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bioRxiv2021

Patterns and Progress of Peninsular Malaysia's Amphibian Research in the 21st Century (2000-2020)

In this study, we review the status, patterns, and progress of Peninsular Malaysias amphibian research in the 21st century with the main goal of identifying areas for improvement that can help focus and prioritize future research initiatives. Between 2000-2020 we found 130 publications that can be broadly categorized into four groups: 1) checklists and biodiversity; 2) new species and taxonomy; 3) ecology and natural history; and 4) evolution and phylogenetics. An average of 6.5 papers was published per year and although the number of papers fluctuated, there was a significant upward trend in the number of papers published. Almost half (49%) of all papers published comprised checklists and biodiversity-related papers. This was followed by new species and taxonomy (25%, 33 papers), evolution and phylogenetics (14%, 18 papers), and ecology and natural history (12%, 16 papers). Amphibian research was conducted most frequently in the states of Kedah, Pahang, and Perak, and most infrequently in the states of Malacca, Negeri Sembilan, Selangor/Kuala Lumpur, Perlis, and Kelantan. Despite being a megadiverse country and a biodiversity hotspot, not a single conservation-centric paper has ever been published on Peninsular Malaysian amphibians, highlighting the urgent need for future research to focus on conservation.

scientific communication and education↗

bioRxiv2021

The Visual Dictionary of Antimicrobial Stewardship, Infection Control, and Institutional Surveillance

ObjectivesData and data visualization are integral parts of (clinical) decision-making in general and stewardship (antimicrobial stewardship, infection control, and institutional surveillance) in particular. However, systematic research on the use of data visualization in stewardship is lacking. This study aimed at filling this gap by creating a visual dictionary of stewardship through an assessment of data visualization in stewardship research. MethodsA random sample of 150 data visualizations from published research articles on stewardship were assessed. The visualization vocabulary (content) and design space (design elements) were combined to create a visual dictionary. Additionally, visualization errors, chart junk, and quality were assessed to identify problems in current visualizations and to provide improvement recommendations. ResultsDespite a heterogeneous use of data visualization, distinct combinations of graphical elements to reflect stewardship data were identified. In general, bar (n=54; 36.0%) and line charts (n=42; 28.1%) were preferred visualization types. Visualization problems comprised colour scheme mismatches, double y-axis, hidden data points through overlaps, and chart junk. Recommendations were derived that can help to clarify visual communication, improve colour use for grouping/stratifying, improve the display of magnitude, and match visualizations to scientific standards. ConclusionsResults of this study can be used to guide data visualization creators in designing visualizations that fit the data and visual habits of the stewardship target audience. Additionally, the results can provide the basis to further expand the visual dictionary of stewardship towards more effective visualizations that improve data insights, knowledge, and clinical decision-making.

scientific communication and education↗

bioRxiv2021

Development of a Bayesian network for probabilistic risk assessment of pesticides

Conventional environmental risk assessment of chemicals is based on a calculated risk quotient, representing the ratio of exposure to effects of the chemical, in combination with assessment factors to account for uncertainty. Probabilistic risk assessment approaches can offer more transparency, by using probability distributions for exposure and/or effects to account for variability and uncertainty. In this study, a probabilistic approach using Bayesian network (BN) modelling is explored as an alternative to traditional risk calculation. BNs can serve as meta-models that link information from several sources and offer a transparent way of incorporating the required characterization of uncertainty for environmental risk assessment. To this end, a BN has been developed and parameterised for the pesticides azoxystrobin, metribuzin, and imidacloprid. We illustrate the development from deterministic (traditional) risk calculation, via intermediate versions, to fully probabilistic risk characterisation using azoxystrobin as an example. We also demonstrate seasonal risk calculation for the three pesticides.

scientific communication and education↗

bioRxiv2021

Tapping into non-English-language science for the conservation of global biodiversity

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,680 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate, and can expand the geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence, especially in biodiverse regions, albeit often based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges.

scientific communication and education↗

bioRxiv2021

Integrating digital and field surveillance to complement efforts to manage epidemic diseases of livestock: African swine fever as a case study

The SARS-CoV-2 pandemic has unveiled the importance of stakeholders and ordinary citizens in managing infectious disease emergencies. Efficient management of infectious diseases requires a top-down approach which must be complemented with a bottom-up response to be effective. Here we investigate a novel approach to surveillance for transboundary animal diseases using African Swine fever as a model. We were able to collect data at a population level on information-seeking behavior and at a local level through a targeted questionnaire-based survey to relevant stakeholders such as farmers and veterinary authorities. Our study shows how information-seeking behavior and resulting public attention during an epidemic, can be addressed through novel data streams from digital platforms such as Wikipedia. We also bring evidence on how field surveys aimed at local workers (e.g. farmers) and public authorities remain a crucial tool to assess more in-depth preparedness and awareness among front-line actors. We conclude that they should be used in combination to maximize the outcome of surveillance and prevention activities for selected transboundary animal diseases.

scientific communication and education↗

bioRxiv2021

Reporting and Misreporting of Sex Differences in the Biological Sciences

As part of an initiative to improve rigor and reproducibility in biomedical research, the U. S. National Institutes of Health now requires the consideration of sex as a biological variable in preclinical studies. This new policy has been interpreted by some as a call to compare males and females with each other. Researchers testing for sex differences may not be trained to do so, however, increasing risk for misinterpretation of results. Using a list of recently published articles curated by Woitowich et al. (eLife, 2020; 9:e56344), we examined reports of sex differences and non-differences across nine biological disciplines. Sex differences were claimed in the majority of the 147 articles we analyzed; however, statistical evidence supporting those differences was often missing. For example, when a sex-specific effect of a manipulation was claimed, authors usually had not tested statistically whether females and males responded differently. Thus, sex-specific effects may be over-reported. In contrast, we also encountered practices that could mask sex differences, such as pooling the sexes without first testing for a difference. Our findings support the need for continuing efforts to train researchers how to test for and report sex differences in order to promote rigor and reproducibility in biomedical research.

scientific communication and education↗

bioRxiv2021

In an "ecological-belonging" intervention to reduce inequities in STEM, context matters

Doubts about belonging in the classroom are often shouldered disproportionately by students from historically marginalized groups, which can lead to underperformance. Ecological-belonging interventions use a classroom-based activity to instill norms that adversity is normal, temporary and surmountable. Building on prior studies, we sought to identify the conditions under which such interventions are effective. In a chemistry course (Study 1), students from underrepresented ethnic backgrounds underperformed relative to their peers in the absence of the intervention. This performance gap was eliminated by the intervention. In an introductory biology course (Study 2), there were no large performance gaps in the absence of the intervention, and the intervention had no effect. Study 2 also explored the role of the instructor that delivers the intervention. The intervention boosted scores in classrooms of instructors with a fixed (versus growth-oriented) intelligence mindset. Our results suggest that ecological-belonging interventions are more effective in more threatening classroom contexts.

scientific communication and education↗

bioRxiv2021

Assessing student success in a Peer Assisted Learning program using propensity score matching

The Peer Assisted Learning program at Sacramento State University (PAL) was established in 2012 with one section supporting introductory chemistry. It now serves 17 gatekeeper courses in Biology, Chemistry, Mathematics, Physics, and Statistics, enrolling approximately 1,400 students annually. Adapting the Peer-Led Team Learning model, PAL Facilitators do not teach, tutor, or even confirm answers; they do ask scaffolding questions, provide encouragement, and ensure that all group members participate in problem-solving. Here we assess the efficacy of the program in terms of student success in the parent course. As PAL is an opt-in program, we employ propensity score matching techniques to account for confounding factors. Our analysis of 11 classes shows that PAL provides an average course GPA bump ranging from .23 to .71 grade points (mean .42). Compared to the non-PAL baseline course GPA, this amounts to an increase of 9% to 51% (mean 23%). We consider data from over 25,000 students, and our propensity score analysis uses over 10,000 students (4,519 PAL, 5,814 non-PAL) for whom appropriate matches could be found.

scientific communication and education↗

bioRxiv2021

Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

Inspired by well-established material and pedagogy provided by The Carpentries (Wilson 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al. 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.

scientific communication and education↗

bioRxiv2021

'Superbugs: A Pop-up Science Shop': Increasing public awareness and knowledge of antimicrobial resistance by taking science to the city

Superbugs: A Pop-up Science Shop was a public engagement event in the school summer holidays of 2019, organised by members of Cardiff Universitys School of Medicine. We transformed an empty retail unit in the centre of Wales largest shopping centre into an interactive and immersive microbiology experience. We aimed to facilitate opportunities for two-way dialogue to impart positive impact on the awareness of antibiotic resistance, whilst concurrently evaluating the efficacy of an engagement strategy focused on the utilisation of public spaces to attract public demographics diverse to those who would normally engage with STEM outreach. Over the course of 14 days, we welcomed 6,566 visitors, with 67% attending as part of the natural footfall of the shopping centre. We created 1,625 young Antibiotic Resistance Champions, located in over 200 schools. Through a multi-lateral evaluation strategy, we were able to collect quantitative and qualitative feedback on the success of our delivery model, and the impact on our stakeholders. Herein, we will discuss the evolution of Superbugs from concept, planning and design, to the logistics of delivering an engagement event of this scale. We will focus in particular on the learning outcomes of the project, and how this will shape the future of our Superbugs project, and engagement events beyond. Key MessagesO_LICreating a multi-disciplinary core team is essential to the success of large-scale engagement events as well as the support and development of large numbers of colleagues/volunteers C_LIO_LIUtilising themes of exhibition and gameplay alongside strong fear-empowerment messages is an impactful way to confer positive influence and behaviour around antimicrobial resistance (AMR) and the use of antibiotics C_LIO_LI Pop-up shop is an effective mode of delivery to capture diverse public demographics far beyond those who would traditionally engage with scientific outreach and science engagement. C_LI

scientific communication and education↗

bioRxiv2021

Long-term quality assessment and monitoring of light microscope performance through accessible and reliable protocols, tools and metrics

Reliable, reproducible and comparable results are what biology requires from microscopy. To achieve that level of confidence, monitoring the stability of the microscope performance over time with standardized quality testing routines is essential for mining quantitative data. Three levels of microscope quality control procedures should be considered: i) usage of accessible and affordable tools and samples, ii) execution of easy and fast, preferably automatized, acquisition protocols, iii) analysis of data in the most automated way possible with adequate metrics for long-term monitoring. In this paper, we test the acquisition protocols on the mainly used microscope techniques (wide-field, spinning disk and confocal microscopy) with simple quality control tools. Seven protocols specify metrics on measuring the lateral and axial resolution (Point-Spread Function) of the system, field flatness, chromatic aberrations and co-registration, illumination power monitoring and stability, stage drift and positioning repeatability and finally temporal and spatial noise sources of camera detectors. We designed an ImageJ/FiJi java plugin named MetroloJ_QC to incorporate the identified metrics and automatize the data processing for the analysis. After processing and comparing the data of microscopes from more than ten imaging facilities, we test the robustness of the metrics and the protocols by determining experimental limit values. Our results give a first extensive characterization of the quality control procedures of a light microscope, with an automated data processing and experimental limit values that can be used by core facility staff and researchers to monitor the microscope performance over time.

scientific communication and education↗

bioRxiv2021

Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of AMR

Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having genomics facilities and adequately trained staff. Training research and public health experts who are directly involved in the establishment of such facilities offers an effective, but limited, solution to a growing need. Instead, training them to impart their knowledge and skills to others provides a sustainable model for scaling up the much needed capacity and capability for genomic sequencing and analysis locally with global impact. We designed and developed a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities. The course was delivered to 18 participants from 12 countries in Africa, Asia, and Latin America. A combination of teaching strategies culminating in a group project created a foundation for continued development at home institutions. Upon follow-up after 6 months, at least 40% of trainees had initiated training programs and collaborations to build capacity at local, national, and regional level. This work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance. 40-word summaryThis work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance. We outline a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities.

scientific communication and education↗

bioRxiv2021

EcoEvoApps: Interactive Apps for Teaching Theoretical Models in Ecology and Evolutionary Biology

O_LIThe integration of theory and data drives progress in science, but a persistent barrier to such integration in ecology and evolutionary biology (EEB) is that theory is often developed and expressed in the form of mathematical models that can feel daunting and inaccessible for students and empiricists with variable quantitative training and attitudes towards math. C_LIO_LIA promising way to make mathematical models more approachable is to embed them into interactive tools with which one can visually evaluate model structures and directly explore model outcomes through simulation. C_LIO_LITo promote such interactive learning of quantitative models, we developed EcoEvoApps, a collection of free, open-source (R/Shiny) apps that include model overviews, interactive model simulations, and code to implement these models directly in R. The package currently focuses on canonical models of population dynamics, species interaction, and landscape ecology. We also outline a vision and approach for growing the collection to include more models from across EEB. C_LIO_LIThese apps help illustrate fundamental results from theoretical ecology and can serve as valuable teaching tools in classroom settings. We present data from student surveys which show that students rate these apps as useful learning tools, and that using interactive apps leads to substantial gains in students interest and confidence in mathematical models. This points to the potential for interactive activities to make theoretical models more accessible to a wider audience, and thus facilitate the feedback between theory and data across ecology and evolutionary biology. C_LI

scientific communication and education↗

bioRxiv2021

Robust Brain State Decoding using Bidirectional Long Short Term Memory Networks in functional MRI

Decoding brain states of the underlying cognitive processes via learning discriminative feature representations has recently gained a lot of interest in brain imaging studies. Particularly, there has been an impetus to encode the dynamics of brain functioning by analyzing temporal information available in the fMRI data. Long-short term memory (LSTM), a class of machine learning model possessing a "memory" component, is increasingly being observed to perform well in various applications with dynamic temporal behavior, including brain state decoding. Because of the dynamics and inherent latency in fMRI BOLD responses, future temporal context is crucial. However, it is neither encoded nor captured by the conventional LSTM model. This paper performs robust brain state decoding via information encapsulation from both the past and future instances of fMRI data via bi-directional LSTM. This allows for explicitly modeling the dynamics of BOLD response without any delay adjustment. The two hidden activations of forward and reverse directions in bi-LSTM are collated to build the "memory" of the model and are used to robustly predict the brain states at every time instance. Working memory data from the Human Connectome Project (HCP) is utilized for validation and was observed to perform 18% better than its unidirectional counterpart in terms of accuracy in predicting the brain states.

scientific communication and education↗

bioRxiv2021

I will teach you here or there, I will try to teach you anywhere: perceived supports and barriers for emergency remote teaching during COVID-19 pandemic

BackgroundDue to the COVID-19 pandemic, many universities moved to emergency remote teaching (ERT). This allowed institutions to continue their instruction despite not being in person. However, ERT is not without consequences. For example, students may have inadequate technological supports, such as reliable internet and computers. Students may also have poor learning environments at home and may need to find added employment to support their families. Additionally, there were consequences to faculty. It has been shown that female instructors are more disproportionately impacted in terms of mental health issues and increased domestic labor. This research aims to investigate instructors and students perceptions of their transition to ERT. Specifically, we wanted to: O_LIIdentify supports and barriers during the transition to ERT C_LIO_LICompare instructors experiences with the student experiences C_LIO_LIExplore these supports and barriers within the context of social presence, teaching presence, and/or cognitive presence during ERT as well as how these supports and barriers relate to scaffolding in emergency remote courses C_LI DesignUsing grounded theory techniques, we applied two-cycle, qualitative analyses to assess the instructor transcripts. In first-cycle analysis, we used open coding to develop initial ideas from the data. We then used second cycle coding to generate categories with definitions and criteria agreed upon during discussion-based consensus building. Finally, these categories and descriptions were used to code student survey data. Analyses/InterpretationsInstructors identified twice as many barriers as supports in their teaching during the transition to ERT and identified casual and formal conversations with colleagues as valuable supports. Emerging categories for barriers consisted of academic integrity concerns as well as technological difficulties. Similarly, students identified more barriers than supports in their learning during the transition to ERT. More specifically, students described pre-existing course structure, classroom technology, and community as best supporting their learning. Barriers that challenged student learning included classroom environment, student availability, and student emotion and comfort. ContributionTogether, this research will help us understand supports and barriers to teaching and learning during the transition to ERT. This understanding can help us better plan and prepare for future emergencies, particularly at MSIs, where improved communication and increased access to resources for both students and instructors are key.

scientific communication and education↗

bioRxiv2021

Analysis of scientific journalism in Nature reveals gender and regional disparities in coverage

Science journalism is a critical way for the public to learn about and benefit from scientific findings. Such journalism shapes the publics view of the current state of science and legitimizes experts. Journalists can only cite and quote a limited number of sources, who they may discover in their research, including recommendations by other scientists. Biases in either process may influence who is identified and ultimately included as a source. To examine potential biases in science journalism, we analyzed 22,001 non-research articles published by Nature and compared these with Nature-published research articles with respect to predicted gender and name origin. We extracted cited authors names and those of quoted speakers. While citations and quotations within a piece do not reflect the entire information-gathering process, they can provide insight into the demographics of visible sources. We then predicted gender and name origin of the cited authors and speakers. We compared articles with a comparator set made up of first and last authors within primary research articles in Nature and a subset of Springer Nature articles in the same time period. In our analysis, we found a skew toward quoting men in Nature science journalism. However, quotation is trending toward equal representation at a faster rate than authorship rates in academic publishing. Gender disparity in Nature quotes was dependent on the article type. We found a significant over-representation of names with predicted Celtic/English origin and under-representation of names with a predicted East Asian origin in both in extracted quotes and journal citations but dampened in citations.

scientific communication and education↗

bioRxiv2021

Inequalities in the Distribution of National Institutes of Health Research Project Grant Funding

Previous reports have described worsening inequalities of National Institutes of Health (NIH) funding of principal investigators. We analyzed data through the end of Fiscal Year 2020, confirming worsening inequalities beginning at the time of the NIH budget doubling (1998-2003), but finding that trends have reversed over the past 3 years. We also find that career-stage trends have stabilized, with equivalent proportions of early-, mid-, and late-career investigators funded from 2017 to 2020. Women continue to constitute a greater proportion of funded principal investigators, though not at parity. Analyses of funding inequalities over time show that inequalities have consistently been greater within groups (i.e., within groups by career stage, gender, race, and degree) than between groups.

scientific communication and education↗

bioRxiv2021

An Experimental Test of the Effects of Redacting Grant Applicant Identifiers on Peer Review Outcomes

Blinding reviewers to applicant identity has been proposed to reduce bias in peer review. This experimental test used 1200 NIH grant applications, 400 from Black investigators, 400 matched applications from White investigators, and 400 randomly selected applications from White investigators. Applications were reviewed by mail in standard and redacted formats. Redaction reduced, but did not eliminate, reviewers ability to correctly guess features of identity. The primary, pre-registered analysis hypothesized a differential effect of redaction according to investigator race in the matched applications. A set of secondary analyses (not pre-registered) used the randomly selected applications from White scientists and tested the same interaction. Both analyses revealed similar effects: Standard format applications from White investigators scored better than those from Black investigators; redaction reduced the size of the difference by about half (e.g. from a Cohens d of 0.20 to 0.10 in matched applications); redaction caused applications from White scientists to score worse but had no effect on scores for Black applications. The primary statistical test of the study hypothesis was not significant; the secondary analysis was significant. The findings support further evaluation of peer review models that diminish the influence of applicant identity.

scientific communication and education↗