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bioRxiv2021

Analysis of Scholarly Discourse in Biosecurity from 1986-2020

Scholarly discourse in Biosecurity is complex and interdisciplinary. The term Biosecurity has different meanings depending on the discipline. This term most often strives to capture efforts to prepare for and respond to threats posed by infectious organisms1. Increasing complexity of discourse in this interdisciplinary field and lack of common definitions can pose communication challenges. We use text mining of scholarly articles to characterize the interdisciplinary field of Biosecurity and the uses of this term over the past 35 years; a context evolution model is built to describe major changes in this field, and it shows a progression toward health security in recent years. Understanding the shifts in discourse predominance helps to illuminate the major challenges facing biosecurity research and academic community, and contributes to enhancing communication across disciplines within the Biosecurity field.

scientific communication and education↗

bioRxiv2021

How to attract and retain health workers in rural areas of a fragile state: findings from a labour market survey in Guinea

Most countries face challenges attracting and retaining health staff in remote areas but this is especially acute in fragile and shock-prone contexts, like Guinea, where imbalances in staffing are high and financial and governance arrangements to address rural shortfalls are weak. The objective of this study was to understand how health staff could be better motivated to work and remain in rural, under-served areas in Guinea. In order to inform the policy dialogue on strengthening human resources for health, we conducted three nationally representative cross-sectional surveys, adapted from tools used in other fragile contexts. We found that the locational job preferences of health workers in Guinea are particularly influenced by opportunities for training, working conditions, and housing. Most staff are satisfied with their work and with supervision, however, financial aspects and working conditions are considered least satisfactory, and worrying findings include the high proportion of staff favouring emigration, their high tolerance of informal user payments, as well as their limited exposure to rural areas during training. Based on our findings, we highlight measures which could improve rural recruitment and retention in Guinea and similar settings. These include offering upgrading and specialization in return for rural service; providing greater exposure to rural areas during training; increasing recruitment from rural areas; experimenting with fixed term contracts in rural areas; and improving working conditions in rural posts. The development of incentive packages should be accompanied by action to tackle wider issues, such as reforms to training and staff management.

scientific communication and education↗

bioRxiv2021

Heterogeneity versus the COVID-19 Pandemic

In this paper, heterogeneity is formally defined, and its properties are explored. We define and distinguish observable versus non-observable heterogeneity. It is proposed that heterogeneity among the vulnerable is a significant factor in the contagion impact of COVID-19, as demonstrated with incidence rates on a Diamond Princess Cruise ship in February 2020. Given the nature of the disease, its heterogeneity and human social norms, pre-voyage and post-voyage quick testing procedures may become the new standard for cruise ship passengers and crew. The technological advances in testing available today would facilitate more humanistic treatment as compared to more archaic quarantine and isolation practices for all onboard ship. With quick testing, identification of those infected and thus not allowed to embark on a cruise or quarantining those disembarking and other mitigation strategies, the popular cruise adventure could be available safely again. Whatever the procedures implemented, the methodological purpose of this study should add valuable insight in the modeling of disease and specifically, the COVID-19 virus.

scientific communication and education↗

bioRxiv2021

Oncofly: A CURE for Cancer

Course-based Undergraduate Research Experiences (CUREs) are emerging as a means to engage large numbers of undergraduate students in meaningful inquiry-based research activities. We describe here a simple laboratory exercise as part of an undergraduate genetics course that illustrates the contributions of oncogenes and tumor suppressors to the formation of neoplasms in an invertebrate model system. In addition, students were challenged to investigate whether flies reared on a diet containing a variety of additives display a higher number of invasive tumors in the larval abdomen. The goal of the exercise was to (i) familiarize students with the multigenic origin of the cancer phenotype, to (ii) introduce some of the fundamental molecular cancer hallmarks, and to (iii) highlight the significance of invertebrate model systems in biomedical research. Furthermore, (iv) students learn to execute a molecular test for transgenic produce and (v) apply statistical tools to test a simple hypothesis. We evaluated student learning and changes in opinions and attitudes relating to environmental versus genetic causes of cancer and several common misconceptions using a questionnaire before and after completing the exercise. Overall, significant improvements in the rate of factually correct responses and reductions in uncertainty were demonstrated. Although resistance to change was apparent in regard to identifying some risk factors, there was clear learning and understanding of the core concepts of carcinogenesis and the utility of basic research with model organisms.

scientific communication and education↗

bioRxiv2021

Comprehensive mapping of local and diaspora scientists: a database and analysis of 63951 Greek scientists

Research policy and planning for a given country may benefit from reliable data on both its scientific workforce as well as the diaspora of scientists for countries with substantial brain drain. Here we use a systematic approach using Scopus to generate a comprehensive country-level database of all scientists in Greece. Moreover, we expand that database to include also Greek diaspora scientists. The database that we have compiled includes 63951 scientists who have published at least 5 papers indexed in Scopus. Of those, 35116 have an affiliation in Greece. We validate the sensitivity and specificity of the database against different control sets of scientists. We also analyze the scientific disciplines of these scientists according to the Science Metrix classification (174 subfield disciplines) and provide detailed data on each of the 63951 scientists using multiple citation indicators and a composite thereof. These analyses demonstrate differential concentrations in specific subfields for the local versus the diaspora cohorts, as well as an advantage of the diaspora cohort in terms of citation indicators especially among top-impact researchers. The approach that we have taken can be applied to map also the scientific workforce of other countries and nations for evaluation, planning and policy purposes.

scientific communication and education↗

bioRxiv2021

An open-source tool to assess the carbon footprint of research

The scrutiny over the carbon footprint of academics has increased rapidly in the last few years. This has resulted in a series of publications providing various estimates of the carbon footprint of one or several research activities, principally at the scale of a university or a research center or, more recently, a field of research. The variety of tools or methodologies - on which these estimates rely - unfortunately prevents from any direct comparison because of the sensitivity of carbon footprint assessments to variations in the scope and to key parameters such as emission factors. In an effort to enabling a robust comparison of research carbon footprints across institutions, contexts or disciplines, we present an open-source web application, GES 1point5 designed to estimate the carbon footprint of a department, research lab or team in any country of the world with a transparent and common methodology. The current version of GES 1point5, open-source and freely available, takes into account the most common and often predominant emission sources in research labs: buildings, digital devices, commuting, and professional travel. GES 1point5 is developed by an interdisciplinary team of scientists from several public research institutions in France as part of the Labos 1point5 project. GES 1point5 is therefore presently tailored for the French context but can be adjusted to any national contexts by adjusting the values of emission factors. The versatility and usability of the software have been empirically validated by its adoption by several hundred research labs in France over the last 18 months. In addition to enabling the estimation and monitoring of greenhouse gas (GHG) emissions at the scale of a research lab, GES 1point5 is designed to aggregate the data entered by the labs and the corresponding GHG emissions estimates into a comprehensive database. GES 1point5 can therefore allow to (i) identify robust determinants of the carbon footprint of research activities across a network of research labs (ii) estimate the carbon footprint of research at the national scale. A preliminary analysis of the carbon footprint of more than one hundred laboratories is presented to illustrate the potential of the approach. While assessments of carbon footprints are often externalized onto extension services and proprietary softwares, GES 1point5 is designed as a hands-on, pedagogic and transparent tool for research labs to monitor and reduce their own carbon footprint. This internalization has strong positive co-benefits for academics in terms of awareness and empowerment. We further expect that international dissemination of GES 1point5 will contribute to establishing a global understanding of the drivers of the research carbon footprint worldwide and an identification of the levers to decrease it. Availability and implementationGES 1point5 is available online at http://labos1point5.org/ges-1point5 and its source code can be downloaded from the GitLab platform at https://framagit.org/labos1point5/l1p5-vuejs.

scientific communication and education↗

bioRxiv2021

Overburdening of peer reviewers. A multi-disciplinary and multi-stakeholder perspective on causes, effects and potential policy implications

Peer review of manuscripts is labour-intensive and time-consuming. Individual reviewers often feel themselves overburdened with the amount of reviewing they are requested to do. Aiming to explore how stakeholder groups perceive reviewing burden and what they believe to be the causes of a potential overburdening of reviewers, we conducted focus groups with early-, mid-, and senior career scholars, editors, and publishers. By means of a thematic analysis, we aimed to identify the causes of overburdening of reviewers. First, we show that, across disciplines and roles, stakeholders believed that the reviewing workload has become so enormous that the academic community is no longer able to supply the reviewing resources necessary to address its demand for peer review. Second, the reviewing workload is distributed unequally across the academic community, thereby overwhelming small groups of scholars. Third, stakeholders believed the overburdening of reviewers to be caused by (i) an increase in manuscript submissions; (ii) insufficient editorial triage; (iii) a lack of reviewing instructions; (iv) difficulties in recruiting reviewers; (v) inefficiencies in manuscript handling and (vi) a lack of institutionalisation of peer review. These themes were assumed to mutually reinforce each other and to relate to an inadequate incentive structure in academia that favours publications over peer review. In order to alleviate reviewing burden, a holistic approach is required that addresses both the increased demand for and the insufficient supply of reviewing resources.

scientific communication and education↗

bioRxiv2021

A national analysis of trends in COVID-19 infection and clinical management in Veterans Health Administration medical facilities

OBJECTIVEWe explored longitudinal trends in sociodemographic characteristics, reported symptoms, laboratory findings, pharmacological and non-pharmacological treatment, comorbidities, and 30-day in-hospital mortality among hospitalized patients with coronavirus disease 2019 (COVID-19). METHODSThis retrospective cohort study included 43,267 patients diagnosed with COVID-19 in the Veterans Health Administration between 03/01/20 and 08/31/20 and followed until 09/30/20. We focused our analysis on patients that were subsequently hospitalized, and categorized them into groups based on the month of hospitalization. We summarized our findings through descriptive statistics. We used a nonparametric rank-sum test for trend to examine any differences in the distribution of our study variables across the six months. RESULTSDuring our study period, 8,240 patients were hospitalized, and 1,081 (13.1%) died within 30 days of admission. Hospitalizations increased over time, but the proportion of patients that died consistently declined from March (N=221/890, 24.8%) to August (N=111/1,396, 8.0%). Patients hospitalized in March compared to August were younger on average, mostly black, and symptomatic. They also had a higher frequency of baseline comorbidities, including hypertension and diabetes, and were more likely to present with abnormal laboratory findings including low lymphocyte counts and elevated creatinine. Lastly, receipt of mechanical ventilation and Hydroxychloroquine declined from March to August, while treatment with Dexamethasone and Remdesivir increased. CONCLUSIONWe found evidence of declining COVID-19 severity and fatality over time within a national health care system.

scientific communication and education↗

bioRxiv2021

Randomized controlled studies comparing traditional lectures versus online modules

We assessed the efficacy of traditional lectures versus online modules with respect to student learning in an undergraduate introductory biochemistry course in two successive years. In the first year, students had the options of attending live lectures by the course instructor and viewing online modules pre-recorded by the instructor, with the lectures and modules covering identical content; in addition, all students had a mandatory weekly application session. Utilizing pre-course and post-course tests as an instrument with which to measure learning during the course, we observed significantly increased learning (0.7 standard deviations) with attendance of traditional lectures and decreased learning with use of online modules, even after adjustment for grade point average. In the second year, the course had the same curriculum, but students were randomized to either live lectures or online modules for the first half of the course, crossing over to the other modality during the second half. With randomization, no difference in learning was observed between the two groups. Furthermore, we found that students self-reported greater engagement when viewing online modules than when attending lectures in person. These findings suggest some aspects of the lecture experience can be shifted to online modules in STEM courses without impacts on student learning so as to use classroom time more fully for application-based active learning interventions.

scientific communication and education↗

bioRxiv2021

COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study

COVID-19 pandemic is the largest unprecedented viral pandemic of the 21st century. We aimed to study the COVID-19 knowledge, attitudes, and practices (KAP) among medical and health sciences students in the United Arab Emirates (UAE). We performed a cross-sectional study between 2nd June and 19th August 2020. The survey was developed using online Survey Monkey. The link was distributed via UAE University to all students and via WhatsApp(C) groups. The self-administered questionnaire was conducted in English and comprised of two parts: socio-demographic characteristics and KAP towards COVID-19. A total of 712 responses to the questionnaire were collected. 90% (n=695) were under-graduate, while 10% (n=81) were post-graduate students. Majority (87%, n=647) stated that they obtained COVID-19 information from multiple reliable sources. They were highly knowledgeable about COVID-19 pandemic but 76% (n=539) did not recognize its routes of transmission. 63% (n=431) were worried of getting COVID-19, while 92% (n=633)) were worried that a family member could get infected with the virus. 97% (n=655) took precautions when accepting home deliveries, 94% (n=637) had been washing their hands more frequently, and 95% (n=643) had been wearing face masks. In conclusion, participants showed high levels of knowledge and awareness about COVID-19. They were worried about getting infected themselves or their family members, and had good practices against COVID-19.

scientific communication and education↗

bioRxiv2021

Alignment of biomedical data repositories with open, FAIR, citable and trustworthy principles

Increasing attention is being paid to the operation of biomedical data repositories in light of efforts to improve how scientific data is handled and made available for the long term. Multiple groups have produced recommendations for functions that biomedical repositories should support, with many using requirements of the FAIR data principles as guidelines. However, FAIR is but one set of principles that has arisen out of the open science community. They are joined by principles governing open science, data citation and trustworthiness, all of which are important aspects for biomedical data repositories to support. Together, these define a framework for data repositories that we call OFCT: Open, FAIR, Citable and Trustworthy. Here we developed an instrument using the open source PolicyModels toolkit that attempts to operationalize key aspects of OFCT principles and piloted the instrument by evaluating eight biomedical community repositories listed by the NIDDK Information Network (dkNET.org). Repositories included both specialist repositories that focused on a particular data type or domain, in this case diabetes and metabolomics, and generalist repositories that accept all data types and domains. The goal of this work was both to obtain a sense of how much the design of current biomedical data repositories align with these principles and to augment the dkNET listing with additional information that may be important to investigators trying to choose a repository, e.g., does the repository fully support data citation? The evaluation was performed from March to November 2020 through inspection of documentation and interaction with the sites by the authors. Overall, although there was little explicit acknowledgement of any of the OFCT principles in our sample, the majority of repositories provided at least some support for their tenets.

scientific communication and education↗

bioRxiv2021

Publication practices during the COVID-19 pandemic: Biomedical preprints and peer-reviewed literature

The coronavirus pandemic introduced many changes to our society, and deeply affected the established in biomedical sciences publication practices. In this article, we present a comprehensive study of the changes in scholarly publication landscape for biomedical sciences during the COVID-19 pandemic, with special emphasis on preprints posted on bioRxiv and medRxiv servers. We observe the emergence of a new category of preprint authors working in the fields of immunology, microbiology, infectious diseases, and epidemiology, who extensively used preprint platforms during the pandemic for sharing their immediate findings. The majority of these findings were works-in-progress unfitting for a prompt acceptance by refereed journals. The COVID-19 preprints that became peer-reviewed journal articles were often submitted to journals concurrently with the posting on a preprint server, and the entire publication cycle, from preprint to the online journal article, took on average 63 days. This included an expedited peer-review process of 43 days and journals production stage of 15 days, however there was a wide variation in publication delays between journals. Only one third of COVID-19 preprints posted during the first nine months of the pandemic appeared as peer-reviewed journal articles. These journal articles display high Altmetric Attention Scores further emphasizing a significance of COVID-19 research during 2020. This article will be relevant to editors, publishers, open science enthusiasts, and anyone interested in changes that the 2020 crisis transpired to publication practices and a culture of preprints in life sciences.

scientific communication and education↗

bioRxiv2021

Signal processing basics applied to Ecoacoustics

Ecoacoustics is a research field that has attracted attention of researchers from areas as diverse as ecology, biology, engineering, and human sciences, to cite a few. Ecoacoustics studies the sounds that emanates from the environments, by gaining insights of landscape dynamics from acoustic patterns and particularities at different places. With recent advance in technology, it is common to obtain sound datasets recorded 24-h a day for several months. The analysis of these long-term sound recordings represents several challenges. Investigators already involved in acoustic are familiar with signal processing methods, which are essential tools for sound analysis. However, in general beginners interested in Ecoacoustics do not share this background formation. The present work illustrates basic topics of digital signal processing in a comprehensible style, and an effective pipeline for long-term sound explorative data analysis (EDA) is presented. Finally, the described signal processing fundamentals are applied for EDA of 1-month underwater acoustic data recorded in a Brazilian marine protected area. The Matlab codes used for the analysis will be available as supplementary material.

scientific communication and education↗

bioRxiv2021

Estimating the societal disease burden of East Coast fever among rural cattle keeping households of Namwala District, Zambia

The study aimed to estimate the disease burden of East Coast fever (ECF) among rural cattle keeping households of Namwala District of Zambia using Productivity Adjusted Life Years (PALYs). We modified Disability Adjusted Life Year (DALY) equations for humans to PALYs to estimate the societal burden of animal diseases. We used a structured questionnaire to collect data on parameters that feed into PALY equations. We coded and entered data from questionnaires directly into Statistical Package of Social Sciences (IBM SPSS Version 20), and entered the estimated values of PALY parameters into Mathematical Calculus Software called Integral Calculator (https://www.integral-calculator.com/). We then used the integral calculator to calculate PALY equations, which we used to estimate the societal disease burden of ECF in cattle. PALYs calculations were done in three categories; PALYs without discounting and age weighting, PALYs with only discounting, and PALYs with discounting and age weighting. Results revealed that the years of productivity lost by a cow, bull, and ox that suffered from ECF were estimated at 15, 10, and 15 years, respectively. In the second category, the years of productivity lost by a cow, bull, and ox were seven, six, and seven years, respectively. In the final category, the years of productivity lost by a cow, bull, and ox were five years. ECF caused a total of 517,165 PALYs in Namwala District. The quality of life reduced in years due to disability (YLD) caused by ECF per cow, bull, and ox was 0.07, 0.07, and 0.02 percent of their life expectancy, respectively. The estimated values for the years of a lifetime lost due to mortality (YLL) caused by ECF were 35, 49, and 35 percent of the life expectancy per cow, bull, and ox. These results are important for measuring outcomes of animal health problems in terms of PALYs. The findings are helpful in future projections for the future burden of any disease and can be used as a basis in policy-making and decision-making, particularly on priorities in animal health research. We recommend that a classification of animal diseases of national economic importance should consider both the societal burden and economic impact instead of the common practice of only considering the economic impact.

scientific communication and education↗

bioRxiv2021

Mentorship as a strategy to improve research ability of students and young researchers in Africa: an exploratory study and initial findings on the CORE Africa Research Mentorship Scheme

Mentorship provides an opportunity to support skill development, improve research ability, promote interest in research and offer career advice. The need for research mentorship in Africa is well-recognised. However, there is scarce literature on the development of such programmes and their potential impacts on students and young researchers in Africa (SYRIA). This study documents the development of the CORE Africa Research Mentorship Scheme (CARMS), and reports the outcomes and challenges experienced over a two-year period, from 2018 to 2020. 41 mentors and mentees from Cameroon, Uganda and Nigeria participated in the programme. Mentors were based in Africa and the UK, while mentees were all based in Africa. Mentees gained knowledge and skills in various research areas including proposal writing, research methods, data analysis, report writing and research publication. Nine mentees gained their first research publication through the CARMS and three successfully completed their first grant proposal. Three mentees were supported by their mentor to develop PhD research proposals and five others gained skills that helped them secure paid research jobs. Eleven mentees have graduated from the programme, seven of which are currently enrolled as trainee mentors. Mentees appreciated the opportunity to improve on their research skills and felt that the programme gave them a safe environment to freely express their concerns. Main challenges encountered were: difficulty finding suitable mentors, communication barriers, poorly defined mentorship goals, dealing with mentees lack of knowledge/experience of basic research concepts and funding limitations. This programme had several positive impacts on the knowledge and skills of mentees and demonstrates the importance of mentorship in research capacity strengthening. Sustaining such programmes requires investments in training and development, to ensure that mentees are continuously and adequately supported.

scientific communication and education↗

bioRxiv2021

The effect of mentee and mentor gender on scientific productivity of applicants for NIH training fellowships

Several studies have suggested that women in science are less productive than men, and that this gap contributes to their under-representation in the ranks of senior researchers. However, few studies have examined the role of mentoring, and in particular mentor gender, on the productivity of female scientists early in their careers. Such efforts are limited by the difficulties of unambiguously linking mentees to their mentors and measuring the research productivity resulting from those relationships. Here we use our novel author disambiguation solution to investigate the role of self-identified gender in mentorship of 12,932 trainees who either successfully or unsuccessfully applied to the National Institutes of Health for research fellowships between fiscal years 2011 and 2017, applying a multi-dimensional framework to assess productivity. We found that, after normalizing for the funding level of mentors, the productivity of female and male mentees is indistinguishable; it is also independent of the gender of the mentor, other than in measures of clinical impact, where women mentored by women outperform other mentee-mentor dyads.

scientific communication and education↗

bioRxiv2021

LIFE AND WORK OF RESEARCHERS TRAPPED IN THE COVID-19PANDEMIC VICIOUS CYCLE

AO_SCPLOWBSTRACTC_SCPLOWCOVID-19 has disrupted researchers work and posed challenges to their life routines. We have surveyed 740 researchers of which 66% experienced a decrease in productivity, 50% indicated increased workload, and 66% reported they have been feeling internal pressure to make progress. Those whose research required physical presence in a lab or the field experienced considerable disruption and productivity decrease. About 82% of this group will try to permanently reduce their work dependency on physical presence. Parents and those taking care of vulnerable dependents have been spending less time on research due to their role conflict. We further observed a gender gap in the overall disruption consequences; more female researchers have been experiencing a reduction in productivity and external pressure to make progress. The results of this study can help institution leaders and policymakers better understand the pandemics challenges for the research community and motivate appropriate measures to instill long-term solutions.

scientific communication and education↗

bioRxiv2021

'Nepotistic journals: a survey of biomedical journals.

ContextConvergent analyses in different disciplines support the use of the Percentage of Papers by the Most Prolific author (PPMP) as a red flag to identify journals that can be suspected of questionable editorial practices. We examined whether this index, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using a large sample of biomedical journals. MethodsWe extracted metadata for all biomedical journals referenced in the National Library of Medicine, with any attributed Broad Subject Terms, and at least 50 authored (i.e. by at least one author) articles between 2015 and 2019, identifying the most prolific author (i.e. the person who signed the most papers in each particular journal). We calculated the PPMP and the 2015-2019 Gini index for the distribution of articles across authors. When the relevant information was reported, we also computed the median publication lag (time between submission and acceptance) for articles authored by any of the most prolific authors and that for articles not authored by prolific authors. For outlier journals, defined as a PPMP or Gini index above the 95th percentile of their respective distributions, a random sample of 100 journals was selected and described in relation to status on the editorial board for the most prolific author. Results5 468 journals that published 4 986 335 papers between 2015 and 2019 were analysed. The PPMP 95th percentile was 10.6% (median 2.9%). The Gini index 95th percentile was 0.355 (median 0.183). Correlation between the two indices was 0.35 (95CI 0.33 to 0.37). Information on publication lag was available for 2 743 journals. We found that 277 journals (10.2%) had a median time lag to publication for articles by the most prolific author(s) that was shorter than 3 weeks, versus 51 (1.9%) journals with articles not authored by prolific author(s). Among the random sample of outlier journals, 98 provided information about their editorial board. Among these 98, the most prolific author was part of the editorial board in 60 cases (61%), among whom 25 (26% of the 98) were editors-in-chief. DiscussionIn most journals publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications. The papers by these authors were more likely to be accepted for publication within 3 weeks of their submission. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

scientific communication and education↗