2018

Gender balance in time-keeping at life science conferences

Scientific conferences are biased against women when selecting speakers, but recent studies showed a positive trend where the ratio of invited female speakers had increased. We have recorded speaking times at 11 different conferences during 2016-2017 to analyze which factors influenced a speakers time keeping. Men and women went over time 47% and 41% of the talks, respectively. In a regression analysis, it was found that the most important factors that influences how long a presenter spoke was 1) their allocated time, 2) their career stage and 3) the level of time keeping enforcement. It was also found that gender and the size of the conference contributed significantly towards the speakers timing. Male speakers exceeded their allocated time more frequently than female speakers, especially at large conferences (60% vs 49%). Since conferences are an important arena for science dissemination this might have a negative impact on female scientists careers.

scientific communication and education↗

bioRxiv2018

Bioscience-scale automated detection of figure element reuse

Scientists reuse figure elements sometimes appropriately, e.g. when comparing methods, and sometimes inappropriately, e.g. when presenting an old experiment as a new control. To understand such reuse, automatically detecting it would be important. Here we present an analysis of figure element reuse on a large dataset comprising 760 thousand open access articles and 2 million figures. Our algorithm detects figure region reuse, while being robust to rotation, cropping, resizing, and contrast changes, and estimates which of the reuses have biological meaning. Then a three-person panel analyzes how problematic these biological reuses are using contextual information such as captions and full texts. Based on the panel reviews, we estimate that 9% of the biological reuses would be unanimously perceived as at least suspicious. We further estimate that 0.6% of all articles would be unanimously perceived as fraudulent, with inappropriate reuses occurring 43% across articles, 28% within article, and 29% within a figure. Our tool rapidly detects image reuse at scale, promising to be useful to a broad range of people that campaign for scientific integrity. We suggest that a great deal of scientific fraud will be, sooner or later, detectable by automatic methods.

scientific communication and education↗

bioRxiv2018

Intellectual Synthesis in Mentorship Determines Success in Academic Careers

As academic careers become more competitive, junior scientists need to understand the value that mentorship brings to their success in academia. Previous research has found that, unsurprisingly, successful mentors tend to train successful students. But what characteristics of this relationship predict success, and how? We analyzed an open-access database of about 20,000 researchers who have undergone both graduate and postdoctoral training, compiled across several fields of biomedical science. Our results show that postdoctoral mentors were more instrumental to trainees success compared to graduate mentors. A trainees success in academia was predicted by the degree of intellectual synthesis with their mentors, resulting from fusing the influence of disparate advisors. This suggests that junior scientists should have increased chances of success by training with and linking the ideas of mentors from different fields. We discuss the implications of these results for choosing mentors and determining the duration of postdoctoral training.

scientific communication and education↗

bioRxiv2018

Persistent Underrepresentation of Women’s Science in High Profile Journals

Yiqin Alicia Shen, Jason M. Webster, Yuichi Shoda, and Ione Fine Department of Psychology, University of Washington Past research has demonstrated an under-representation of female editors and reviewers in top scientific journals, but less is known about the representation of women authors within original research articles. We collected research article publication records from 15 high-profile multidisciplinary and neuroscience journals for 2005-2017 and analyzed the representation of women over time, as well as its relationship with journal impact factor. We find that women authors have been persistently underrepresented in high-profile journals. This under-representation has persisted over more than a decade, with glacial improvement over time. Even within our limited group of high profile journals, the percent of female first and last authors is negatively associated with journal impact factor. Since publishing in high-profile journals is a gateway to academic success, this underrepresentation of women may contribute to the lack of women at the top of the academic ladder.

scientific communication and education↗

bioRxiv2018

Automation of citation screening in pre-clinical systematic reviews

BackgroundThe amount of published in vivo studies and the speed researchers are publishing them make it virtually impossible to follow the recent development in the field. Systematic review emerged as a method to summarise and analyse the studies quantitatively and critically but it is often out-of-date due to its lengthy process. MethodWe invited five machine learning and text-mining groups to build classifiers for identifying publications relevant to neuropathic pain (33814 training publications). We kept 1188 publications for the assessment of the performance of different classifiers. Two groups participated in the next stage: testing their algorithm on datasets labeled for psychosis (11777/2944) and datasets labeled for Vitamin D in multiple sclerosis (train/text: 2038/510). ResultThe performances (sensitive/specificity) of the most promising classifier built for neuropathic pain are: 95%/84%. The performance for psychosis and Vitamin D in multiple sclerosis datasets are 95%/73% and 100%/45%. ConclusionsMachine learning can significantly reduce the irrelevant publications in a systematic review, and save the scientists time and money. Classifier algorithms built for one dataset can be reapplied on another dataset in different field. We are building a machine learning service at the back of Systematic Review & Meta-analysis Facility (SyRF).

scientific communication and education↗

bioRxiv2018

Changes in Acceptance of Evolution and Associated Factors during a Year of Introductory Biology: The Shifting Impacts of Biology Knowledge, Politics, Religion, Demographics, and Understandings of the Nature of Science

Recent research has identified many factors influencing student acceptance of biological evolution, but few of these factors have been measured in a longitudinal context of changing knowledge and acceptance of evolution over a period of instruction. This study investigates factors previously associated with evolution acceptance as well as other potential factors among students over the course of a year-long majors and non-majors introductory biology sequence at a private, research-intensive university in the northeastern United States. Acceptance of evolution was measured using the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and other factors were measured using well-established instruments and a demographic survey. As expected given the context, evolution was widely accepted among the population (71% of our sample scored in the \"high\" or \"very high\" acceptance range), but 160 students were in the very low to moderate acceptance range. Over the course of the academic year, regressions on measures of normalized change revealed that as knowledge of the Nature of Science (NOS) increased, evolution acceptance increased (R2 = .378, p << 0.001). Increasing levels of genetic literacy (R2 = .214, p << 0.001) and Evolutionary Knowledge (R2 = .177, p << 0.001) were also significantly associated with increases in acceptance of evolution. We also examined the longitudinal effect of combining various factors into unified working models of acceptance of evolution, and this is the first study by our knowledge to do so. From fall to spring, the influence of student knowledge of NOS on evolution acceptance increased, as did the influence of genetic literacy. Conversely, the influence of religious variables decreased, as did the influence of political inclinations and race/ethnicity. Our results indicate that as students learn more about the nature of science, they may rely more on scientific explanations for natural phenomena. This study also underscores the importance of using longitudinal, multifactorial analyses to understand acceptance of evolution.

scientific communication and education↗

bioRxiv2018

A Measure of Open Data: A Metric and Analysis of Reusable Data Practices in Biomedical Data Resources

Data is the foundation of science, and there is an increasing focus on how data can be reused and enhanced to drive scientific discoveries. However, most seemingly \"open data\" do not provide legal permissions for reuse and redistribution. Not being able to integrate and redistribute our collective data resources blocks innovation, and stymies the creation of life-improving diagnostic and drug selection tools. To help the biomedical research and research support communities (e.g. libraries, funders, repositories, etc.) understand and navigate the data licensing landscape, the (Re)usable Data Project (RDP) (http://reusabledata.org) assesses the licensing characteristics of data resources and how licensing behaviors impact reuse. We have created a ruleset to determine the reusability of data resources and have applied it to 56 scientific data resources (i.e. databases) to date. The results show significant reuse and interoperability barriers. Inspired by game-changing projects like Creative Commons, the Wikipedia Foundation, and the Free Software movement, we hope to engage the scientific community in the discussion regarding the legal use and reuse of scientific data, including the balance of openness and how to create sustainable data resources in an increasingly competitive environment.

scientific communication and education↗

bioRxiv2018

Bibliometric analysis of the trends of Zika related research from 2015 to 2017

BackgroundZika virus (ZIKV) is a mosquito-borne disease discovered in 1947, which did not cause public concern for the next 68 years. However, when ZIKV emerged in Brazil 2015 the attention increased rapidly. The announcement by Brazilian authorities, that ZIKV infection was associated with severe congenital disease e.g. microcephaly, surged public interest. Because of the accumulation of evidence that showed the magnitude of the ZIKV outbreak in the Americas, the World Health Organization declared a Public Health Emergency of International Concern February 1, 2016.\n\nResultsDuring 2015-2017, we witnessed one of the most active and cooperated research responses against an emerging disease. To investigate the impact of ZIKV research during those years we decided to perform a bibliometric analysis of ZIKV research. The search for research articles on ZIKV was performed by bibliometric analysis from the scientific databases PubMed and Scopus. We found that the number of ZIKV related publications increased 38-41 times in 2016-2017 compared to 2015. During the three years there was a temporal shift in ZIKV research trends, from reports of ZIKV case studies and diagnostic methods, to development of ZIKV prevention and treatment. In addition, the number of countries involved in ZIKV research increased from 25 in 2015 to 111 in 2016 and 139 in the following year, showing that ZIKV research became global during three years.\n\nConclusionsThe results from our study highlighted the importance of gathering public interest to global health issues, and how it can act as a powerful catalyzer to trigger the research field. However, despite the progress in ZIKV research, many questions remain to be addressed to accelerate the development of effective ZIKV countermeasures. Nevertheless, as long as we remember the importance of support and collaboration that we have experienced during the multidisciplinary effort against the current ZIKV outbreak, we will have an idea on how to handle the next inevitable and yet unknown infectious disease threat.

scientific communication and education↗

bioRxiv2018

Science podcasts: analysis of global production and output from 2004 to 2018

1.Since 2004, podcasts have emerged as a decentralised medium for science communication to the global public. However, to-date, there have been no large-scale quantitative studies of the production and dissemination of science podcasts. This study identified 952 English language science podcasts available between January and February 2018 and analysed online textual and visual data related to the podcasts and classified and noted key production parameters. It was found that the total number of science podcast series available grew linearly between 2004 and 2010, and then exponentially between 2010 and 2018. 65% of science podcast series were hosted by scientists and 77% were targeted to public audiences. Although a wide range of primarily single-subject science podcasts series were noted, 34% of science podcast series were not dedicated to a science subject. Compared to biology and physics, chemistry may be under-represented by science podcasts. Only 24% of science podcast series had any overt financial income. 62% of science podcast series were affiliated to an organisation; producing a greater number of episodes (median = 24, average = 96) than independent science podcast series (median = 16, average = 48). This study provides the first snapshot of how science podcasts are being used to communicate science to public audiences around the globe.

scientific communication and education↗

bioRxiv2018

Predicting the time needed to conduct an environmental systematic review or systematic map: analysis and decision support tool

Systematic reviews aim to maximise transparency and comprehensiveness, whilst also minimising subjectivity and sources of bias. Because of these time-consuming and complex tasks, systematic reviews are perceived as being resource-intensive. To date, published estimates of systematic review resource requirements have been largely anecdotal, being imprecise and not based on evidence. However, it is valuable to provide reliable means of estimating the resource and time requirements of systematic reviews and maps. We analysed all CEE systematic reviews (n=66) and maps (n=20) published or registered between 2012 and 2017 to estimate the average time needed to complete a systematic review and map. We then surveyed 33 experienced systematic reviewers to collate information on time needed for each stage of the review process. Our results show that the average CEE systematic review takes 157 days (SD; {+/-}22), whilst the average CEE systematic map takes 209 days (SD; {+/-}53). While screening of titles and abstracts is widely accepted to be time-consuming, in practice meta-data extraction and critical appraisal can take as long (or even longer) to complete, especially when producing systematic maps. Finally, we present a tool that allows the user to predict the time requirements of a review or map given information known about the planned methods and evidence base likely to be identified. Our tool uses evidence-based defaults as a useful starting point for those wishing to predict the time requirements for a particular review. Our analyses shed light on the most time-consuming stages of the systematic review and map process, and highlight key bottlenecks from the perspective of time requirements, helping future reviewers to plan their time accordingly. Future predictions of effort required to complete systematic reviews and maps could be improved if CEE and CEE review authors provided more detailed reporting of the methods and results of their reviewing processes.

scientific communication and education↗