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Research Productivity and Training Support for Doctoral Students in the Biological and Biomedical Sciences

Training of doctoral students as part of the next generation of the biomedical workforce is essential for sustaining the scientific enterprise in the US. Training of doctoral students primarily occurs at institutions of higher education and these trainees comprise an important part of the workforce at these institutions. Federal investment in the support of doctoral students in the biological and biomedical sciences is distributed differently than the distribution of students across different types of institutions, e.g. Public vs Private. Institutions in states that historically receive less federal support for research also receive less support for doctoral student training. Analysis of F31 awardees at different types of institution reveal little difference in research productivity and subsequent receipt of additional NIH awards. Analysis of a large cohort of doctoral students at different types of institutions also reveal little difference in research productivity, with the exception of citations. Thus, training outcomes, which are related to the quality of the student and training environment, are similar across different institutions. Factors that correlate with F31 funding include R01 funding levels and program size. The findings suggest strategies for institutions to increase success at securing F31s and modification of policy to promote more equitable distribution of F31s across institutions.

scientific communication and education↗

3D Digitizing An Animal Organ Could Make It Possible To Work With Anatomy Classes In The Metaverse Or With A 3D-Printed Real-Scale Organ On Demand

Organ scanning is not a novel technology but the unique part of this study is to eliminate the need for expensive devices by using free iOS/Android applications. The apps allow users to create high-quality 3D models from photos taken with a phone or tablet. Metaverse and 3D digitization are the future of technology. Implementation of these approaches into the anatomy can change education style. Also, 3D printing technology along with the digitization of real-sized organs enables researchers and clinicians to study with 3D printed organs in class, even with augmented reality glasses. In this study, we first aimed to 3D digitized an animal organ with its real sizes to print in a 3D printer. Next, we wanted to digitize decellularized form of the organ, which suggests researchers study extracellular matrix and vascularization. This digitization of the different organ forms can improve the progression of artificial organ studies. Free and easy-to-use iOS or Android applications for 3D digitization enable medical students to study not only animal organs but cadavers. Hereby, we are suggesting organ scanning can be done on a daily basis in a standard laboratory. It is aimed to enable medical students to work effectively in anatomy lessons in Metaverse or in real cases, thanks to the anatomical library created with the accessibility brought by easy usability.

scientific communication and education↗

The Effects of Practice-based Training on Graduate Teaching Assistants’ Classroom Practices

Evidence-based teaching is a highly complex skill, requiring repeated cycles of deliberate practice and feedback to master. Despite existing well characterized frameworks for practice-based training in K-12 teacher education, the major principles of these frameworks have not yet been transferred to instructor development in higher educational contexts, including training of graduate teaching assistants (GTAs). We sought to determine whether a practice-based training program could help GTAs learn and use evidence-based teaching methods in their classrooms. We implemented a weekly training program for introductory biology GTAs, which included structured drills of techniques selected to enhance student practice, logic-development, and accountability and reduce apprehension. GTAs received regular performance feedback based on classroom observations. To quantify use of target techniques and levels of student participation, we collected and coded 160 hours of video footage. We found that, although GTAs adopted and utilized many of the target techniques with high frequency, techniques which enforced student participation were not stably adopted and their use was unresponsive to formal feedback. We also found that techniques discussed in training, but not practiced, were not used at quantifiable frequencies, further supporting the importance of practice-based training for influencing instructional practices.

scientific communication and education↗

Students Attitudes Surrounding STEM: A Social Cognitive Career Theory Instrument for High School

To broaden participation in science, technology, engineering, and math (STEM), we must understand the factors that shape perspectives and beliefs around career selection. Good measurement of these factors is crucial to quantify how effectively educational interventions impact student attitudes towards STEM. Adolescents are particularly suited for quantifying intervention efficacy because students build their identities during these formative years and make important career choices. To better quantify intervention efficacy at the high school level, we developed an instrument entitled Student Attitudes Surrounding STEM (SASS), which builds upon the social cognitive career theory (SCCT) framework for understanding career selection. Questionnaire responses were collected from 932 high school students and split into samples of 400 for exploratory factor analysis and 532 for confirmatory factor analysis. The 37 questions clustered into six factors: Self-Efficacy-Experience, Self-Efficacy-Academic, Outcome Expectations, Interests, Negative Perceptions of Scientists, and Career Awareness. Adequate construct validity for the factors indicated in the SASS model was suggested by the fit indices and theoretical considerations. Furthermore, the analyses supported criterion validity, internal consistency, and test-retest reliability. This tool represents a novel integration of three latent variables into SCCT: Negative Perceptions of Scientists, Career Awareness, and an experience factor for Self-Efficacy.

scientific communication and education↗

Evaluation of Postgraduate Educational Environment of Doctors Training in Psychiatry: a mixed method study

IntroductionEducational Environment (EE) is of paramount importance in Medical Education, but can be intangible and hard to clearly determine. Professional satisfaction and patient care improve in a pleasant learning environment; where postgraduate physicians are encouraged, suitably supervised, and fostered. A negative learning environment can be detrimental to trainees and teams morale and can jeopardize the multidisciplinary working relationship. ObjectivesThe objective of this study was to measure the Educational Environment (EE) of Psychiatry postgraduate training in the Midwest of Ireland training Deanery; what aspects of training are working well and what areas are seen as not optimal. MethodsThis study took place between April and June 2021. A mixed methods approach was adopted, using the Postgraduate Hospital Educational Environment Measure (PHEEM) and semi-structured one-to-one interviews. ResultsResponse rate was 88% (n=22). The total PHEEM score was 105.64{+/-}23.52, indicating a postgraduate EE with more positive than negative aspects, but with room for improvement. There were no differences in overall PHEEM and subscale scores between trainees gender, training grades or years of working experience. Three themes were identified that contribute to trainees perception of EE: the commitment of the trainees supervisors to the role they play in trainees overall development, the clinical workload of the trainee, and the day-to-day working conditions of the trainee. Definite disparities between work placements were evident in the collected data across these three themes. ConclusionsAlthough the training program had an overall positive EE, specific answers and interview themes indicated some areas of weakness that may contribute to trainee dissatisfaction and possible burnout. Planned interventions targeting these areas and tracking changes in EE and burnout rates over time may be useful measures going forward. Declaration of InterestNone

scientific communication and education↗

Graphicacy across age, education, and culture: a new tool to assess intuitive graphics skills

Data plots are widely used in science, journalism and politics, since they efficiently allow to depict a large amount of information. Graphicacy, the ability to understand graphs, thus became a fundamental cultural skill. Here, we introduce a new measure of graphicacy that assesses the ability to detect a trend in noisy scatterplots ("does this graph go up or down?"). In 3943 educated participants, responses vary as a sigmoid function of the t-value that a statistician would compute to detect a significant trend. We find a minimum level of core graphicacy even in unschooled participants living in remote Namibian villages (N=87) and 6-year-old 1st-graders who never read a graph (N=27). However, the sigmoid slope (the "graphicacy index") varies across participants, increases with education, and tightly correlates with statistical knowledge, showing that experience contributes to refining graphical intuitions. Our tool is publicly available online and allows to quickly evaluate intuitive graphics skills. STATEMENT OF RELEVANCEThe rising cost of gas, the number of Covid deaths, the evolution of temperatures during the summer months: we often face graphs depicting these phenomena. The scientific literature has shown that human adults can intuit, within milliseconds, the statistical trend of these graphs. However, we do not know if these intuitions generalized to unschooled people and, most importantly, how to measure their variations in the population. In this study we show that intuitive graphics skills are present even in 6-year-old children who never saw a graph and in the Himba of Namibia, an indigenous people with no access to formal schooling. Furthermore, we developed a quantitative assessment of such intuitive graphics skills (which we called the "graphicacy index"), that everyone can easily obtain for free, through a short (10 minutes) online test: https://neurospin-data.cea.fr/exp/lorenzo-ciccione/graphicacy-index/. In summary, our study provides the first attempt to formally quantify human intuitions of statistical graphs.

scientific communication and education↗

Establishing Normative Reference Values for the Utah Seated Medicine Ball Throw Protocol in Adolescents

The seated medicine ball throw (SMBT) is a field test intended to assess upper-body muscular power by measuring the maximal distance an individual can throw a medicine ball from an isolated, seated position (25). The SMBT has been used to assess upper-body power in various populations and to establish concurrent validity for other measures of upper-body power such as the bench press power test and the plyometric push-up. The SMBT is less costly and simpler to incorporate into a field test battery than other upper body power assessments. While the SMBT is a valid, reliable field test for upper-body power, normative reference standards for most populations, including adolescent (12-15 years old) physical education students, do not exist. PurposeThis study reports distances thrown in the SMBT to establish normative reference values in male and female physical education students, ages 12-15 years old. MethodsOne hundred thirteen untrained male and female physical education students aged 12-15 years performed the SMBT field test three times on a single testing day. Participants threw a 2kg medicine ball with a 19.5 cm diameter while seated at a 90{degrees} after recording height, body mass, and BMI. ResultsParticipant data was separated by age gender for analysis. Mean and standard deviation for the SMBT for males was 4.3{+/-}0.7m and 5.2{+/-}0.8 m for ages 12-13 and 14-15, respectively, and for females was 3.4{+/-}0.5m and 3.7{+/-}0.5m for ages 12-13 and 14-15, respectively. Pearson correlation coefficients for between-trials comparisons for males and females ranged from r=0.85-0.97. Pearson correlation coefficients for average SMBT and age of participants was r=0.93. Normative reference values as percentile ranks for the SMBT scores for age groups 12-13 and 14-15 among males and females, respectively, were also established. ConclusionThe data presented provides an initial set of normative reference standards for coaches and students to determine upper-body muscular power using the SMBT.

scientific communication and education↗

Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom

Laboratory pedagogy is moving away from step-by-step instructions and toward inquiry-based learning (IBL), but only now developing methods for integrating inquiry-based writing (IBW) practices into the laboratory course. Based on an earlier proposal (Science 332:919 (2011)), we designed and implemented an IBW sequence in a university bioinformatics course.\n\nWe automatically generated unique, double-blinded, biologically plausible DNA sequences for each student. After guided instruction, students investigated sequences independently and responded through IBW writing assignments. IBW assignments were structured as condensed versions of a scientific research paper, and because the sequences were double blinded, they were also assessed as authentic science and evaluated on clarity and persuasiveness.\n\nWe piloted the approach in a seven-day workshop (35 students) at Perdana University Graduate School of Medicine in Kuala Lumpur. We observed dramatically improved student engagement and indirect evidence of improved learning outcomes over a similar workshop without IBW. Based on student feedback, initial discomfort with the writing component abated in favor of an overall positive response and increasing comfort with the high demands of student writing. Similarly encouraging results were found in a semester length undergraduate module at the National University of Singapore (155 students).

scientific communication and education↗

Caffeinated Coli: Inspiring the Next Generation of Scientists through Synthetic Biology

The Caffeinated Coli Educational Module brings inquiry-driven learning to high schools, introducing students to scientific research, synthetic biology, and genetic engineering. The module focuses on the exploration of a genetically engineered strain of E. coli modified to grow exclusively on caffeine and, as such, can be used as a measurement device to determine the amount of caffeine in a liquid or beverage. Students conduct two bioassay experiments using these bacteria. During this process, they learn to create cultures and then measure bacterial growth followed by calculating the caffeine concentrations of unknown samples using their own data. This flexible module contains five weeks of original lectures and student learning materials that follow Next Generation Science Standards (NGSS), allowing the content to be adapted for basic, intermediate, or advanced biology courses. Upon completion of the module, students and teachers expressed that the most memorable aspects of the module include collaboration with peers, hands-on learning of content, and the opportunity to interact with the professor/mentors through office hours. Already implemented in 8 Texas high schools over the past two academic years, our module inspires STEM learning while bringing 21st century biology research to new audiences.

scientific communication and education↗

A Study of Secondary School Students Participation in a Novel Course on Genomic Principles and Practices.

This paper presents the design, development, and validation of a study among secondary school students’ participation in a novel course on genomic principles and practices by analyzing and documenting evidence of their participation, and educational outcomes, in a novel course on genomic principles and practices. A mixed methods approach, using qualitative and quantitative methods, was used to address three research questions. 1) Based on affective evidence, how did secondary school students perceive and critically judge, content topics learned in a course on modern genomic principles and practices? 2) Based on cognitive evidence, how much of the content did secondary school students learn when they participated in a course on modern genomic principles and practices? 3) Using individual interview evidence, what are the major perceptions that the secondary school students expressed throughout the duration of the course? The participants were provided an opportunity to comment on the course through individual and collaborative interviews, in order to find out to what extent they perceived the course to be interesting and challenging. Future inquiry expanding from this research would help to establish the foundational pathway for designing a more inclusive genomics curriculum. In conclusion, the course offered real-life/real-world applications that encourage all students to conceptualize genomics, human health, diseases, medicine, ethics, beliefs, research, and careers.View Full Text

scientific communication and education↗

Forging Sustainable Research: Integrating Sustainability into Neuroscience Education

The health and wellbeing of living organisms and the environment are irrevocably interconnected. Animals constantly shape the environments in which they live, and environmental factors, in turn, shape the minds and behaviours of animals. The emerging discipline of environmental neuroscience studies this reciprocal interaction and offers a unique opportunity to integrate sustainability into undergraduate training. Here, we present and evaluate Forging Sustainable Research, an interdisciplinary undergraduate course that integrates teaching of neuroscience, biology, psychology, environmental science, and sustainable development. Students explore how research in these fields can be interlinked 24 and re-oriented towards addressing emerging environmental challenges. In parallel, students learn how to measure and mitigate the environmental impact of research activities. Student feedback suggests that the course is effective at raising awareness and understanding of sustainability in research, while also enhancing student perception of their own ability to promote positive change. As climate and ecosystem change impact all sectors, sustainability awareness in academic and professional spaces is increasingly sought after. Students in the course therefore receive training in transferable skills relevant for diverse career paths. In the long term, this course may serve as model for direct integration of sustainability training into undergraduate curricula in the natural sciences.

scientific communication and education↗

Roles matter: Graduate student perceptions of active learning in the STEM courses they take and those they teach

Despite many calls to reform undergraduate science, technology, engineering, and math (STEM) education to incorporate active learning into classes, there has been little attention paid to graduate level classrooms or courses taught by graduate students. Here, we set out to understand if and how STEM graduate students perceptions of active learning change in the classes they take versus those they teach by administering surveys to STEM graduate students at our institution. We found that graduate students had taken relatively few graduate level classes using active learning and they felt that more time should devoted to active learning in the courses they were taking. Teaching assistants felt that they were devoting the right amount of class time to active learning in the classes they taught. Graduate students also felt that they were using teaching methods in the classes they taught that were different from those they thought should be used when teaching undergraduates and were different from how they preferred to learn when taking classes. These findings suggest that graduate students perceptions of teaching and learning changed based on their role in the classroom, which have implications for graduate level course work and professional development programs.

scientific communication and education↗

Datelife: leveraging databases and analytical tools to reveal the dated Tree of Life.

Achieving a high-quality reconstruction of a phylogenetic tree with branch lengths proportional to absolute time (chronogram) is a difficult and time-consuming task. But the increased availability of fossil and molecular data, and time-efficient analytical techniques has resulted in many recent publications of large chronograms for a large number and wide diversity of organisms. Knowledge of the evolutionary time frame of organisms is key for research in the natural sciences. It also represent valuable information for education, science communication, and policy decisions. When chronograms are shared in public and open databases, this wealth of expertly-curated and peer-reviewed data on evolutionary timeframe is exposed in a programatic and reusable way, as intensive and localized efforts have improved data sharing practices, as well as incentivizited open science in biology. Here we present DateLife, a service implemented as an R package and an R Shiny website application available at www.datelife.org, that provides functionalities for efficient and easy finding, summary, reuse, and reanalysis of expert, peer-reviewed, public data on time frame of evolution. The main DateLife workflow constructs a chronogram for any given combination of taxon names by searching a local chronogram database constructed and curated from the Open Tree of Life Phylesystem phylogenetic database, which incorporates phylogenetic data from the TreeBASE database as well. We implement and test methods for summarizing time data from multiple source chronograms using supertree and congruification algorithms, and using age data extracted from source chronograms as secondary calibration points to add branch lengths proportional to absolute time to a tree topology. DateLife will be useful to increase awareness of the existing variation in alternative hypothesis of evolutionary time for the same organisms, and can foster exploration of the effect of alternative evolutionary timing hypotheses on the results of downstream analyses, providing a framework for a more informed interpretation of evolutionary results.

scientific communication and education↗

Promising or problematic? Perceptions of active learning from STEM students with ADHD and specific learning disabilities

STEM instructors are encouraged to adopt active learning in their courses, yet our understanding of how active learning affects different groups of students is still developing. One group often overlooked in higher education research is students with disabilities. Two of the most commonly occurring disabilities on college campuses are attention-deficit/hyperactivity disorder (ADHD) and specific learning disorders (SLD). We investigated how the incorporation of active-learning practices influences the learning and self-advocacy experiences of students with ADHD and/or SLD (ADHD/SLD) in undergraduate STEM courses. Semi-structured interviews with 25 STEM majors with ADHD/SLD were conducted and data were analyzed using qualitative methods. Most participants perceived themselves to learn best in a STEM course with at least some elements of active learning. Participants described how they perceived active learning to support or hinder their learning and how active learning affected their self-advocacy. Active-learning barriers could be attributed to a combination of instructional factors. These factors included how a particular active-learning practice was implemented within a STEM course and limited awareness of universal design for learning. Defining the supports and barriers perceived by students with ADHD/SLD is a crucial first step in developing more inclusive active-learning STEM courses. Suggestions for research and teaching are provided.

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Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars

Universities are at long last undertaking efforts to collect and disseminate information about student career outcomes, after decades of calls to action. Organizations such as Rescuing Biomedical Research and Future of Research brought this issue to the forefront of graduate education, and the second Future of Biomedical Graduate and Postdoctoral Training conference (FOBGAPT2) featured the collection of career outcomes data in its final recommendations, published in this journal (Hitchcock et al., 2017). More recently, 26 institutions assembled as the Coalition for Next Generation Life Science, committing to ongoing collection and dissemination of career data for both graduate and postdoc alumni. A few individual institutions have shared snapshots of the data in peer-reviewed publications (Mathur et al., 2018; Silva, des Jarlais, Lindstaedt, Rotman, Watkins, 2016) and on websites. As more and more institutions take up this call to action, they will now be looking for tools, protocols, and best practices for ongoing career outcomes data collection, management, and dissemination. Here, we describe UCSF's experiences in conducting a retrospective study, and in institutionalizing a methodology for annual data collection and dissemination. We describe and share all tools we have developed, and we provide calculations of the time and resources required to accomplish both retrospective studies and annual updates. We also include broader recommendations for implementation at your own institutions, increasing the feasibility of this endeavor.

scientific communication and education↗

Ethical Shades of Gray: Questionable Research Practices in Health Professions Education

PurposeTo maintain scientific integrity and engender public confidence, research must be conducted responsibly. Whereas scientific misconduct, like data fabrication, is clearly irresponsible and unethical, other behaviors--often referred to as questionable research practices (QRPs)--exploit the ethical shades of gray that color acceptable practice. This study aimed to measure the frequency of self-reported QRPs in a diverse, international sample of health professions education (HPE) researchers.\n\nMethodIn 2017, the authors conducted an anonymous, cross-sectional survey study. The web-based survey contained 43 QRP items that asked respondents to rate how often they had engaged in various forms of scientific misconduct. The items were adapted from two previously published surveys.\n\nResultsIn total, 590 HPE researchers took the survey. The mean age was 46 years (SD=11.6), and the majority of participants were from the United States (26.4%), Europe (23.2%), and Canada (15.3%). The three most frequently reported QRPs were adding authors to a paper who did not qualify for authorship (60.6%), citing articles that were not read (49.5%), and selectively citing papers to please editors or reviewers (49.4%). Additionally, respondents reported misrepresenting a participants words (6.7%), plagiarizing (5.5%), inappropriately modifying results (5.3%), deleting data without disclosure (3.4%), and fabricating data (2.4%). Overall, 533 (90.3%) respondents reported at least one QRP.\n\nConclusionsNotwithstanding the methodological limitations of survey research, these findings indicate that a substantial proportion of HPE researchers report a range of QRPs. In light of these results, reforms are needed to improve the credibility and integrity of the HPE research enterprise.\n\nO_QD\"Researchers should practice research responsibly. Unfortunately, some do not.\" -Nicholas H. Steneck, 20061\n\nC_QD

scientific communication and education↗

Results from a conservation initiative for parrotfishes in the Colombian Caribbean

Parrotfish (Family Scaridae) are a family of herbivorous fishes crucial to coral reef health, particularly for Caribbean reefs due to their declining coral cover. However, despite parrotfish are fully protected in some countries, they are still heavy fished in most of their Caribbean range. The consequences of this targeted fishery in the Colombian Caribbean are not fully understood due to a lack of local conservation and management resources. This research aimed to evaluate and enhance the conservation status and protection of parrotfish among local communities in the National Natural Park Corales del Rosario and San Bernardo. Underwater visual census surveys (UVC) were undertaken to evaluate reef fish community structure, and participatory education campaigns and activities were carried out with local communities to raise awareness about parrotfish ecology and their functional role in conserving Caribbean coral reef ecosystems of Colombia. UVC showed parrotfish to be dominant in the fish community, yet there was evidence of exploitation of large adults by selective fishing. Conflicts exist between the community and environmental authorities because fishing regulations are not clear, and the level of enforcement is insufficient. Parrotfish are sold to tourists, as red snapper to fulfil high seafood demand since commercially valuable fish are now scarce. However, following intensive awareness-raising activities developed as part of this study, the community has started to recognize the vital ecological role of parrotfish in coral reef systems, and are suggesting a redrafting of fishing legislation by the environmental authorities, in order to recognise and incorporate the traditional fishing rights of human communities living within the MPA. Lobbying for the protection of parrotfish and inclusion of local communities in decision-making will take time, but this research represents the crucial first steps towards sustainable practice and cooperative alliances in the Colombian Caribbean.

scientific communication and education↗

FAIRsharing: working with and for the community to describe and link data standards, repositories and policies

In this modern, data-driven age, governments, funders and publishers expect greater transparency and reuse of research data, as well as greater access to and preservation of the data that supports research findings. Community-developed standards, such as those for the identification1 and reporting2 of data, underpin reproducible and reusable research, aid scholarly publishing, and drive both the discovery and evolution of scientific practice. The number of these standardization efforts, driven by large organizations or at the grass root level, has been on the rise since the early 2000s. Thousands of community-developed standards are available (across all disciplines), many of which have been created and/or implemented by several thousand data repositories. Nevertheless, their uptake by the research community, however, has been slow and uneven. This is mainly because investigators lack incentives to follow and adopt standards. The situation is exacerbated if standards are not promptly implemented by databases, repositories and other research tools, or endorsed by infrastructures. Furthermore, the fragmentation of community efforts results in the development of arbitrarily different, incompatible standards. In turn, this leads to standards becoming rapidly obsolete in fast-evolving research areas.\n\nAs with any other digital object, standards, databases and repositories are dynamic in nature, with a life cycle that encompasses formulation, development and maintenance; their status in this cycle may vary depending on the level of activity of the developing group or community. There is an urgent need for a service that enhances the information available on the evolving constellation of heterogeneous standards, databases and repositories, guides users in the selection of these resources, and that works with developers and maintainers of these resources to foster collaboration and promote harmonization. Such an informative and educational service is vital to reduce the knowledge gap among those involved in producing, managing, serving, curating, preserving, publishing or regulating data. A diverse set of stakeholders-representing academia, industry, funding agencies, standards organizations, infrastructure providers and scholarly publishers-- both national and domain-specific as well global and general organizations-- have come together as a community, representing the core adopters, advisory board members, and/or key collaborators of the FAIRsharing resource. Here, we introduce its mission and community network. We present an evaluation of the standards landscape, focusing on those for reporting data and metadata - the most diverse and numerous of the standards - and their implementation by databases and repositories. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We report on the ongoing challenge to recommend resources, and we discuss the importance of making standards invisible to the end users. We present guidelines that highlight the role each stakeholder group must play to maximize the visibility and adoption of standards, databases and repositories.

scientific communication and education↗