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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 19 recordsLinked to original sources

bioRxiv2023

MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR

MolecularWebXR is a new website for education, science communication and scientific peer discussion in chemistry and biology, based on modern web-based Virtual Reality (VR) and Augmented Reality (AR). With no installs as it is all web-served, MolecularWebXR enables multiple users to simultaneously explore, communicate and discuss concepts about chemistry and biology in immersive 3D environments, by manipulating and passing around objects with their bare hands and pointing at different elements with natural hand gestures. User may either be present in the same real space or distributed around the world, in the latter case talking naturally with each other thanks to built-in audio features. Although MolecularWebXR is most immersive when running in the web browsers of high-end AR/VR headsets, its WebXR core also allows participation by users with consumer devices such as smartphones, possibly inserted into cardboard goggles for deeper immersivity, or even in computers and tablets. MolecularWebXR comes with preset VR rooms that cover topics from general, inorganic and organic chemistry, biophysics and structural biology, and general biology; besides, new content can be added at will through moleculARwebs PDB2AR tool or by contacting the lead authors. We verified MolecularWebXRs ease of use and versatility by people aged 12-80 years old in entirely virtual sessions or in mixed real-virtual sessions at various science outreach events, in courses at the bachelor, masters and early doctoral levels, in scientific collaborations, and in conference lectures. MolecularWebXR is available for free use without registration at https://molecularwebxr.org, and a blog post version of this preprint with embedded videos is available at https://go.epfl.ch/molecularwebxr-blog-post.

scientific communication and education↗

bioRxiv2022

CellScape: Protein structure visualization with vector graphics cartoons

MotivationIllustrative renderings of proteins are useful aids for scientific communication and education. Nevertheless, few software packages exist to automate the generation of these visualizations. ResultsWe introduce CellScape, a tool designed to generate 2D molecular cartoons from atomic coordinates and combine them into larger cellular scenes. These illustrations can outline protein regions in different levels of detail. Unlike most molecular visualization tools which use raster image formats, these illustrations are represented as vector graphics, making them easily editable and composable with other graphics. Availability and ImplementationCellScape is implemented in Python 3 and freely available at https://github.com/jordisr/cellscape. It can be run as a command-line tool or interactively in a Jupyter notebook. Contactjordisr@berkeley.edu

bioinformatics↗

bioRxiv2021

Lecture-based, problem-based, digital problem-based and distance learning on knowledge improvement in medical education: a meta-analysis

Problem-based learning (PBL), an educational approach well applied in education, was believed as a deep method that can promote problem solving, and critical thinking. Varies implementation of PBL across different settings were introduced. How to objectively evaluate knowledge effectiveness of PBLs remains a challenge. The present study is aiming to systematically investigate the knowledge improvement between types of PBL in medical education. Our meta-analysis showed that distance learning using digital PBL could be a good alternative to traditional learning in medical education.

scientific communication and education↗

bioRxiv2025

Comparing AI and Human Mentoring in Supporting Dental Student Well-being: A Mixed-Methods Study

BackgroundDental education is associated with high psychological distress among students, exacerbated by intensive clinical training and variable institutional support. Traditional mentoring programs mitigate such challenges, yet faculty shortages and resource constraints necessitate exploration of alternative models. Artificial intelligence (AI) platforms such as ChatGPT offer potential supplemental mentoring support; however, their comparative effectiveness in health professions education remains underexplored. MethodsThis comparative, convergent mixed-methods study was conducted at SEGi University, Malaysia, involving 31 Year 4 dental students receiving human mentoring and 36 Year 5 students utilizing ChatGPT as an AI mentor. Quantitative outcomes were assessed using the Depression, Anxiety, and Stress Scale (DASS-21), the Perceived Mentor Support Scale (PMSS), and the Mentoring Effectiveness Scale (MES). Qualitative data were collected through focus groups and analysis of ChatGPT interaction logs. Statistical analyses included paired t-tests and ANOVA, while thematic analysis was used for qualitative data integration. ResultsYear 4 students demonstrated significant reductions in stress, anxiety, and depression scores (p < 0.001) and greater improvements in perceived mentor support (p < 0.001) and mentoring effectiveness (p < 0.001) compared to Year 5 students. Year 5 students reported modest gains following ChatGPT mentoring, highlighting strengths in accessibility and immediacy but limitations in emotional resonance. Qualitative themes underscored human mentors superior capacity for emotional attunement, while ChatGPT was valued for availability and practical support. ConclusionsWhile AI-based mentoring via ChatGPT shows promise in enhancing mentoring accessibility, human mentorship remains critical for addressing the emotional and relational needs of dental students. Careful integration of AI tools into hybrid mentorship models could optimize support systems, particularly in resource-constrained educational environments. Future research should explore ethical frameworks and training strategies to enhance empathetic AI mentorship in health professions education.

scientific communication and education↗

bioRxiv2020

Acculturation stressors and academic adjustment among Nepalese students in South Korean higher education institutions

IntroductionInternational students are steadily increasing in South Korean higher education institutions. How well international students in South Korea are adjusted academically and the relationship between acculturation stressors and academic adjustment has not yet been determined. The study aimed to fill this research gap by examining the relationship between acculturation stressors and academic adjustment among Nepalese international students in South Korean higher education institutions. MethodsThe sample of the study consisted of Nepalese international students who enrolled in 36 universities in South Korea. Students background characteristics and acculturation stressors (e.g., discrimination, homesickness, hate/rejection, fear, cultural shock, and guilt) were selected to assess the association of these characteristics and stressors with academic adjustment. Pearson correlation and hierarchical multiple regression were utilized to examine the association between acculturation stressors and academic adjustment. ResultsThe results from the Pearson correlation revealed the negative correlation of perceived discrimination (r = -.23, p< 0.01), perceived hate/rejection (r = -.18, p< 0.05), perceived fear (r = -.24, p< 0.01), and perceived cultural shock (r = -.17, p< 0.05) with academic adjustment. Further, the hierarchical regression model revealed that marital status ({beta} = .223, p <.01) had a positive association with academic adjustment, whereas perceived fear ({beta} = -.206, p <.05) had a negative association with academic adjustment even after including students background characteristics and other acculturation stressors. ConclusionAddressing acculturation stressors among international students in higher education institutions is essential to facilitate positive academic adjustment. Mainly, perceived fear has negatively affected students academic adjustment. Based on these findings, tailored programs must be developed to curtail students perceived fear in order to enhance their academic performance in South Korean higher education institutions.

scientific communication and education↗

bioRxiv2020

Combining formal education and citizen science: A case study on students' perceptions of learning and interest in an urban rat project

Citizen science is a valuable tool in environmental and formal education in creating scientific knowledge for the researchers and facilitating learning and fostering a positive relationship toward the environment and study species. We present a case study on the Helsinki Urban Rat Project in which students surveyed rat occurrence in their own near environments. According to our results, experientiality, involvement, meaningfulness, freedom to choose, ease of participation, and the rats themselves contributed to students increased interest in participation. Furthermore, students described diverse factual, conceptual, procedural, and metacognitive knowledge that they acquired during their participation. In general, students described negative attitudes toward rats, but they described fewer negative views on rats after participation. We reflect on the success of the citizen science project and implications of planning a future citizen science project and incorporating citizen science in formal education.

scientific communication and education↗

bioRxiv2022

Second Climate Survey of Biomedical PhD Students in the Time of Covid

In July 2021, sixteen months into the Covid-19 pandemic, the institutional climate for PhD training in the School of Medicine was assessed for a second time. This survey of graduate students occurred 1 year after initial surveys of graduate students and training faculty in July 2020. The 2021 survey was completed by 99 PhD students in 11 PhD-granting programs. To allow comparisons between years, most of the 2021 questions were repeated with only minor edits. A few items were added to assess impacts of school-wide town hall meetings, a new PhD career club program, and enlarged mental health services. Several themes emerged. Students remain extremely concerned about the pandemics impact upon their training and long-term career prospects. They worry specifically about pandemic related reductions in research productivity and networking opportunities. Many students successfully adapted to laboratory research under pandemic restrictions but suffer from the continuing lack of social interaction even after in-person work hours increased. Symptoms of anxiety and/or depression persist amongst 46% of the students, as compared to 51% in 2020. Nearly 80% of students continue to report strong satisfaction with mentoring relationships with their dissertation advisors, but to lesser extents with programs (66%), departments or centers (71%), the School of Medicine (32%) and the University (49%). Students (26%) express interest in the Ombuds office that was announced in late 2021. Some students wrote that the medical school could do a better job in embracing diversity and inclusion and in mentor training, and many stated that town hall meetings do not serve them well. Coping mechanisms shared by some students demonstrate impressive resilience. These results present a mixed picture. While aspects of biomedical PhD training have begun to recover as the pandemic continues, long-term consequences of the disruption raise challenges that must be addressed by efforts to restore and improve the learning environment required for 21st century research education.

scientific communication and education↗

bioRxiv2018

Four assessment methods to measure student gains in a graduate course on mathematical modeling in cell biology

The push for mathematics and quantitative skill development in biology is greater than ever before. The perceptions of these techniques are a barrier to their implementation on a grand scale. Methods to assess the efficacy of approaches to teaching quantitative skills are needed to determine if they effectively overcome social stereotypes and fears of math. In our project we study the effect of a mathematical modeling course in cell biology. We developed four assessments to understand if hands-on modeling increases student understanding of the concepts while simultaneously reducing fear of math. Two concept inventories track students learning gains both in general and specific knowledge to the course content. Two surveys quantify students quantitative confidence and opinions of the usefulness of these techniques in biology. We discuss the effectiveness of our methods and the implications for assessment development in mathematical biology education.

scientific communication and education↗

bioRxiv2021

Instructor-learner neural synchronization during elaborated feedback predicts learning transfer

The provision of feedback with complex information beyond the correct answer, i.e., elaborated feedback, can powerfully shape learning outcomes such as transfer, i.e., the ability to extend what has been learned in one context to new contexts. However, an understanding of neurocognitive processes of elaborated feedback during instructor-learner interactions remains elusive. Here, a two-person interactive design is used during simultaneous recording of functional near-infrared spectroscopy (fNIRS) signals from adult instructor-learner dyads. Instructors either provided elaborated feedback (i.e., correct answer and an example) or simple feedback (i.e., correct answer only) to learners during a concept learning task. Our results showed that elaborated feedback produced comparable levels of retention to simple feedback, however, transfer was significantly enhanced by elaboration. We also noted significant instructor-learner neural synchronization in frontoparietal regions during the provision of elaborated feedback, especially when examples were provided. Further, interpersonal neural synchronization in the parietal cortex successfully predicted transfer of knowledge to novel contexts. This prediction was retained for both learner-delayed and learner-preceding neural synchronization. These findings point toward transfer effects of elaborated feedback provided in a social context can be predictable through interpersonal neural synchronization, which may hold important implications for real-world learning and pedagogical efficacy. Educational Impact and Implications StatementFeedback provides learners with crucial information regarding the gap between what has currently been achieved and what remains to be achieved, and thus plays a critical role in any learning process. In real-world settings, feedback is typically provided and received through social interaction, and high-quality "elaborated feedback" contains complex information that goes beyond the correct answer. This study aims to elucidate the neurocognitive processes underpinning elaborated feedback during instructor-learner interactions. We detected significant instructor-learner neural synchronization in mutual frontoparietal brain regions during elaborated feedback, particularly during the provision of specific elaborated information (i.e., concrete examples). Moreover, this synchronization (including learner-delayed and learner-preceded synchronization) in the parietal region predicted whether the learners transferred learning to novel examples of learned psychology concepts. This study advances current understanding on the neural mechanisms for elaborated feedback and the role of social interaction in feedback effects. These results may have important implications for successful real-world learning and communication, and related pedagogical applications in educational settings.

scientific communication and education↗

bioRxiv2025

Improving science communication and organization visibility through Wikipedia: A case study of the American Association for Anatomy

Wikipedia is one of the most widely accessed sources of scientific information globally, serving as a critical platform for public understanding and engagement with science. Despite its influence, many scientific societies are underrepresented or insufficiently described on the platform, limiting their visibility, outreach potential, and opportunities for public scholarship. This gap is particularly significant given Wikipedias high placement in search engine results and its role in shaping perceptions of scientific institutions. To address this issue, a structured case study was conducted focusing on the Wikipedia article for the American Association for Anatomy (AAA). A baseline evaluation revealed major deficiencies in article structure, historical coverage, citation quality, and alignment with Wikipedias editorial standards. Using a methodical editing process informed by science communication principles and content guidelines, the article was substantially revised. High-quality secondary sources were used to develop new sections on AAAs mission, governance, publications, awards, meetings, and outreach efforts. Following these edits, the articles classification improved from Stub to Start-class, its visibility and connectivity within Wikipedia increased, and the number of internal and external references, links, and structural elements grew substantially. This outcome demonstrates that scholarly engagement with Wikipedia can meaningfully enhance institutional presence and public accessibility of scientific knowledge. This case study offers a transparent and replicable model for scientific organizations and educators seeking to improve digital visibility and contribute to open-access science. It also highlights the potential for Wikipedia editing to serve as a form of public scholarship and a high-impact educational practice within the anatomical sciences.

scientific communication and education↗

bioRxiv2023

Detecting signals of critical transition in inclusive teaching in biology education: A computational text analysis of CourseSource

We examine every Inclusive Teaching section in articles published by the journal CourseSource - undergraduate biology teaching materials and related essays - from 2014 to 2022 to understand the evolution of inclusive teaching ideas as expressed through language. We find a rapid shift in attention to inclusive teaching occurs between 2018 and 2019, marked by an increase in section length, increased use of inclusive teaching keywords, and an increase in complexity of ideas in the semantic network. This critical transition occurs before many of the recent events in 2020 which have renewed conversation on equity in education. Some effect is associated with Writing Workshop Faculty Mentoring Networks, which provide participants with authoring resources and support. However, this alone is not enough to explain the observed shift, suggesting that many other structures, conversations, and investments were already providing the fertile ground for educational equity in biology education.

scientific communication and education↗

bioRxiv2025

THE IMPACT OF ARTIFICIAL INTELLIGENCE ON UNIVERSITY STUDENTS PERCEPTIONS OF ENVIRONMENTAL CHALLENGES AND SUSTAINABLE SOLUTIONS

In the context of Vietnams higher education strongly transforming towards digitalization and sustainability, this study aims to analyze the impact of artificial intelligence (AI) on students awareness and intention to act for the environment. Based on the Extended Planned Behavior (TPB) model, the research model integrates two input factors: environmental awareness (EA) and the level of interaction with AI in environmental learning (AEEL), affecting three mediating factors: attitude (AT), subjective norm (SN) and perceived behavioral control (PBC), thereby predicting students green action intention (GAI). Data collected from 521 students at private university in Vietnam were processed using EFA, CFA and SEM. The results showed that both EA and AEEL had positive effects on AT, SN and PBC (p < 0.001). Among them, AEEL had the strongest influence on SN ({beta} = 0.281) and PBC ({beta} = 0.252). PBC had the strongest influence on GAI ({beta} = 0.312), followed by AT ({beta} = 0.274) and SN ({beta} = 0.267). Bootstrapping mediation analysis confirmed that the mediating variables (AT, SN, PBC) played an important role in linking EA and AEEL with GAI. In addition, cluster analysis showed that female students and senior students had significantly higher levels of AI engagement and action intention. These results suggest that AI not only serves as a learning support tool but also as a catalyst for sustainable behavior in higher education.

scientific communication and education↗

bioRxiv2020

Developing bio-technical reliability among future researchers and industrial work-force in developing countries: a success story

A common problem in the biotech sector of developing countries is that a large portion of students attain a poor conceptual understanding of the basic theory and/or lack proficiency in basic laboratory skills even as they complete higher studies such as a masters degree. A small scale solution was developed in the form of a unique post-graduate diploma program that imparted reliable skills in students with good theoretical knowledge. The course of 6 to 8 months duration, with an optional 6 months internship, was successfully conducted for 8 batches. Most students of this course inculcated the right laboratory practices. This was evident by safe operations, and precise as well as accurate results of quantitative experiments conducted by them. They learned to work independently as well as in teams. They could create and follow standard operating procedures, and contribute to general laboratory maintenance. Every student also designed, prepared and conducted routine molecular biology experiments. The following aspects are suggested for successfully dealing with the patchy and varied capacities of life science students during higher (post bachelors) studies: a) careful selection of students, b) training with prioritized objectives, c) attention to basic lab-practices, d) opportunities to self-learn, e) structured group discussions, f) teacher(s) with genuine interest and passion, g) reasonable infrastructure, and h) maintaining a good student-instructor ratio. The course objectives, structure, teaching methods, and experiences are presented here along with some of the relevant data, including statistics about improvement in the precision and accuracy in experimental results by students. Limitations in this course and a general critical perspective of the routine higher education have also been discussed briefly.

scientific communication and education↗

bioRxiv2024

The influence of visual attention on letter recognition and reading acquisition in Arabic

The present study sets out to explore the cognitive underpinnings of reading acquisition in Arabic. Previous studies have identified phonological awareness and rapid automatized naming as early predictors. However, the graphic complexity of Arabic letters imposes particular constraints on the visual system, which should mobilize visual attention. To test this hypothesis, 101 Arabic-speaking children who just began their formal reading instruction in Arabic were administered tests of syllable and word reading. Their nonverbal reasoning, vocabulary, phonological awareness, rapid automatized naming and letter knowledge were measured. Their visual attention was estimated through tasks of visual attention span. We found that phonological awareness, visual attention span and letter knowledge were associated with reading outcomes. However, regression analyses showed that the relationship between visual attention span and reading disappeared when letter knowledge was taken-into-account. We used structural equation modeling to examine the direct and indirect effects of visual attention span to reading. Results showed that phonological awareness and letter knowledge were significant and independent predictors of reading while visual attention span contributed only indirectly through its influence on letter knowledge. Our findings suggest that beginning readers rely on visual attention to identify and discriminate visually-complex Arabic letters. In turn, more efficient letter identification in children with higher visual attention facilitates reading acquisition. These findings support the cognitive models of word recognition that include visual attention as a component of the reading system. They open new perspectives for cross-language studies, suggesting that visual attention might contribute differently to reading depending on the orthographic system. They also provide a foundation for innovative teaching methodologies in Arabic language education.

scientific communication and education↗

bioRxiv2018

A Strategy Study on Risk Communication of Pandemic Influenza ----A Mental Model Study of College Students in Beijing

Understanding the risk perception of pandemic influenza can improve the risk communication efficiency of the government and ultimately reduce losses caused by the disaster. A mental model interview of 28 individuals who discussed pandemic influenza was analyzed in this paper. The interviewees were college students in Beijing, China who were evaluated to understand their views on the risk perception of pandemic influenza. Referring to the mental model theory, the researchers using Delphi method to identify the key risk factors and concepts to examine the public understanding of these contents; then, the researchers identify the deviations in their understanding so that suggestions and countermeasures have been put forward to enhance the effectiveness of risk communication. Most of the conceptual content was mentioned by most interviewees. However, some interviewees showed misunderstanding including excessive optimism about the consequences of pandemic influenza, a lack of detailed mitigation measures, and negative attitudes toward health education and vaccination. Once faced with threats, this may lead to the failure of risk communication. In Beijing City, the center of domestic and international education, the historical SARS epidemic and this years seasonal flu peak are all hints of the potential risk of a pandemic outbreak. Beijings college students one-sided understanding and misunderstanding of the relevant risk information may increase the risk during an influenza pandemic. The results highlight the necessity for the government to clearly focus on the communication content of the student group, provide an official reference plan for the public and update health education on this topic.

scientific communication and education↗

bioRxiv2022

Perception of RNA Nanotechnology among students and recommendations towards improved educational outreach

Translating new technologies to industrial and biomedical applications requires a highly skilled workforce. In the past, colleges and graduate schools played a primary role in preparing students for various areas of industry and medicine. The learning process and introduction of new concepts have recently extended beyond college education. High schools saw the rise of specialized career programs, while both high and middle school curricula got infused with challenging concepts. Nucleic acids, such as DNA and RNA, are broadly known for their role in the foundation of life. However, nucleic acid nanotechnology, an area of material science manipulating DNA and RNA to create complex structures with controlled properties, is less known. Herein, I report the results of a study investigating the perception of RNA nanotechnology among school students and suggest educational resources to improve understanding of RNA nanotechnology.

scientific communication and education↗

bioRxiv2026

Aesthetic Appreciation and Environmental Values: A Cross-Cultural Study of Teachers in 34 Countries

BackgroundThe relationship between aesthetic appreciation and environmental values remains a critical yet under-researched area in environmental psychology. Although the Two-Major Environmental Values (2-MEV) model--encompassing preservation and utilization dimensions--serves as a standard framework for assessing environmental attitudes, the integration of aesthetic perception within this structure has largely remained unexplored. This study investigates the conceptual linkages across a diverse international sample to determine whether aesthetic appreciation functions independently of a traditional environmental value framework. Methods and FindingsWe conducted a large-scale, cross-sectional survey involving 11,800 pre- and in-service teachers across 34 countries. Participants environmental values were evaluated using the 2-MEV scale, while their aesthetic appreciation of nature and the built environment was assessed using Osgoods semantic differential technique. Employing principal component analysis, hierarchical exploratory factor analysis (EFA), analysis of variance (ANOVA), and within-class analysis (WCA), we accounted for cross-national variations and evaluated response consistency. The results demonstrate that aesthetic appreciation comprises two distinct dimensions-- focusing separately on nature and the built environment--that operate independently of traditional preservation and utilization values, showing only weak correlations. Furthermore, while the overarching psychological structure remains consistent globally, our findings reveal significant cross-national variations in respondent scores, particularly concerning utilization-related values. ConclusionsThese findings establish that aesthetic appreciation constitutes a distinct psychological construct separate from conventional environmental value frameworks. The observed cross-cultural variability underscores the necessity of accounting for national and cultural contexts when designing environmental education programs. By leveraging a robust, comprehensive global dataset, this study provides a vital empirical foundation for integrating aesthetic and value-based dimensions into future environmental research and educational policy.

scientific communication and education↗

bioRxiv2021

Sleep Medicine Knowledge Among Graduating Medical Students in Lebanon During an Economic and Political Crisis

ObjectivesSleep disorders are prevalent and underrecognized during both economic and political crises. They are a major reason for poor overall health and decreased quality of life. Sleep medicine education is limited at most medical schools, resulting in limited awareness of this important aspect of healthcare. The aim of the study is to assess sleep medicine knowledge of graduating medical students in Lebanon and to assess their readiness to tackle sleep health issues in a country during an unprecedented crisis. MethodsFinal-year medical students at 7 medical schools in Lebanon were invited to fill a survey between January 2020 and March 2021. The Assessment of Sleep Knowledge in Medical Education survey was used to assess their knowledge in sleep medicine. The curriculum organizers at the medical schools were also surveyed. Students t-test was used for analysis. Results158 and 58 students completed the survey during 2020 and 2021, with a mean overall score on sleep knowledge of was 17.5 and 15.9 /30, respectively. There was no difference in mean knowledge scores by gender, age, American versus European medical school systems, and between medical schools that included sleep medicine in their curriculum versus those that did not. ConclusionsPresence of sleep medicine education in the curriculum was associated with higher scores on ASKME among graduating Lebanese medical students. Overall, the new crop of physicians in Lebanon possesses a relatively good knowledge base in sleep medicine. Nevertheless, more effort should be made to uniformly maintain this level of sleep education.

scientific communication and education↗