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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Sociality enhances survival in science, especially for female researchers

Intense competition for limited opportunities means the career path of a scientist is a challenging one, and female scientists in particular are less likely to survive in academia. Collaboration is a key factor in scientific advances, and in social species enhanced sociality improves fitness and longevity. Yet whether sociality influences career progression and survival in science, and how this might differ between genders, is largely unknown. We built authorship social networks from publication records to test how sociality predicts career progression and survival in a cohort of biologists contributing to three international conferences in the 1990s. We show that sociality has the strongest effect for female researchers but, regardless of gender, publishing with many diverse co-authors significantly reduces time to become a principal investigator and increases career duration. Publishing repeatedly with co-authors also enhances career progression in both genders, but reduces career length for men. These findings demonstrate that the value of collaboration extends beyond scientific advances, and can directly benefit the career progression and longevity of research scientists themselves. Efforts to encourage researchers at all levels to invest in collaborations, particularly with female researchers, will help to close the gender gap in science and academia.

scientific communication and education↗

No Relationship Between Perceived Health Anomalies and Perceived Experimental Success in Retired Breeder Male Hartley Albino Guinea Pigs

Guinea pigs used in our laboratory for cardiac research sometimes exhibit physical abnormalities. These issues may abate or intensify during the time they are housed in our facility. After using a guinea pig for research, experimentalists note the apparent health of an animal based on visible features and/or abnormal electrophysiology of the heart. There was an existing anecdotal observation that the health of the Guinea Pigs, and subsequently the experimental success rate, had a seasonal variation; therefore we sought to determine if there is a time of year in which our guinea pigs are more likely to be perceived as unhealthy, and whether any determined monthly pattern correlates with an experimentalists ability to complete an experimental protocol. An electronic log was created to record the perceived health of the animal and the ability to complete the experiment successfully. Irregular symptoms included, but were not limited to, severe weight or hair loss and irregularities with the heart found post thoracotomy or during baseline electrophysiological recordings of whole-heart preparations. Animals that did not exhibit significant weight or hair loss, or other ailments were considered "healthy". Overall, our results indicate that there are no monthly variations in perceived Hartley Albino guinea pig health or correlations with experimental completion rates, suggesting mild hair or weight loss that is common when shipping animals may not significantly affect the ability to conduct ex vivo whole-heart electrophysiological studies.

scientific communication and education↗

Quantifying and contextualizing the impact of bioRxiv preprints through social media audience segmentation

Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a papers social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each users followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from non-specialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the highly tweeted preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints intentionally espouse any right-wing extremist messages, cases exist where extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing research evaluation as well as shedding light on the unavoidable challenges of scientific discourse afforded by social media.

scientific communication and education↗

Who reviews for predatory journals? A study on reviewer characteristics

BackgroundWhile the characteristics of scholars who publish in predatory journals are relatively well-understood, nothing is known about the scholars who review for these journals. We aimed to answer the following questions: Can we observe patterns of reviewer characteristics for scholars who review for predatory journals and for legitimate journals? Second, how are reviews for potentially predatory journals distributed globally? MethodsWe matched random samples of 1,000 predatory journals and 1,000 legitimate journals of the Cabells Scholarly Analytics journal lists with the Publons database of review reports, using the Jaro-Winkler string metric. For reviewers of matched reviews, we descriptively analysed meta-data on reviewing and publishing behaviour. ResultsWe matched 183,743 unique Publons reviews that were claimed by 19,598 reviewers. 6,077 reviews were conducted for 1160 unique predatory journals (3.31% of all reviews). 177,666 were claimed for 6,403 legitimate journals (96.69% of all reviews). The vast majority of scholars either never or only occasionally submitted reviews for predatory journals to Publons (89.96% and 7.55% of all reviewers, respectively). Smaller numbers of scholars claimed reviews predominantly or exclusively for predatory journals (0.26% and 0.35% of all reviewers, respectively). The two latter groups of scholars are of younger academic age and have fewer publications and fewer reviews than the first two groups of scholars.Developing regions feature larger shares of reviews for predatory reviews than developed regions. ConclusionThe characteristics of scholars who review for potentially predatory journals resemble those of authors who publish their work in these outlets. In order to combat potentially predatory journals, stakeholders will need to adopt a holistic approach that takes into account the entire research workflow.

scientific communication and education↗

Assessing the impact of introductory programming workshops on the computational reproducibility of biomedical workflows

IntroductionAs biomedical research becomes more data-intensive, computational reproducibility is a growing area of importance. Unfortunately, many biomedical researchers have not received formal computational training and often struggle to produce results that can be reproduced using the same data, code, and methods. Programming workshops can be a tool to teach new computational methods, but it is not always clear whether researchers are able to use their new skills to make their work more computationally reproducible. MethodsThis mixed methods study consisted of in-depth interviews with 14 biomedical researchers before and after participation in an introductory programming workshop. During the interviews, participants described their research workflows and responded to a quantitative checklist measuring reproducible behaviors. The interview data was analyzed using a thematic analysis approach, and the pre and post workshop checklist scores were compared to assess the impact of the workshop on computational reproducibility of the researchers workflows. ResultsPre and post scores on a checklist of reproducible behaviors did not increase in a statistically significant manner. The qualitative interviews revealed that several participants had made small changes to their workflows including switching to open source programming languages for their data cleaning, analysis, and visualization. Overall many of the participants indicated higher levels of programming literacy and an interest in further training. Factors that enabled change included supportive environments and an immediate research need, while barriers included collaborators that were resistant to new tools and a lack of time. ConclusionWhile none of the participants completely changed their workflows, many of them did incorporate new practices, tools, or methods that helped make their work more reproducible and transparent to other researchers. This indicate that programming workshops now offered by libraries and other organizations contribute to computational reproducibility training for researchers

scientific communication and education↗

Sorry, we're open: Golden Open Access and inequality in the natural sciences

Global Open Access (GOA) journals make research more accessible and therefore more citable; however, the publication fees associated with GOA journals can be costly and therefore not a viable option for many researchers seeking high-impact publication outlets. In this study, I collect metadata from 237 open-access natural science journals and analyze them in terms of Article Processing Charges (APC), Impact Factor (IF), Eigen Factor (EF), citability, and country of publisher. The results of this study provide evidence that with IF, EF, and citability all increase as APC increases, and each of these metrics are higher in publishers from developed countries in comparison to developing countries. Implications of these trends are discussed in regards to natural sciences and inequality within the global scientific community.

scientific communication and education↗

Biodiverse food plants in the semiarid region of Brazil have unknown potential: A systematic review

Food biodiversity presents one of the most significant opportunities to enhance food and nutrition security today. The lack of data on many plants, however, limits our understanding of their potential and the possibility of building a research agenda focused on them. Our objective with this systematic review was to identify biodiverse food plants occurring in the Caatinga biome, Brazil, strategic for the promotion of food and nutrition security. We selected studies from the following databases: Web of Science, Medline/PubMed (via the National Library of Medicine), Scopus and Embrapa Agricultural Research Databases (BDPA). Eligible were original articles, published since 2008, studying food plants occurring in the Caatinga. We assessed the methodological quality of the studies we selected. We reviewed a total of fifteen studies in which 65 plants that met our inclusion criteria were mentioned. Of this amount, 17 species, including varieties, subspecies, and different parts of plants, had data on chemical composition, in addition to being mentioned as food consumed by rural communities in observational ethnobotanical studies. From the energy and protein data associated with these plants, we produced a ranking of strategic species. The plants with values higher than the average of the set were: Dioclea grandiflora Mart. ex Benth (mucuna), Hymenaea courbaril L. (jatoba), Syagrus cearensis Noblick (coco-catole), Libidibia ferrea (Mart. ex Tul.) L.P.Queiroz (juca), Sideroxylon obtusifolium (Roem. & Schult.) T.D.Penn. (quixabeira). We suggest that the scientific community concentrates research efforts on tree legumes, due to their resilience and physiological, nutritional, and culinary qualities.

scientific communication and education↗

Trachomatous Trichiasis (TT) management in Tanzania: a mixed method study investigating barriers and facilitators to obtaining treatment

BackgroundProlonged ocular Chlamydial infection, known as trachoma, can lead to trachomatous trichiasis (TT). TT is the stage of trachoma where the eyelid turns inwards, resulting in lashes rubbing against the cornea. TT can damage the cornea, leading to vision impairment or blindness. Treatment for TT includes epilation or surgery. Trachoma is targeted for elimination as a public health problem. One criterion of trachoma elimination is less than 0.2% prevalence of TT unknown to the health system in adults >= 15 years. There are several districts in Tanzania that have not attained this target. MethodologyWe selected six districts across three regions in Tanzania. Our mixed-methods approach included a retrospective review and analysis of program data and implementation of key informant interviews (KII) and focus group discussions (FGD). The desk review collated data on district-level indicators and generated estimates around number and proportion of cases not identified by case finders and cases lost along the continuum of care. KIIs and FGDs guides were structured to enlist responses around case finding techniques, linkage to services and TT surgery process. ConclusionWe found a substantial proportion (13%) of TT positive people were not being identified by case finders, and of those identified, majority (72%) were lost along the continuum of care. These factors likely contribute to high TT prevalence in districts where surgical interventions are ongoing. Engaging community leaders to share TT information and enlisting people who have received surgery to witness in communities may encourage consent of examination by case finders and increase surgical uptake. After witnessing positive effects of surgery, many interviewees who had previously declined surgery changed their mind. Increasing frequency of surgical camps would improve access to these populations. Additionally, giving more notice about surgical camps and extending duration is important to enable remote populations to obtain services. Author SummaryTreatment for trachomatous trichiasis (TT) includes epilation or surgery. There are several districts in Tanzania that have struggled to link people with TT to services. It is important for the program to understand why this is the case to inform program adaptations for improved linkage to services. We implemented a mixed methods approach to address this knowledge gap. We found a large portion of TT positive people are not being identified by case finders and of those identified, many are lost along the continuum of care. These factors are likely contributing to the unexpectedly high TT prevalence in districts where surgical interventions are ongoing. Barriers to identifying cases included remoteness, case finder credibility, knowledge of TT, and case finder motivation. Once cases are identified, the largest gap along the continuum of care is the link between being identified and screened. We found barriers to attending screenings and subsequently obtaining treatment to be fear of surgery, distance from surgical camps, agricultural season, time to plan, awareness and frequency of camps, and lack of assistance after surgery.

scientific communication and education↗

Prevalence of scabies and its associated factors among school age children in Arba Minch zuria district, Southern Ethiopia, 2018.

BackgroundScabies, a common human skin disease with a prevalence range of 0.2% to 71.4% in the world. It can have considerable impact on general health leading to illness and death not only through direct effect of its infestation and as a result of secondary bacterial infection. The aim of this study was to assess the prevalence of scabies and its associated factors among school age children in Arba Minch zuria district, Gamo zone, Southern Ethiopia. MethodsA community based cross sectional study was carried out in 845 school age children from February 20 to March 30, 2018. Multi-stage sampling technique was used to select study populations. Logistic regression an analysis was used to identify factors associated with scabies. Findings were presented using 95% CI of Crude Odds Ratios (COR) and Adjusted Odds Ratios (AOR. To declare statistical significance, p-value less than 0.05 was used. ResultA total of 825 children participated in the study with response rate of 97.6%. The overall prevalence of scabies was 16.4% [95% CI: 13.9%, 18.9%]. overcrowding index, family history of itching in the past two weeks, wealth index, knowledge of scabies, climatic zone, frequency of washing body, frequency of washing clothes, finger nails cutting practice, history of skin contact with scabies patient, washing hair more than once weekly, and sharing of clothes were significantly associated scabies disease. ConclusionIn conclusion, the prevalence of scabies in Arba Minch lies at 16.4% in the global scabies range 0.2% to 71.4%. The prevalence was highest in highlands followed by midland and then lowland. This represents a significant scabies burden which we recommend warrants health service intervention. Authors summaryScabies, a common human skin disease with a prevalence range of 0.2% to 71.4% in the world. It can have considerable impact on general health leading to illness and death not only through direct effect of its infestation and as a result of secondary bacterial infection. Conducting a research on this neglected tropical disease would contribute in designing a policies and strategies on prevention and control measures in the study area. Therefore, the aim of this study was to assess the prevalence of scabies and its associated factors among school age children in Arba Minch zuria district, Gamo zone, Southern Ethiopia.

scientific communication and education↗

Evaluating institutional open access performance: Methodology, challenges and assessment

Open Access to research outputs is becoming rapidly more important to the global research community and society. Changes are driven by funder mandates, institutional policy, grass-roots advocacy and culture change. It has been challenging to provide a robust, transparent and updateable analysis of progress towards open access that can inform these interventions, particularly at the institutional level. Here we propose a minimum reporting standard and present a large-scale analysis of open access progress across 1,207 institutions world-wide that shows substantial progress being made. The analysis detects responses that coincide with policy and funding interventions. Among the striking results are the high performance of Latin American and African universities, particularly for gold open access, whereas overall open access levels in Europe and North America are driven by repository-mediated access. We present a top-100 of global universities with the worlds leading institutions achieving around 80% open access for 2017 publications.

scientific communication and education↗

Evaluating institutional open access performance: Sensitivity analysis

In the article “Evaluating institutional open access performance: Methodology, challenges and assessment” we develop the first comprehensive and reproducible workflow that integrates multiple bibliographic data sources for evaluating institutional open access (OA) performance. The major data sources include Web of Science, Scopus, Microsoft Academic, and Unpaywall. However, each of these databases continues to update, both actively and retrospectively. This implies the results produced by the proposed process are potentially sensitive to both the choice of data source and the versions of them used. In addition, there remain the issue relating to selection bias in sample size and margin of error. The current work shows that the levels of sensitivity relating to the above issues can be significant at the institutional level. Hence, the transparency and clear documentation of the choices made on data sources (and their versions) and cut-off boundaries are vital for reproducibility and verifiability.View Full Text

scientific communication and education↗

A comparative analysis reveals irreproducibility in searches of scientific literature

Repeatability is the cornerstone of science and it is particularly important for systematic reviews. However, little is known on how database and search engine choices influence replicability. Here, we present a comparative analysis of time-synchronized searches at different locations in the world, revealing a large variation among the hits obtained within each of the several search terms using different search engines. We found that PubMed and Scopus returned geographically consistent results to identical search strings, Google Scholar and Web of Science varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls.View Full Text

scientific communication and education↗

Inflated citations and metrics of journals discontinued from Scopus for publication concerns: the GhoS(t)copus Project

Background Scopus is considered a leading bibliometric database. It contains the largest number of abstracts and articles cited in peer reviewed publications. The journals included in Scopus are periodically re-evaluated to ensure they meet indexing criteria. Afterwards, some journals might be discontinued for publication concerns. Despite their discontinuation, previously published articles remain indexed and continue to be cited. The metrics and characteristics of journals discontinued for publication concerns have yet to be studied. This study aimed (1) to evaluate the main features and citation metrics of journals discontinued from Scopus for publication concerns, before and after discontinuation, and (2) to determine the extent of predatory journals among the discontinued journals.Materials and Methods Eight authors surveyed a list of discontinued journals from Scopus (version July 2019). Data regarding metrics, citations and indexing were extracted from Scopus or other scientific databases, for the journals discontinued for publication concerns.Results A total of 317 journals were evaluated. The mean number of citations per year after discontinuation was significantly higher than before (median of difference 64 citations, p<0.0001), and so was the number of citations per document (median of difference 0.4 citations, p<0.0001). The total number of citations after discontinuation was 607,261, with a median of 713 citations (IQR 254-2056, range 0-19468) per journal. The open access publishing model was declared for 93% (294/317) of the journals, but only nine of these are currently indexed in the Directory of Open Access Journals (DOAJ). Twenty-two percent (72/317) of the journals were included in the Cabell blacklist.Conclusions The citation count of journals discontinued for publication concerns, increases despite discontinuation. Countermeasures should be taken to ensure the validity and reliability of Scopus metrics both at journal- and author-level for the purpose of scientific assessment of publishing.View Full Text

scientific communication and education↗

Interpretative guides for interacting with tissue atlas and digital pathology data using the Minerva browser

The recent development of highly multiplexed tissue imaging promises to substantially accelerate research into basic biology and human disease. Concurrently, histopathology in a clinical setting is undergoing a rapid transition to digital methods. Online tissue atlases involving highly multiplexed images of research and clinical specimens will soon join genomics as a systematic source of information on the molecular basis of disease and therapeutic response. However, even with recent advances in machine learning, experience with anatomic pathology shows that there is no immediate substitute for expert visual review, annotation, and description of tissue images. In this perspective we review the ecosystem of software available for analysis of tissue images and identify a need for interactive guides or "digital docents" that allow experts to help make complex images intelligible. We illustrate this idea using Minerva software and discuss how interactive image guides are being integrated into multi-omic browsers for effective dissemination of atlas data.

scientific communication and education↗

Scientometric correlates of high-quality reference lists in ecological papers

It is said that the quality of a scientific publication is as good as the science it cites, but the properties of high-quality reference lists have never been numerically quantified. We examined seven numerical characteristics of reference lists of 50,878 primary research articles published in 17 ecological journals between 1997 and 2017. Over this 20-years period, there have been significant changes in reference lists’ properties. On average, more recent ecological papers have longer reference lists, cite more high Impact Factor papers, and fewer non-journal publications. Furthermore, we show that highly cited papers across the ecology literature have longer reference lists, cite more recent and impactful papers, and account for more self-citations. Conversely, the proportion of ‘classic’ papers and non-journal publications cited, as well as the temporal range of the reference list, have no significant influence on articles’ citations. From this analysis, we distill a recipe for crafting impactful reference lists.View Full Text

scientific communication and education↗

Access to Scientific Literature by the Conservation Community

Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ∼97% need to use the scientific literature in order to support their IUCN-related conservation work, with ∼50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and gender (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ∼50% in Asia and Latin America, and ∼40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but prefer to read books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.View Full Text

scientific communication and education↗

Evaluating features of scientific conferences: A call for improvements

Scientific conferences provide valuable opportunities for researchers across career stages and disciplines to present their latest work, and to network with their peers. These meetings have largely been held in-person with rapid proliferation in the number of meetings and attendees. Yet the format and quality of their organization lag behind what is possible and as a result, the current experience of attending conferences in many disciplines remains unchanged in many respects. We created a database of 270 national and international academic conferences held in-person during 2018-2019 in various disciplines and examined them for their features, costs and impact on the community. We found that many meetings could still be improved significantly in terms of diversity, inclusivity, promoting early career researcher (ECR) networking and career development, venue accessibility, and importantly, reducing the meetings carbon footprint. It is important to accelerate and mandate efforts to improve conferences so that researchers in all disciplines, in particular ECRs, consistently benefit from scientific gatherings, for years to come. We discuss a combination of approaches and recommendations to make conferences more modern, effective, equitable and intellectually productive for the research community and environmentally sustainable for our planet. "They always say time changes things, but you actually have to change them yourself." -- Andy Warhol

scientific communication and education↗

On Biases of Attention in Scientific Discovery

How do nuances of scientists’ attention influence what they discover? We pursue an understanding of the influences of patterns of attention on discovery with a case study about confirmations of protein-protein interactions over time. We find that modeling and accounting for attention can help us to recognize and interpret biases in databases of confirmed interactions and to better understand missing data and unknowns in our fund of knowledge.View Full Text

scientific communication and education↗