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bioRxiv2020

Assessment of transparency indicators across the biomedical literature: how open is open?

Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify five indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central. Our results indicate remarkable improvements in some (e.g. conflict of interest disclosures, funding disclosures), but not other (e.g. protocol registration, code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand and promote transparency and reproducibility in science.

scientific communication and education↗

bioRxiv2020

Relating farmers perceptions to long term dynamics in maize (Zea mays L.) production: The production of improved maize is coming to a standstill in central Malawi

Maize production, area and yield dynamics were assessed based on farmer perceptions and production data from 2004/05-2018/19 using 36 000 households in Salima, central Malawi. The results showed that farmers used 16, six and two varieties for hybrid, Open-pollinated varieties (OPV) and local maize respectively. Farmers sourced Hybrid and OPV maize seed from Private Agro dealers while local maize was own-sourced. Farmers preferred local maize for being cheap, good taste, low storage costs, and pest resistance although low yielding. They preferred hybrid and OPV maize for high yielding and early maturity despite demanding high storage costs, pest susceptibility, and low flour. From 2004/05-2018/19, the area under local and OPV maize reduced by 61% and 12% respectively, while that of hybrid maize increased by 49%. However, the consistent decrease in area for hybrid and OPV and significant increase of that of local maize from 2014/15-2018/19 may signal a catastrophic maize production in the region. From 2019/20-2025/26 production of all maize was projected at 44 172 tons by 2025/26, representing a 1.6% increase from the base year 2019/20. This increase will be due to favorable climatic conditions and not increase in area or yield. If maize yield was improved by 30% production would increase to 110 430 tons representing 67% of the food requirement in the study area. The current maize production trend in Salima does not guarantee food security prospects. Therefore, policymakers should consider reviewing the past interventions (input pricing, promotion strategies, sustainable practices, policies) in the maize subsector to enhance maize productivity.

scientific communication and education↗

bioRxiv2020

Risk perceptions and preventive practices of COVID-19 among healthcare professionals in public hospitals in Ethiopia

Healthcare professionals are at higher risk of contracting the novel coronavirus due to their work exposure in the healthcare settings. Practicing appropriate preventive measures to control COVID-19 infection is one of the most important interventions that healthcare workers are expected to use. The aim of this study was to assess the level of risk perception and practices of preventive measures of COVID-19 among health workers in Addis Ababa, Ethiopia. A hospital-based cross-sectional study was conducted from 9th to 26th June 2020 among healthcare professionals working at six public hospitals in Addis Ababa. Data were collected using a self-administered structured questionnaire. Frequency, percentage, and mean were used to summarize the data. A binary logistic regression analyses were performed to identify factors associated with risk perception about COVID-19. A total of 1,134 participants were surveyed. Wearing facemask (93%), hand washing for at least 20 seconds (93%), covering mouth and nose while coughing or sneezing (91%), and avoiding touching eyes, nose, and mouth (91%) were the commonly self-reported preventive practices. About 88% perceived that they were worried about the risk of becoming infected with coronavirus, and majority (91%) worried about the risk of infection to their family. The mean score of overall fear and worry of COVID-19 was 2.37 on a scale of 1 to 3. Respondents who ever provided clinical care to COVID-19 patients were more likely to report fear and worry (adjusted OR=1.34, 95% CI:1.02-1.91), however those who ever participated in Ebola or SARS outbreaks were less likely to report fear and worry due to COVID-19 crisis (adjusted OR=0.66, 95% CI:0.48-0.90). This study has revealed widespread practices of preventive measures and the highest perceived risk of COVID-19 among healthcare workers. Therefore, an effective risk communication intervention should be implemented to ensure the maintenance of appropriate practices during the current COVID-19 pandemic.

scientific communication and education↗

bioRxiv2020

Matchathon: A guide to student-faculty connections in PhD programs

Relevant and impactful mentors are essential to a graduate students career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy. The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

scientific communication and education↗

bioRxiv2020

Mental Health Status of Adolescents During the COVID-19 Pandemic: A Cross-sectional Survey among the Bangladeshi Graduate Students at Dhaka City

ObjectivesTo identify the level of Mental Health Status of Adolescents During the COVID-19 Pandemic among the Bangladeshi Graduate Student at Dhaka MethodA cross-sectional survey was conducted with 330 students from different public and Private Universities in Dhaka, Bangladesh between April 01, 2020 and July 31, 2020 amid the COVID-19 lockdown period in Bangladesh. A standard, self-administered online questionnaire consisting of questions on socio-demographic variables, mental health status, as well as stress management sent to the respondents through social networking platforms. Data were analyzed using descriptive statistics, t-test, one-way ANOVA and correlation tests. ResultsThe mean score of mental health status was 2.08 based on four points scale. They felt problem in decision making (3.04), in doing the things well (2.92), in enjoying normal day to day life (2.88), in playing a useful part in life (2.85), in doing their task (2.75), living in perfectly well and in good health (2.70). The respondents also developed a suicidal tendency (2.55), felt nervous in strung-up (2.24), took longer time to do things (2.14), felt tightness and pressure in head (2.12), and found themselves pressurized by various stuff (2.05). This study also found a significant positive relationship between mental health status and age, living with parents, and parents attitude. Finally, this study revealed that the respondents managed their stress by chatting with their friends, parents and siblings, and by sleeping. ConclusionMental health status of adolescents was found moderate in this study. This study suggests further large-scale study including different socio-economic settings in order to figure out the real scenario of adolescents mental health status of the country during the pandemic.

scientific communication and education↗

bioRxiv2020

Supporting Student Learning and Experiences in the Lab: (How) Should We Design Their Groups?

Undergraduate science students spend a substantial amount of time working in their laboratory groups, and instructors want to make evidence-based decisions on how to best set up these groups. Despite several studies on group composition, the evidence appears to be quite context-specific, and very little has been published about lab groups. Further, many studies focus solely on conceptual learning; however, the lab is an important venue for also supporting non-content outcomes such as confidence, process skills, team skills, and attitudes. Thus, in our introductory course on molecules, cells, and physiology we were interested in the impact of group composition, on a spread of student outcomes. Students were either placed into groups by the instructor, or self-selected into groups. To assess the impact of group composition on student outcome, we collected pre/post data from >500 students over 2 semesters. Our measures assess conceptual knowledge, confidence in lab skills, attitudes toward group learning, lab grades, gender, year of study, and (via open-ended questions) student perspectives. Using a multiple regression approach, we established models that predict student outcomes based on their individual attributes and on their lab group attributes. Surprisingly, the hetero/homogeneity of the initial group, and whether the groups were student- or instructor-selected, did not affect student outcomes in these models. Further MANCOVA analysis demonstrated that student interaction outside of the lab time was the strongest predictor of positive student attitudes toward group learning. Student perspectives on group formation are mixed, and suggest that a simple and flexible choice approach may best support our students. Overall, these findings have clear implications for our course design and instructional choices: we should focus our efforts to promote positive student interactions, rather than worrying about initial composition.

scientific communication and education↗

bioRxiv2020

Exploring and illustrating the mouse embryo: virtual objects to think and create with

The teaching, learning, communication, and practice of Developmental Biology require interested parties to be at ease with the considerable spatial complexity of the embryo, and with its evolution over time as it undergoes morphogenesis. In practice, the four dimensionality of embryonic development (space and time) calls upon strong visual-spatial literacy and mental manipulation skills, generally expected to be innate or to come through experience. Yet it has been argued that Developmental Biology suffers the most from available traditional media of communication and representation. To date, few resources exist to engage with the embryo in its 3D and 4D aspects, to communicate such aspects in ones work, and to facilitate their exploration in the absence of live observations. I here provide a collection of readily-usable volumetric models for all tissues and stages of mouse peri-implantation development as extracted from the eMouse Atlas Project (E5.0 to E9.0), as well as custom-made models of all pre-implantation stages (E0 to E4.0). These models have been converted to a commonly used 3D format (.stl), and are provided in ready-made files for digital exploration and illustration. Further provided is a step-by-step walkthrough on how to practically use these models for exploration and illustration using the free and open source 3D creation suite Blender. I finally outline possible further uses of these very models in outreach initiatives of varying levels, virtual and augmented reality applications, and 3D printing.

scientific communication and education↗

bioRxiv2020

The multidisciplinary nature of COVID-19 research

ObjectiveWe analyzed the scientific output after COVID-19 and contrasted it with studies published in the aftermath of seven epidemics/pandemics: Severe Acute Respiratory Syndrome (SARS), Influenza A virus H5N1 and Influenza A virus H1N1 human infections, Middle East Respiratory Syndrome (MERS), Ebola virus disease, Zika virus disease, and Dengue. Design/Methodology/ApproachWe examined bibliometric measures for COVID-19 and the rest of studied epidemics/pandemics. Data were extracted from Web of Science, using its journal classification scheme as a proxy to quantify the multidisciplinary coverage of scientific output. We proposed a novel Thematic Dispersion Index (TDI) for the analysis of pandemic early stages. Results/DiscussionThe literature on the seven epidemics/pandemics before COVID-19 has shown explosive growth of the scientific production and continuous impact during the first three years following each emergence or re-emergence of the specific infectious disease. A subsequent decline was observed with the progressive control of each health emergency. We observed an unprecedented growth in COVID-19 scientific production. TDI measured for COVID-19 (29,4) in just six months, was higher than TDI of the rest (7,5 to 21) during the first three years after epidemic initiation. ConclusionsCOVID-19 literature showed the broadest subject coverage, which is clearly a consecuence of its social, economic, and political impact. The proposed indicator (TDI), allowed the study of multidisciplinarity, differentiating the thematic complexity of COVID-19 from the previous seven epidemics/pandemics. Originality/ValueThe multidisciplinary nature and thematic complexity of COVID-19 research were successfully analyzed through a scientometric perspective.

scientific communication and education↗

bioRxiv2020

Publishing of COVID-19 Preprints in Peer-reviewed Journals, Preprinting Trends, Public Discussion and Quality Issues

IntroductionCOVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals. We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues. MethodsManuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data. The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. ResultsWith adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR=2.04, 95%CI 1.87-2.23) as well as over the entire observed period (OR=1.42, 95%CI 1.33-1.52). Submission-to-acceptance was by 38.67 days (95%CI 34.96-42.39) shorter for COVID-19 articles. Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. ConclusionCurrent data suggest a preference for publication of COVID-19-related preprints over the observed period.

scientific communication and education↗

bioRxiv2020

Emerging Concern of Scientific Fraud: Deep Learning and Image Manipulation

Scientific fraud by image duplications and manipulations within western blot images is a rising problem. Currently, problematic western blot images are mainly detected by checking repeated bands or through visual observation. However, the completeness of the above methods in detecting problematic images has not been demonstrated. Here we show that Generative Adversarial Nets (GANs) can generate realistic western blot images that indistinguishable from real western blots. The overall accuracy of researchers for identifying synthetic western blot images is 0.52, which almost equal to blind guess (0.5). We found that GANs can generate western blot images with bands of the expected lengths, widths, and angles in desired positions that can fool researchers. For the case study, we find that the accuracy of detecting the synthetic western blot images is related to years of researchers performed studies relevant to western blots, but there was no apparent difference in accuracy among researchers with different academic degrees. Our results demonstrate that GANs can generate fake western blot images to fool existing problematic image detection methods. Therefore, more information is needed to ensure that the western blots appearing in scientific articles are real. We argue to require every western blot image to be uploaded along with a unique identifier generated by the laboratory machine and to peer review these images along with the corresponding submitted articles, which may reduce the incidence of scientific fraud.

scientific communication and education↗

bioRxiv2020

Grant Review Feedback: Appropriateness and Usefulness

The primary goal of the peer review of research grant proposals is to evaluate their quality for the funding agency. An important secondary goal is to provide constructive feedback to applicants for their resubmissions. However, little is known about whether review feedback achieves this goal. In this paper, we present a mixed methods analysis of responses from grant applicants regarding their perceptions of the effectiveness and appropriateness of peer review feedback they received from grant submissions. Overall, 56%-60% of applicants determined the feedback to be appropriate (fair, well-written, and well-informed), although their judgments were more favorable if their recent application was funded. Importantly, independent of funding success, women found the feedback better written than men, and more white applicants found the feedback to be fair than non-white applicants. Also, perceptions of a variety of biases were specifically reported in respondents feedback. Less than 40% of applicants found the feedback to be very useful in informing their research and improving grantsmanship and future submissions. Further, negative perceptions of the appropriateness of review feedback were positively correlated with more negative perceptions of feedback usefulness. Importantly, respondents suggested that highly competitive funding pay-lines and poor inter-panel reliability limited the usefulness of review feedback. Overall, these results suggest that more effort is needed to ensure that appropriate and useful feedback is provided to all applicants, bolstering the equity of the review process and likely improving the quality of resubmitted proposals.

scientific communication and education↗

bioRxiv2020

Attitudes and Practices of Open Data, Preprinting, and Peer-review - a Cross Sectional Study on Croatian Scientists

Attitudes towards open peer review, open data and use of preprints influence scientists engagement with those practices. Yet there is a relatively small number of validated questionnaires that measure these attitudes. The goal of our study was to construct and validate such a questionnaire. Using a sample of Croatian scientists (N=541), from a wide range of disciplines, we developed a questionnaire titled Attitudes towards Open data sharing, preprinting, and peer-review (ATOPP). The questionnaire has 21 item with a four-factor structure (attitudes towards: open data, preprint servers, open peer-review and open peer-review in small scientific communities). Based on the questionnaire, the attitudes of Croatian scientists towards these topics were generally neutral, with a median of 3.3 out of 5 of the total attitude score. Croatian scientist attitudes were lowest for open peer-review in small scientific communities (Md 2.0) and highest for open data (Md 3.9).

scientific communication and education↗

bioRxiv2020

Modeling Research Project Grant Success Rates from NIH Appropriation History: Extension to 2020

Communication of the likelihood that a grant proposal is funded is important for individual researchers and academic institutions. For research project grants (RPGs) funded by the US National Institutes of Health (NIH), this is measured by the success rate, the fraction of grants reviewed in a given fiscal year that are funded. In 2016, I posted a relatively simple computational model that allowed estimation of these success rates from historical data of NIH appropriations and associated data, based largely on the fact that commitments to fund NIH grants are typically made over four fiscal years rather than coming from a single fiscal years appropriations. Data for appropriations and success rates for fiscal years 2016-2020 are now available, allowing this model to be tested without no adjustable parameters. Over this period, the NIH appropriation increased by 29.7% to $39.313 billion, yet the RPG success rate increased from 0.183 to 0.201, a relative increase of only 9.8%. This difference is accurately reproduced by the model, indicating that the modest changes in success rate despite large appropriation increases reflect the consequences of the funding grants from multiple fiscal years and the response of the biomedical research community in submitting an increased number of proposals. The model can also be extended to estimate the success rates for individual institutes with reasonable accuracy.

scientific communication and education↗

bioRxiv2020

Global Trends in eHealth Research: Analysis and Visualization of Author and Indexer-Supplied Keywords

This article examined the growth and development of ehealth research based on the headcount and analysis of the characteristics of keywords used by authors and indexers to represent their research content during 1945-2019 as indexed in the Elseviers Scopus database. The results show that although the term ehealth originated in the late 1990s, but it has become an envelope term for much older terms such as telemedicine, and its variants which originated much earlier. The keywords were spread in 27 Scopus Subject Areas, with medicine (44.04%), engineering (12.84%) and computer science (11.47%) leading while by Scopus All Science Journal Classification, Health Sciences accounted for 55.83% of the keywords and physical sciences followed with 30.62%. The rest two classifications namely social sciences and life sciences made only single digit contributions. Although the primary essence of ehealth was how to meet health needs, the work of engineers who either initially deployed telephone to meet their health needs or, and, computer scientists, who addressed the need to design technologies for medical services is very significant. It is concluded that ehealth is a multidisciplinary area that is attractive to researchers from all disciplines because of its sensitive focus on health, and therefore requires pooling and integrating of resources and expertise, methods and approaches.

scientific communication and education↗

bioRxiv2020

How to best evaluate applications for junior fellowships? Remote evaluation and face-to-face panel meetings compared

ObjectivesTo test a simplified evaluation of fellowship proposals by analyzing the agreement of funding decisions with the official evaluation, and to examine the use of a lottery-based decision for proposals of similar quality. DesignThe study involved 134 junior fellowship proposals (Postdoc.Mobility). The official method used two panel reviewers who independently scored the application, followed by triage and discussion of selected applications in a panel. Very competitive/uncompetitive proposals were directly funded/rejected without discussion. The simplified procedure used the scores of the two panel members, with or without the score of an additional, third expert. Both methods could further use a lottery to decide on applications of similar quality close to the funding threshold. The same funding rate was applied, and the agreement between the two methods analyzed. SettingSwiss National Science Foundation (SNSF). ParticipantsPostdoc.Mobility panel reviewers and additional expert reviewers. Primary outcome measurePer cent agreement between the simplified and official evaluation method with 95% confidence intervals (95% CI). ResultsThe simplified procedure based on three reviews agreed in 80.6% (95% CI 73.9-87.3) with the official funding outcome. The agreement was 86.6% (95% CI 80.8-92.4) when using the two reviews of the panel members. The agreement between the two methods was lower for the group of applications discussed in the panel (64.2% and 73.1%, respectively), and higher for directly funded/rejected applications (range 96.7% to 100%). The lottery was used in eight (6.0%) of 134 applications (official method), 19 (14.2%) applications (simplified, three reviewers) and 23 (17.2%) applications (simplified, two reviewers). With the simplified procedure, evaluation costs could have been halved and 31 hours of meeting time saved for the two 2019 calls. ConclusionAgreement between the two methods was high. The simplified procedure could represent a viable evaluation method for the Postdoc.Mobility early career instrument at the SNSF.

scientific communication and education↗

bioRxiv2020

Demographics and Employment of Max-Planck Society's Postdocs

The recently founded Max Planck PostdocNet brings together postdoctoral researchers (or postdocs) from the Max Planck Society (MPS), provides representation for the postdoctoral community across all Max Planck Institutes (MPI) and associated institutes, and advocates for their interests on their behalf. At the 2019 founding meeting, MPS postdocs quickly raised their concerns about their employment situation and their associated social and working conditions. Subsequently, the PostdocNet conducted the first survey targeting exclusively postdoctoral researchers to gather information on their demographics, employment situations and social conditions. This report presents the results of this survey, providing a thorough characterization of the postdoc demographics as well as the working conditions experienced by the postdoctoral community of the MPS. Remarkably, the survey analysis revealed a number of disparities in the access to employment type, wage level and social benefits. These results will guide future and present MPS postdoctoral researchers and their employers at the MPS to thrive for equality and fairness. Moreover, these results should be of help to the MPS to establish, improve and maintain optimal working conditions for MPS postdocs.

scientific communication and education↗

bioRxiv2020

Latent class regression improves the predictive acuity and clinical utility of survival prognostication amongst chronic heart failure patients.

The present study aimed to compare the predictive acuity of latent class regression (LCR) modelling with: standard generalised linear modelling (GLM); and GLMs that include the membership of subgroups/classes (identified through prior latent class analysis; LCA) as alternative or additional candidate predictors. Using real world demographic and clinical data from 1,802 heart failure patients enrolled in the UK-HEART2 cohort, the study found that univariable GLMs using LCA-generated subgroup/class membership as the sole candidate predictor of survival were inferior to standard multivariable GLMs using the same four covariates as those used in the LCA. The inclusion of the LCA subgroup/class membership together with these four covariates as candidate predictors in a multivariable GLM showed no improvement in predictive acuity. In contrast, LCR modelling resulted in a 10-14% improvement in predictive acuity and provided a range of alternative models from which it would be possible to balance predictive acuity against entropy to select models that were optimally suited to improve the efficient allocation of clinical resources to address the differential risk of the outcome (in this instance, survival). These findings provide proof-of-principle that LCR modelling can improve the predictive acuity of GLMs and enhance the clinical utility of their predictions. These improvements warrant further attention and exploration, including the use of alternative techniques (including machine learning algorithms) that are also capable of generating latent class structure while determining outcome predictions, particularly for use with large and routinely collected clinical datasets, and with binary, count and continuous variables.

scientific communication and education↗

bioRxiv2020

Valid statistical approaches for clustered data: A Monte Carlo simulation study

The translation of preclinical studies to human applications is associated with a high failure rate, which may be exacerbated by limited training in experimental design and statistical analysis. Nested experimental designs, which occur when data have a multilevel structure (e.g., in vitro: cells within a culture dish; in vivo: rats within a litter), often violate the independent observation assumption underlying many traditional statistical techniques. Although previous studies have empirically evaluated the analytic challenges associated with multilevel data, existing work has not focused on key parameters and design components typically observed in preclinical research. To address this knowledge gap, a Monte Carlo simulation study was conducted to systematically assess the effects of inappropriately modeling multilevel data via a fixed effects ANOVA in studies with sparse observations, no between group comparison within a single cluster, and interactive effects. Simulation results revealed a dramatic increase in the probability of type 1 error and relative bias of the standard error as the number of level-1 (e.g., cells; rats) units per cell increased in the fixed effects ANOVA; these effects were largely attenuated when the nesting was appropriately accounted for via a random effects ANOVA. Thus, failure to account for a nested experimental design may lead to reproducibility challenges and inaccurate conclusions. Appropriately accounting for multilevel data, however, may enhance statistical reliability, thereby leading to improvements in translatability. Valid analytic strategies are provided for a variety of design scenarios.

scientific communication and education↗