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bioRxiv2021

Establishing CREATE: Lessons learned in setting up a training environment for early-career researchers in respiratory medicine

BackgroundThe purpose of the National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis (CRE-PF) is to improve and extend the lives of patients living with pulmonary fibrosis through the development of a comprehensive and integrated program of basic and clinical research and education across Australia. A key objective of the CRE-PF was establishment of a unique national training scheme, CREATE, for early-career researchers (ECRs) in respiratory research. CREATE ECRs are broadly drawn from two main fields of researchers: clinicians and scientists, where clinicians tend to be involved in part-time translational research and scientists are involved in broad scientific research including laboratory or genetic research, health economics or population research. MethodsWe describe the CREATE Program which, with limited budget and the assistance of key organisations, has provided funding opportunities (scholarships, fellowships, prizes, travel and collaboration grants), professional development (mentoring program, symposia, presentation opportunities and on-line training) and fostered a connected, supportive research community for respiratory ECRs. ResultsThe CREATE program has successfully fostered the development of the supported researchers, contributing substantially to the future of pulmonary fibrosis research in Australia. During the life of the program the CRE-PF has offered 10 PhD scholarships and five postdoctoral fellowships, awarded 13 travel grants and three grants to promote collaboration between ECRs from different institutes. A mentoring program has been established and CREATE Symposia have been held in association with key meetings. During COVID-19 restrictions, a series of virtual research meetings has offered 12 CREATE ECRs from seven universities the opportunity to present their research to a national audience. CREATE research-related achievements are impressive, including over 80 first-author publications by ECRs, and many conference presentations. Contributions to the research community, measured by committee membership, is also strong. ConclusionsIn spite of a very limited budget, wide geographic distribution of participants and the multi-disciplinary nature of the cohort, we have succeeded in providing a unique, supportive academic development environment for CREATE ECRs. Lessons learned in the process of developing this program include the importance of leveraging funding, being flexible, building networks and seeking and responding to ECR input.

scientific communication and education↗

bioRxiv2022

Discussion-based DEI education to help create inclusive and open BME research lab environments

Diversity in teams has been shown to enhance creativity and innovation, particularly in teams where all members felt a sense of belonging. Creating an inclusive environment in a lab setting that provides a sense of belonging to all is challenging. This is particularly true in a field like Biomedical Engineering/Bioengineering where diversity is multifaceted and includes peoples diverse personal/cultural backgrounds and also diverse scientific backgrounds. In a research lab, there is additional diversity in training, as most labs contain trainees at different levels (undergrad, grad, postdoc, high school). To aid in creating a sense of belonging in a research lab, we have devised a novel initiative based upon open group discussions on diversity, equity, and inclusion topics. The initiative included a first presentation/discussion by the PI to set the stage for defining diversity, equity, and inclusion, and provided examples of existing DEI issues within our field, such as lack of racial diversity in awards like the NIH New Innovator Award and among conference speakers. After the initial presentation, trainee-led, bi-weekly-structured discussions were maintained. First, discussions focused broadly on any DEI related topic to enhance general knowledge on DEI issues and provide discussion comfort among the group. Second, there was a period to deepen knowledge of a specific topic (in our example, microaggressions), which was followed up with a period of discussions on potential solutions (such as how to react when observing a microaggression and what to do in response to realizing ones own microaggression). Students reported that our discussions were the only ones they have had in their training thus far, and felt that these discussions made them feel like they belonged in the lab, made the lab more inclusive, enhanced their awareness of how to create inclusive spaces, and taught them about a variety of DEI topics. Overall, our DEI discussions have fostered open conversations within our lab group about DEI-related issues and topics at the lab, department, university, and countrywide levels and has established a space where students feel safe to voice their opinions and ask questions. We hope to ultimately use these DEI discussions to create actionable steps for addressing topics, e.g., microaggressions, in different scenarios that can be applied by group members in their future careers.

scientific communication and education↗

bioRxiv2023

Undergraduates' reactions to errors mediates the association between growth mindset and study strategies

BackgroundStudents employ a variety of study strategies to learn and master content in their courses. Strategies vary widely in their effectiveness for promoting deep, long-term learning, yet most students use ineffective strategies frequently. Efforts to educate students about effective study strategies have revealed that knowledge about effective strategies is by itself insufficient for encouraging widespread and lasting changes. An important next step is to uncover factors that influence the decisions students make about study strategy use. We explored the association between beliefs about intelligence (mindset, universality, and brilliance) and study strategies. The most effective study strategies are error-prone, and beliefs about intelligence carry implications for whether errors are a normal and even beneficial part of the learning process (e.g., growth mindset) or signs of insufficient intelligence (e.g., fixed mindset). Therefore, we hypothesized that beliefs about and reactions to errors would mediate a relationship between beliefs about intelligence and study strategies. We tested this hypothesis by surveying 345 undergraduates enrolled in an introductory biology class at a public, research-active university in northwestern United States. ResultsConfirmatory factor analysis indicated that the internal structure of all measures functioned as expected in our sample. We fit a structural equation model to evaluate our hypothesized model. We found that mindset, but not universality nor brilliance, predicts variance in both beliefs about errors and reactions to errors. In turn, adaptive reactions to errors (but not beliefs about errors) are associated with the use of highly effective study strategies and spacing study sessions. There was a significant indirect relationship between growth mindset and spacing of study sessions. ConclusionsOur results provide evidence for a mechanism explaining the association between students mindset beliefs and academic outcomes: believing that intelligence is improvable is associated with more adaptive reactions to making errors, which correlates with choosing more error-prone and therefore more effective study strategies. Future interventions aimed at improving students study strategies may be more effective if they simultaneously target reacting adaptively to errors and emphasize that intelligence is improvable.

scientific communication and education↗

bioRxiv2020

Institutionalizing an Evidence-Based Practice in a Selected Government Agency in Nigeria

The need to tackle the discrepancy between research outputs and the execution of the findings into real practice is a crucial factor in establishing evidence-based practice in a selected government agency. There is a need to increase the number of experts in our education sector who can synthesise, translate, and package the evidence for ready use by decision-makers and to foster entrepreneurship in Africa. To achieve this, the activities of a 28-man Evidence Leaders in Africa (ELA) team were recruited to drive the project through capacity building training and workshop sessions. Thereafter, a non-random purposive sampling technique targeted at policy makers at various government and non-governmental organizations was adopted as the study design. In all, purposive administration of 424 copies of questionnaire to individuals in different governmental and non-governmental organizations was done by the recruited personnel. The retrieved data from the questionnaire were analyzed using standard statistical method. Socio-demographic characteristics of respondents reveal 34% representation of (31-40 years) age bracket, with (57%) of them working in the University spanning over 2 to 5years (47%) work experience. Approximately 64% of the respondents are not aware of EIDM while 71% had no understanding of EIDM. As regards knowledge of EIDM, 36% had no knowledge of EIDM, 29% had moderate knowledge, 34% were beginners while approximately 1% had advanced knowledge of EIDM. Also, approximately 99% of the respondents have neither been trained nor involved in training others in EIDM. It was also observed that 8.5% of the respondents were policy-makers in the organization, yet 90.7% of the respondents agree that EIDM is useful in policy-making while 81.3% of the respondents engage their colleagues in EIDM. From this study, it is safe to infer that institutionalizing EIDM in NNMDA has numerous benefits as shown by the findings of this study. This will only be possible when all parties involved in producing and using research evidence are well informed and knowledgeable in EIDM.

scientific communication and education↗

bioRxiv2023

Purchases dominate the carbon footprint of research laboratories

Despite increasing interest for the carbon footprint of higher education institutions, little is known about the carbon footprint associated to research activities. Air travel and attendance to conferences concentrate recent data and debates but purchases have attracted little attention. Here we develop a hybrid method to estimate the greenhouse gas emissions (GHG) associated to research purchases. To do so, we combine macroe-conomic databases, research-centered companies footprints and life-cycle assesments to construct a public database of monetary emission factors (EF) for research purchases. We apply it to estimate the purchases emissions of a hundred of research laboratories in France, belonging to the Labos 1point5 network and gathering more than 20000 staff, from all disciplines. We find that purchases dominate laboratory emissions, accounting for more than 50% of emissions, with a median of 2.7 t CO2e/pers, which is 3 to 4-fold the separate contribution from travel, commutes and heating. Median electricity emissions are 5-fold lower in our dataset of laboratories using low carbon electricity but they become preponderant for high carbon electricity mixes (3.5 t CO2e/pers). Purchases emissions are very heterogeneous among laboratories and are linearly correlated with budget, with an average carbon intensity of 0.31 {+/-} 0.07 kg CO2e/{euro} and differences between research domains. Finally, we quantify the effect of a series of demand-driven mitigation strategies obtaining up to -20 % in total emissions (-40 % in purchases emissions), suggesting that effectively reducing the carbon footprint of research activities calls for systemic changes. Significance statementResearch activities are recently interrogating their contribution to global warming, mainly through the impact of air travel but neglecting the emissions embodied in scientific purchases. However, goods and services used in a research laboratory emit greenhouse gases when they are produced. Here we construct a public and robust database of emission factors to quantify purchases emissions in a laboratory and we use it to assess emissions from a hundred of laboratories in France, from all disciplines. We find that purchases emissions represent half of the of the 6.3 t CO2e/pers per year emitted on average per laboratory. Emissions, however, vary greatly between laboratories and disciplines and an analysis of mitigation strategies shows that decreasing demand may significantly reduce purchases emissions.

scientific communication and education↗

bioRxiv2019

A qualitative study exploring researchers’ perspectives on authorship decision-making

BackgroundAuthorship has major implications for a researchers promotion and tenure, future funding, and career opportunities. Due in part to these high-stakes consequences, many journals require authors to meet formal authorship criteria, e.g. the International Committee of Medical Journal Editors (ICMJE) criteria for authorship. Yet on multiple surveys, researchers admit to violating these criteria, suggesting that authorship practices are a complex issue. Using qualitative methods, we aimed to unpack the complexities inherent in researchers conceptualizations of questionable authorship practices and to identify factors that make researchers vulnerable to engaging in such practices.\n\nMethods and FindingsWe conducted an interview study with a purposeful sample of 26 North American medical education researchers holding MD (n=17) and PhD (n=9) degrees and representing a range of career stages. We asked participants to respond to two vignettes - one portraying honorary authorship, the other describing an author order scenario - and then to describe related authorship experiences. Through thematic analysis, we found that participants, even when familiar with ICMJE criteria, conceptualized questionable authorship practices in various ways and articulated several ethical gray areas. We identified personal and situational factors, including hierarchy, resource dependence, institutional culture and gender, that contributed to participants vulnerability to and involvement in questionable authorship practices. Participants described negative instances of questionable authorship practices as well as situations in which these practices occurred for virtuous purposes. Participants rationalized that engagement in questionable authorship practices, while technically violating authorship criteria, could be reasonable when the practices seemed to benefit science and junior researchers. Participants described negative instances of questionable authorship practices as well as situations in which these practices occurred for virtuous purposes. Participants rationalized that engagement in questionable authorship practices, while technically violating authorship criteria, could be reasonable when the practices seemed to benefit science and junior researchers.\n\nConclusionAuthorship guidelines, such as the ICMJE criteria, portray authorship decisions as black and white, effectively sidestepping key dimensions that create ethical shades of gray. Our findings show that researchers generally recognize these shades of gray and in some cases acknowledge breaking or bending the rules themselves. Sometimes, their flexibility in applying rules of authorship is driven by benevolent aims that align with their own values or prevailing norms such as generosity and inclusivity. Other times, their participation in questionable authorship practices is framed not as a choice, but rather as a consequence of their vulnerability to individual or system factors beyond their control. Taken together, the findings reported here provide insights that may help researchers and institutions move beyond recognition of the challenges of authorship and contribute to the development of informed, evidence-based solutions for questionable authorship practices.

scientific communication and education↗

bioRxiv2023

Beyond performance, competence, and recognition: Forging a science researcher identity in the context of research training

Background Studying science identity development has been useful for understanding students continuation in science-related education and career paths. Yet, how science contexts shape students science identity development, especially as students engage in research at the undergraduate and graduate level, is still largely unexplored. Here we integrate science identity and professional identity theories to investigate how research training shapes science identity. We focus on a specialized form of science identity we call science researcher identity. We characterize how the features of an individuals research experience, and their personal characteristics interact to influence whether and how they see themselves as a science researcher. We accomplished this in two phases of qualitative research. First, we surveyed 548 undergraduate researchers about how their research experience influenced their identity as a scientist. Then we interviewed 30 early career researchers, including undergraduate, postbaccalaureate, and doctoral students, about their views of themselves as researchers and how elements of their research training shaped their views. ResultsEarly career researchers (ECRs) viewed themselves as either science students or science researchers. How ECRs recognized themselves depended on how they viewed the purpose of their daily work and the extent to which they perceived autonomy and intellectual responsibility in their research. Individual-level factors, including research and researcher conceptions, research skill perceptions, and career intentions, influenced whether ECRs identified as science students or science researchers. ECRs also recognized themselves more or less as researchers based on contextual factors like the nature of their work, social interactions, and their perceptions of the norms within their research group and institution. ECRs considered how individual and contextual factors affected their science researcher identity through a lens we call sense-making. We further detail the processes ECRs use to make sense of their science identity and the factors that influence it. ConclusionsWe synthesized our findings to form a conceptual model of science researcher identity development, which hypothesizes relationships among constructs related to science identity and professional identity development. Our results advance theory related to science identity, offer avenues for future investigation, and inform efforts to promote science researcher identity development.

scientific communication and education↗

bioRxiv2022

Putting on academic armor: How Black physicians and trainees take stances to make racism visible amidst publishing constraints

IntroductionWhile there are a growing number of empirical studies of Black physicians and trainees experiences of racism, there are still few accounts from a first-person perspective. These personal commentaries or editorials require taking a delicate stance, balancing the professional, social, and individual. Black authors in the medical publishing space, who already experience microaggressions and racial trauma in their work spaces, must put on their academic armor to further experience them in publishing spaces. Medicine and medical education interpellate each of us, including the authors and readers of this piece, as a particular kind of subject. Beginning with a narrative grounding in the authors personal stances, this study seeks to understand the stances Black physicians and trainees take as they share their personal experiences of racism while protecting the institution of medicine from racisms irreparable harms. MethodsThe authors searched four databases identifying 29 articles authored by Black physicians and trainees describing their experiences. During initial analysis, the authors identified three sets of discursive strategies: identification (introducing and tracking themselves throughout the article); intertextuality (dialoguing and drawing on other "texts" beyond the focus of the articles); and space-time (social constructions of space and time linked to a network of social practices). The authors used a Google form to capture these strategies and direct quotes from the articles. Throughout the study, the authors reflected on their own stances in relation to the experience of conducting the study and its findings. ResultsAuthors engaged in stance taking, which aligned with the concept of donning academic armor, by evaluating and positioning themselves with respect to racism and the norms of academic discourse in response to ongoing conversations both within medicine and in the broader US culture. They did this by (a) positioning themselves as being Black and, therefore, qualified to notice and name personal racist experiences while also aligning themselves with the reader through shared professional experiences and goals, (b) intertextual connections to other related events, people, and institutions that they-and their readers-value and (c) aligning themselves with a hoped-for future rather than a racist present. DiscussionBecause the discourses of medicine and medical publishing interpellate Black authors as Others they must carefully consider the stances they take, particularly when naming racism. The academic armor they put on must not only be able to defend them from attack, but help them slip unseen through institutional bodies replete with mechanisms to eject them. In addition to analyzing their own personal stance, authors leave readers with thought provoking questions regarding this armor as they return to narrative grounding.

scientific communication and education↗

bioRxiv2025

Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a secure cloud-based environment where research and education communities can analyze genomic and biomedical data. The platform supports a wide range of data analysis as well as the ability to safely store and access data in compliance with NIH policies. Work on the AnVIL platform can be easily shared to promote reproducible science and collaboration. The purpose of this study is to better understand the current user base of the AnVIL platform. The AnVIL Community Poll aimed to collect baseline information, identify development opportunities, guide the prioritization of user support strategies, and succinctly but comprehensively describe the current AnVIL Community. The AnVIL Team disseminated the inaugural AnVIL Community Poll by sharing it broadly on social media and through AnVIL and related consortia mailing lists. We categorized respondents as either returning or potential users of the AnVIL platform (based on their provided usage description) and examined user experiences: specifically user backgrounds, technological comfort, research interests, computational needs, and preferences for training and support. Our sample of the AnVIL community found opportunities for platform adoption beyond the current user base and identified areas where training should be enhanced, training preferences, and user computational needs. Specifically, while most respondents were involved in human genomics research, there may be potential for growth in adoption of the platform by prioritizing materials to support clinical researchers. All respondents felt availability of specific tools or datasets was a key feature of the platform. The broader community may also benefit from further development or showcasing of resources to facilitate cost management, finding and incorporating analysis tools, and data import. Our sample greatly preferred virtual training opportunities and returning users of the platform foresaw needing large amounts of storage. This poll provided an insightful snapshot of the current state of the AnVIL and demonstrated areas where the AnVIL Team can take specific steps to address barriers related to platform adoption and further support the existing and varied AnVIL Community. This work can be built upon through user interviews, community discussion, and coordinating a recurring poll.

scientific communication and education↗

bioRxiv2025

Enhancing CRISPR Education: A Plug-And-Play Framework for Teaching Gene Editing in Plant Biology

Modern molecular biology tools and technologies such as CRISPR have sped up scientific discovery. From an educational perspective, these advancements are both exciting and overwhelming. Educators shaping these future scientists face the ongoing challenge of staying compliant with the latest developments in molecular biology while finding effective ways to teach these discoveries. As the use of CRISPR gene editing technology continues to expand globally, there is an increasing need for a workforce that is both knowledgeable about its theoretical foundations and trained in its practical use. While advanced, technology-driven STEM courses have the potential to improve student retention, they are often lecture-heavy and lack intentional engagement strategies that support deeper learning. Moreover, agriculture is the second most impacted sector by this technology, yet there is a significant lack of teaching materials focused on CRISPR in plant biology. To address these gaps, we developed a framework for teaching gene editing that incorporates multiple engagement strategies beyond traditional lecture-based instruction. This framework was implemented over two semesters in an Introduction to Gene Editing course at Tennessee State University, offered to both undergraduate and graduate students enrolled in a degree in Agricultural Sciences. This manuscript outlines the various strategies used in the course including active learning, multimodal instructional approaches and experiential learning strategies that can be adopted in other classrooms to effectively teach gene editing. Survey-based results from the course indicate a measurable increase in student comfort with designing and executing CRISPR-Cas based experiments. Societal Impact StatementPlant biology lacks accessible teaching materials for CRISPR, a powerful gene-editing technology widely used to improve agriculture. We developed an engaging framework to teach CRISPR concepts to advanced undergraduates and graduate students in plant sciences, which can be readily adopted by other instructors. The approach increased self-reported confidence in students and comfort in explaining CRISPR. Since instructors often have limited time to design interactive lessons, this framework offers a ready-to-use, effective strategy that makes CRISPR more widely available in classrooms, ultimately strengthening CRISPR literacy in the future agricultural workforce.

scientific communication and education↗

bioRxiv2026

PREP-aring is worth it: Success of the Case Western Reserve University Post-baccalaureate Research Education Program and its Scholars

The Post-baccalaureate Research Education Program (PREP), established by the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health in 2000, was a research-intense, one-year training program for recent college graduates from backgrounds uncommon in science who intended to matriculate with a PhD or MD/PhD program in preparation for an eventual career in biomedical research. Case Western Reserve University had an NIGMS-supported PREP (CasePREP) from 2007 to 2025, the year NIGMS terminated the PREP funding mechanism. A major goal of CasePREP was to prepare post-baccalaureate trainees (termed Scholars) for graduate school, and major metrics of success were measured as Scholars who a) matriculated in and b) completed PhD or MD/PhD programs. A major goal of NIGMS-supported PREPs was the retention of these scientists in the biomedical research workforce. We report here the extent that CasePREP met program goals as well as the economic and scientific impact NIGMS-supported PREP has had for a variety of stakeholders. Data from 18 CasePREP cohorts included self-reported (surveys, interviews, questionnaires) and public data (websites, PubMed, NIH Reporter). Descriptive statistics and large language models were used to describe the major outcomes related to program goals and a new resilience course as well as Scholar productivity and contribution to science. Between 2007 and 2025, CasePREP was awarded $5.6 million USD and trained 108 Scholars. Most (89%) Scholars resided outside of Ohio prior to the start of CasePREP, with 38.89% from Puerto Rico. Almost all (98%) Scholars completed the one-year program in Cleveland, Ohio, and of those, 83% entered a PhD or MD/PhD program. As of September 2025, 46 Scholars have completed a PhD program, two Scholars have completed an MD/PhD program, and 27 are still in training. The attrition rate for CasePREP Scholars in graduate school is currently 14.77%, much lower than the attrition rates of national PhD programs. Most CasePREP Scholars (69.44%) are co-authors on one or more published manuscripts, and these 406 published works have garnered 14,261 total citations, with an average 35.04 citations per publication. Termination of PREP represents a five-year loss of [~]$2.7 million USD to CasePREP, a budget that would have trained an additional 30 Scholars. CasePREP was a great success as measured by its major outcomes. CasePREP Scholars have persisted in science and have made substantial contributions to the scientific workforce and enterprise. PREPs in general provided a crucial bridge for research talents who had little prior research opportunities to realize their potential and career goals. NIGMS termination of PREP support has negative economic consequences and endangers an important pathway to a career in science for Americans who would not otherwise have similar opportunities.

scientific communication and education↗

bioRxiv2024

Deepening biomedical research training: Community-Building Wellness Workshops for Post-Baccalaureate Research Education Program (PREP) Trainees

ProblemAll trainees, especially those from historically minoritized backgrounds, experience stresses that may reduce their continuation in science, technology, engineering, math, and medicine (STEMM) careers. The Johns Hopkins University School of Medicine is one of [~]45 institutions with a National Institutes of Health funded Postbaccalaureate Research Education Program (PREP) that provides mentoring and a year of fulltime research to prepare students from historically excluded groups for graduate school. Having experienced the conflation of stresses during the COVID-19 pandemic and related shutdown, we realized our program lacked a component that explicitly helped PREP Scholars recognize and cope with non-academic stresses (financial, familial, social, mental) that might threaten their confidence and success as scientists and future in STEMM. InterventionWe developed an early-intervention program to help Scholars develop life-long skills to become successful and resilient scientists. We developed a year-long series comprised of 9 workshops focused on community, introspection, financial fitness, emotional intelligence, mental health, and soft-skills. We recruited and compensated a cohort of PhD students and postdoctoral fellows to serve as Peer Mentors, to provide a community and the safest space for Scholars to discuss personal concerns. Peer Mentors were responsible for developing and facilitating these Community-Building Wellness Workshops (CBWW). ContextCBWW were created and exectued as part of the larger PREP program. Workshops included a PowerPoint presentation by Peer Mentors that featured several case studies that prompted discussion and provided time for small-group discussions between Scholars and Peer Mentors. We also included pre- and post-work for each workshop. These touch-points helped Scholars cultivate the habit of introspection. ImpactThe CBWW exceeded our goals. Both Peer Mentors and Scholars experienced strong mutual support, and Scholars developed life-long skills. Notably, several Scholars who had been experiencing financial, mental or mentor-related stress immediately brought this to the attention of program leadership, allowing early and successful intervention. At the completion of CBWW, PREP Scholars reported implementing many workshop skills into practice, were reshaping their criteria for choosing future mentors, and evaluating career decisions. Strikingly, Peer Mentors found they also benefitted from the program as well, suggesting a potential larger scope for the role of CBWW in academia. Lessons LearnedPeer Mentors were essential in creating a safe supportive environment that facilitated discussions, self-reflection, and self-care. Providing fair compensation to Peer Mentors for their professional mentoring and teaching contributions was essential and contributed meaningfully to the positive energy and impact of this program.

scientific communication and education↗

bioRxiv2014

How many digits in a mean are worth reporting?

Most bioscientists need to report mean values, yet many have little idea of how many digits are significant, and at what point further digits are mere random junk. Thus a recent report that the mean of 17 values was 3.863 with a standard error of the mean (SEM) of 2.162 revealed only that none of the seven authors understood the limitations of their work. The simple rule derived here by experiment for restricting a mean value to its significant digits (sig-digs) is this: the last sig-dig in the mean value is at the same decimal decade as the first sig-dig (the first non-zero) in the SEM. An extended rule for the mean, and a different rule for the SEM itself are also derived. For the example above the reported values should be a mean of 4 with SEM 2.2. Routine application of these simple rules will often show that a result is not as compelling as one had hoped.

Scientific Communication and Education↗

bioRxiv2014

A plea for evidence in ecosystem service science: a framework and its application

The ecosystem service concept is at the interface of ecology, economics and politcs, with scientific results rapidly translated into management or political action. This emphasises the importance of reliable recommendations provided by scientist. We propose to use evidence-based practice in ecosystem service science in order to evaluate and improve the reliability of scientific statements. For this purpose, we introduce a level-of-evidence scale ranking study designs (e.g. review, case-control, descriptive) in combination with a study quality checklist. For illustration, the concept was directly applied to 12 case studies. We also review criticisms levered against evidence-based practice and how it applies to ecosystem services science. We further discuss who should use the evidence-based concept and suggest important next steps, with a focus on the development of guidelines for methods used in ecosystem service assessments.

Scientific Communication and Education↗

bioRxiv2014

Characterization of the Peer Review Network at the Center for Scientific Review, National Institutes of Health

The National Institutes of Health (NIH) is the largest source of funding for biomedical research in the world. This funding is largely effected through a competitive grants process. Each year the Center for Scientific Review (CSR) at NIH manages the evaluation, by peer review, of more than 55,000 grant applications. A relevant management question is how this scientific evaluation system, supported by finite resources, could be continuously evaluated and improved for maximal benefit to the scientific community and the taxpaying public. Towards this purpose, we have created the first system-level description of peer review at CSR by applying text analysis, bibliometric, and graph visualization techniques to administrative records. We identify otherwise latent relationships across scientific clusters, which in turn suggest opportunities for structural reorganization of the system based on expert evaluation. Such studies support the creation of monitoring tools and provide transparency and knowledge to stakeholders.

Scientific Communication and Education↗

bioRxiv2014

An evidence assessment tool for ecosystem services and conservation studies

Reliability of scientific findings is always important, but even more so in ecosystem service science, where results can directly lead to policy implementations. The assessment of reliability resulted in the introduction of the evidence-based concept in the medical sciences. It aims at identifying the best available information to answer the question of interest. In environmental sciences, the evidence-based concept is well developed [very few people actually use it!] in conservation, but so far no guidelines exists for ecosystem services science. To apply the evidence-based concept in practice we need a scale to rank study designs commonly used in ecosystem services science as well as an assessment of the actual quality of implementation in a specific study. Here, we define a framework for evidence-based ecosystem service science, together with a design scale and a critical-appraisal checklist. The approach is described with detailed examples and specific suggestions for different user groups.

Scientific Communication and Education↗

bioRxiv2014

From peer-reviewed to peer-reproduced: a role for data standards, models and computational workflows in scholarly publishing

MotivationReproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP) and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.\n\nResultsExecutable workflows were developed using Galaxy which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata.\n\nAvailabilitySOAPdenovo2 scripts, data and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/. Contact: philippe.rocca-serra@oerc.ox.ac.uk and susanna.assunta-sansone@oerc.ox.ac.uk

Scientific Communication and Education↗

bioRxiv2015

Association of TSH level above 2.1 mlU/L and first trimester pregnancy loss in anti-TPO antibody negative women

Although the exact level of TSH that is indicative of risk of pregnancy loss is not known, a number of studies have suggested a range of values for TSH level that are associated with first trimester pregnancy loss. We conducted an unmatched case-control study to test if a TSH level above 2.1 mlU/L is associated with first trimester pregnancy loss in anti-TPO antibody negative women. We found relatively higher number of women in the case group (18) whose TSH level was above 2.1 mlU/L compared to 7 women in control group. When considered patients in Group I (TSH [≤] 2.1 mlU/L), 45.74% had miscarriage while 54.26% did not have miscarriage within first trimester of pregnancy. Among the Group II patients (TSH > 2.1 mlU/L), 78% had miscarriage and 28% did not have miscarriage. Noticeably there is a larger proportion of miscarriage among the women with TSH level above 2.1 mlU/L. The association between TSH level and first trimester pregnancy loss was statistically significant (p=.0196). From the multivariate analysis, odds ratio for TSH level (OR 4.0, 95% CI: 1.44-11.16) indicates that odds of having miscarriage whose TSH level is above 2.1 mlU/L is 4 times compared to those with TSH level below 2.1 mlU/L after adjusting for the effects of age and BMI. At a global level, the findings of this study provide evidence to the existing discussion on redefining the upper limit of TSH level that is related to first trimester pregnancy loss. At the local level, the results will have direct implication in facilitating management of future pregnancies particularly during the first trimester among Bangladeshi thyroid autoantibody negative women. (268 words)

Scientific Communication and Education↗