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bioRxiv2024

Enhancing student comprehension of paternity assignment in molecular primatology: a pilot study using a Shiny web application in Kenya

Kinship is a major determinant of affiliative and mating behavior in primates. In field studies, identifying kin typically relies in part on genetic analysis, especially for discriminating paternal relationships. Such analyses assume knowledge of Mendelian inheritance, genotyping technologies, and basic statistical inference. Consequently, they can be difficult for students to grasp, particularly through traditional lecture formats. Here, we investigate whether integrating an additional active learning approach--interaction with a Shiny web application, DadApp, which implements a popular paternity inference approach in an accessible graphical user interface--improves student understanding of genetic kinship analysis in molecular primatology. We do so in the context of a non-traditional learning environment in Kenya, a developing nation in which students have limited access to technology, and where the efficacy of educational Shiny apps has never been assessed. Twenty-eight (28) participants with diverse educational backgrounds attended an introductory lecture on genetics and paternity inference, completed a pre-test, interacted with DadApp via a structured set of exercises and questions, and then completed a post-test and survey about their experience and subjective understanding. Post-test scores significantly improved relative to pre-test scores (p-value=3.75 x 10-6 . Further, student interest and confidence in the subject matter significantly increased after the practical session with DadApp. Our results suggest that Shiny web app-based active learning approaches have potential benefits in communicating complex topics in molecular primatology, including in resource-limited settings where such methods have not yet experienced high penetrance. Graphical Abstract*Images in the graphical abstract are courtesy of publicdomainpictures.net O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/610690v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@5ce036org.highwire.dtl.DTLVardef@18429a0org.highwire.dtl.DTLVardef@1c8d997org.highwire.dtl.DTLVardef@1456624_HPS_FORMAT_FIGEXP M_FIG C_FIG

scientific communication and education↗

bioRxiv2020

Trends in scientific research on Environmental Education: A scientometric review

Given the need to understand the current approaches to Environmental Education (EE) in the world, we answer the following questions: (i) Have the studies directed to EE received attention from the scientific community? (ii) what are the trends in EE publications? In the past years, there has been an increase in the number of publications on EE. Brazil stood out in the number of publications, reflecting the concern of Brazilian researchers to promote sustainability and biodiversity maintenance. As for the approaches, the studies are broad, ranging from the influence of policies on environmental protection to the importance of reflection at a global level, proposing international agreements. However, regarding the EE application, given the multiple existing currents, it is worth emphasizing the importance of the teaching-learning process to take place critically so that there is no favoring of the contents promoted and supported by a hegemonic class.

scientific communication and education↗

bioRxiv2021

What is the main driver of unsustainable natural resource use in the Comoro Islands?

The Comoros archipelago is a biodiversity hotspot by virtue of its high level of endemism. However, it suffers one of the highest rates of forest loss worldwide, mainly due to strong anthropogenic pressures. As Comorian populations depend on forest resources for subsistence, establishing relevant conservation strategies for their sustainable management requires the consideration of multiple stakeholders perspectives toward biodiversity and habitat conservation. To better understand the relationships between humans and nature; how comorian people use natural resource and the relevance of a protected area for long-term biodiversity conservation, we used Q-methodology to assess local people s perceptions regarding biodiversity and conservation actions. Three discourses are identified during analysis: "Pro-environment discourse", "Keeping things as usual" and "Social and environmental concerns". According to the results, employed respondents, were favorable to long-term forest and biodiversity conservation. In contrast, unemployed respondents were in favor of more immediate benefits while unemployed but educated respondents were in favor to both long-term forest conservation and immediate benefits from forests. This suggests that the lack of livelihoods for rural people is the main factor leading them to overharvest natural resources. These results suggest that biodiversity conservation of the Comoros archipelagos may benefit for plan aiming at (1) developing tourism and maintaining sustainable production of crops and livestock that could allow enhancing the livelihoods and well-being of all social groups, (2) developing projects such as local markets that could allow villagers to sell their agricultural production, (3) setting up awareness campaign for tree-planting and reforestation. Reforestation could allow re-establishing natural plants and make large trees available for long-term purposes.

scientific communication and education↗

bioRxiv2021

Using a Champion-Oriented Mindset to Overcome the Challenges of Graduate School

Despite efforts to increase diversity, a glaring underrepresentation of minorities (URM) persists in the fields of science, technology, engineering, and mathematics (STEM). Graduate school can be a stressful step in the STEM pipeline, especially for students previously unaware of the structure and challenges of post-graduate education. To promote successful minority participation in STEM and prepare prospective students for the impending challenges of graduate school, we developed a workshop based on the mentoring and fostering of a champion-oriented mindset entitled, "The Trials and Tribulations of Graduate School: How Do You Make an Impact?". We administered the workshop to a cohort of university undergraduates and conducted pre- and post-workshop surveys to measure students perceived need for instruction on specific workshop topics. The results suggest that the workshop was well received by the students and provided information that they considered helpful to help navigate the graduate school process.

scientific communication and education↗

bioRxiv2022

Life-course social disparities in body mass index trajectories across adulthood: cohort study evidence from China Health and Nutrition Survey

BackgroundThe social disparities in obesity may originate in early life and adult social class. There are various developmental trajectories of overweight/obesity in adulthood. It is unclear how the intergenerational mobility of socioeconomic status influences adult overweight/obesity in China. MethodsWe used longitudinal data from ten waves of the China Health and Nutrition Survey (CHNS) between 1989 and 2015 for our analysis. The group-based trajectory modeling was used to identify BMI trajectories in adulthood. Multinomial logistic regression was adopted to assess the associations between SES and adult BMI trajectories. ResultsAmong a total of 3,138 participants, three latent clusters, including normal-stable BMI (51.4%), progressive overweight group (39.8%), and progressive obesity group (8.8%), were identified. High fathers occupational position, high participants occupation position and educational attainment, respectively, were associated with greater obesity risk. Compared to a stable low life course SES trajectory, a stable high life course SES trajectory was associated with a 2.35-fold risk of obesity, and upward and downward social mobility trajectories increased the risk for overweight/obesity. Individuals in the highest relative to the lowest life course cumulative socioeconomic score group had around twice risk of obesity. ConclusionsThe results emphasize the role of the high SES in early life and life-course SES accumulation, in the obesity intervention in China. FundingAll the work was supported by the National Natural Science Foundation of China (Grant Nos. 72174167, 81602928) and Natural Science Foundation of Shaanxi (2021JM-031).

scientific communication and education↗

bioRxiv2022

A Pilot Survey of Authors' Experiences with Poor Peer Reviews

ObjectivesTo develop a typology of poor peer review practices (PPRP) and assess researchers experiences with PPRP. DesignExploratory analysis of cross-sectional internet-based survey. ParticipantsWe solicited 500 researchers funded by the NIH extramural grants in 2018 by direct email and 600 bioethicists on a bioethics discussion forum (mcw.bioethics). 112 respondents (~10%) completed the survey. Primary and Secondary Outcomes MeasuresThe total number of reported PPRP and a five-point scale to assess participants views about the effect of PPRP on their ability to disseminate their research. ResultsThe mean number of PPRP experienced per author was 12.5 of 28 (44.6%; range 0-27; 95% CI = 11.2-13.8), with fourteen PPRP experienced by 50% or more of the sample. The number of reported PPRP increased with age (P = 0.01) and total number of published peer-reviewed manuscripts (P = 0.02). Authors belonging to underrepresented groups reported more PPRP compared to represented groups (P = 0.05). Most authors viewed the peer review process favorably, with 67% (74/111) of authors responding "sometimes" or "often" to having received insightful peer reviews that improved the quality of their final papers. However, a total of 57% (63/111) of respondents admitted to previously abandoning a manuscript after receiving what they perceived to be unfair peer reviews. ConclusionsThis study introduces a practical list of PPRP and a framework for a typology of PPRP, which could serve as an educational tool for editors and reviewers and further our understanding of poor peer review practices. Future researchers will expand authors experiences with constructive or helpful peer review practices. STRENGTHS AND LIMITATIONS OF THIS STUDYO_LIThe sample consisted primarily of experienced researchers from diverse fields, which aided in capturing a wide variety of poor peer review examples. C_LIO_LIThis survey included a core set of 28 poor peer review practices and allowed respondents to add other practices they had experienced, which helped to generate an extensive list of poor peer review practices. C_LIO_LIThe generalizability of the prevalence of poor review types and the degree of negative impact on authors should be interpreted with caution due to the low response rate and the potential for response bias. C_LI

scientific communication and education↗

bioRxiv2021

Introducing Conflict Resolution and Negotiation Training into a Biomedical Sciences Graduate Curriculum

Analysis of the biomedical workforce and graduate education have produced recommendations for modifications of pre-doctoral training to broadly prepare trainees for wider ranging scientific careers. Increased exposure to career opportunities and development of training in professional skills is widely recommended, but details of implementation are not widely available. In alignment with these recommendations, we have incorporated professional skills training into the biomedical science graduate curriculum at West Virginia University. An important component of the training is developing conflict resolution and negotiation skills. This training will provide useful skills for academic careers, non-academic careers and life situations outside of the workplace. Conflict resolution/negotiation skills are also relevant in managing issues in diversity, equity and inclusivity. We report our experience in developing this component of the training program, provide an overview of the approach to delivery and practice of skills, and provide an analysis of the reception and effectiveness of the training.

scientific communication and education↗

bioRxiv2022

Preprint peer review enhances undergraduate biology students' disciplinary literacy and sense of belonging in STEM

Undergraduate education on science publishing and peer review is limited compared to the focus on experimental research. Since peer review is integral to the scientific process and central to the identity of a scientist, we envision a paradigm shift that makes teaching peer review integral to undergraduate science education, and hypothesize that this may facilitate the development of students scientific literacy and identity formation. To this end, we developed a curriculum for biology undergraduates to learn about the mechanisms of peer review, then write and publish their own peer reviews as a way to authentically join the scientific community of practice. The curriculum was implemented as a semester-long intervention in one class and as a module intervention embedded into a discipline-based class on vaccines. Before and after both interventions, we measured students scientific literacy, including peer review ability, using quantitative methods. We also carried out a longitudinal qualitative assessment of students perceptions of their scientific literacy and identity using thematic analysis of students writing. Here, we present data on the improvement in peer review ability of undergraduates in both classes, and data on the curriculums interrelated impact on students development of scientific literacy, identity, and belonging in academic and professional spaces. These data suggest that undergraduates can and should be trained in peer review to foster the interrelated development of their scientific literacy, scientific identity, and sense of belonging in science.

scientific communication and education↗

bioRxiv2023

Beyond Active Learning: Using 3-Dimensional Learning to Create Scientifically Authentic, Student-Centered Classrooms

In recent years, much of the emphasis for transformation of introductory STEM courses has focused on "active learning", and while this approach has been shown to produce more equitable outcomes for students, the construct of "active learning" is somewhat ill-defined, and can encompass a wide range of pedagogical techniques. Here we present an alternative approach for how to think about the transformation of STEM courses that focuses instead on what students should know and what they can do with that knowledge. This approach, known as three-dimensional learning (3DL), emerged from the National Academys "A Framework for K-12 Science Education", which describes a vision for science education that centers the role of constructing productive causal accounts for phenomena. Over the past 10 years, we have collected data from introductory biology, chemistry, and physics courses to assess the impact of such a transformation on higher education courses. Here we report on an analysis of video data of class sessions that allows us to characterize these sessions as active, 3D, neither, or both 3D and active. We find that 3D classes are likely to also involve student engagement (i.e. be active), but the reverse is not necessarily true. That is, focusing on transformations involving 3DL also tends to increase student engagement, whereas focusing solely on student engagement might result in courses where students are engaged in activities that do not involve meaningful engagement with core ideas of the discipline.

scientific communication and education↗

bioRxiv2024

Building Inclusive Leadership: A Biosciences Approach

One-size-fits-all Equity, Diversity, and Inclusion (EDI) strategies and provisioning are no longer suitable for a growing and diversifying higher education landscape; as each research discipline faces its own unique challenges to inclusion. High impact research needs reliable, decisive, and holistic approaches to leadership, but managerial and leadership skills are often considered an add-on as opposed to a necessity in modern research environments. An estimated 70% of EDI initiatives in UK Higher Education Institutions fail to flourish (Marchiondo et al. 2023) - a combinatory effect of conservative approaches to change, cultural adaptation, and departmental stability. We developed an Inclusive Leadership Programme to empower bioscientists to work autonomously and inclusively. Using a co-creation approach, the Inclusive Leadership Programme collectively defined inclusive leadership traits to create a resource. The interactive resource shares inclusive approaches to communication, feedback, recognition, and development - prioritising the experiences of those typically excluded from leadership conversations. By embedding a self-reflective scoring system, we share changes in approaches to inclusivity. After using the resource, self-perception normalises in distribution, indicating the resource provides a baseline for best practice, and space to understand personal approaches to inclusive practice in biosciences. Ultimately, the Inclusive Leadership Programme and Resource offers a template for other biological research, learning, and teaching environments to build their own tailored approach to integrating inclusivity and empowering all members to work as autonomous and inclusive leaders, regardless of seniority.

scientific communication and education↗

bioRxiv2022

Public exams provide opportunities for deeper thought with less anxiety

Assessment methods across post-secondary STEM education are traditionally constrained by logistics and likely contribute to the widespread inequities in STEM education outcomes. As part of attempts to improve and diversify the methods used in assessment, the authors have developed a flexible and low-tech style known as public exams based in educational best practices. Public exams attempt to authentically involve students into the process of assessment through the use of pre-released portions of the exam. Using mixed-methods research techniques at a closely matched pair of institutions (a research-intensive university and a community college classroom), we observed signals of positive impact from the public exam on student learning experiences. Public exams appear to promote deeper thought, to direct students more efficiently to the core concepts in the discipline, and to decrease student anxiety around exams. The public exam experience does not show evidence for exacerbating gaps in exam outcomes for students from underrepresented backgrounds. This suggests that public exams are worth deeper investigation as an evidence-based and effective assessment style.

scientific communication and education↗

bioRxiv2018

Genie: An interactive real-time simulation for teaching genetic drift

Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is specially challenging. Here we present Genie, a browser-based educational tool that facilitates demonstration of concepts such as genetic drift, population isolation, gene flow, and genetic mutation. Because it does not need to be downloaded and installed, Genie can scale to large groups of students and is useful for both in-person and online instruction. Genie was used to teach genetic drift to Evolution students at Arizona State University during Spring 2016 and Spring 2017. The effectiveness of Genie to teach key genetic drift concepts and misconceptions was assessed with the Genetic Drift Inventory developed by Price et al. (2014). Overall, Genie performed comparably to that of traditional static methods across all evaluated classes. We have empirically demonstrated that Genie can be successfully integrated with traditional instruction to reduce misconceptions about genetic drift.

scientific communication and education↗

bioRxiv2019

Can scientists fill the science journalism void? Online public engagement with science stories authored by scientists

In many countries the publics main source of information about science and technology is the mass media. Unfortunately, in recent years traditional journalism has experienced a collapse, and science journalism has been a major casualty. One potential remedy is to encourage scientists to write for news media about science. On these general news platforms, scientists stories would have to compete for attention with other news stories on hard (e.g. politics) and entertaining (e.g. celebrity news) topics written by professional writers. Do they stand a chance?\n\nThis study aimed to quantitatively characterize audience interactions as an indicator of interest in science news stories authored by early career scientists (henceforth scientists) trained to function as science reporters, as compared to news items written by reporters and published in the same news outlets.\n\nTo measure users behavior, we collected data on the number of clicks, likes, comments and average time spent on page. The sample was composed of 150 science items written by 50 scientists trained to contribute popular science stories in the Davidson Institute of Science Education reporters program and published on two major Israeli news websites - Mako and Ynet between July 2015 to January 2018. Each science item was paired with another item written by the websites organic reporter, and published on the same channel as the science story (e.g., tourism, health) and the same close time. Overall significant differences were not found in the publics engagement with the different items. Although, on one website there was a significant difference on two out of four engagement types, the second website did not have any difference, e.g., people did not click, like or comment more on items written by organic reporters than on the stories written by scientists. This creates an optimistic starting point for filling the science news void by scientists as science reporters.

scientific communication and education↗

bioRxiv2025

Teaching good agronomic practices to strengthen pigeon pea cultivation and value chains through farmer-to-farmer education in Zambia

Farmer field schools (FFSs) are transformative, participatory approaches to adult agricultural education that effectively promote farmers learning and capacity building and empower farming communities with practical knowledge. Here, we present a case study of FFS in the Katete district, Eastern province of Zambia, focused on good pigeon pea agronomic practices and the value chain. Three FFSs were established, focusing on a variety of trials, bio-pesticides, and a pigeon pea-specific rhizobial inoculant. Extreme weather conditions, an underdeveloped pigeon pea seed value chain, and a poor seed system hindered the implementation of the FFSs. To strengthen the pigeon pea seed value chain, a seed dehuller is now available to farmers. Our results highlight the importance of the design, implementation, monitoring, and evaluation of the FFSs. Pigeon pea FFSs will support crop and food diversification, improve soil fertility and sustainable agriculture, and may increase household income.

scientific communication and education↗

bioRxiv2025

Community, Belonging, and Peer-Engagement: Participant Experiences Reflect Consistency of Facilitation Practices in Inclusive STEM Teaching Learning Communities

A primary reason for the persistent underrepresentation of minoritized people in STEM careers are their marginalizing experiences in STEM courses, which has spurred efforts to prepare STEM faculty to implement inclusive teaching practices. The Inclusive STEM Teaching Project (ISTP) addresses this nationwide challenge by providing STEM faculty a free, online course and associated learning communities (LCs) led by project-trained facilitators. ISTP centers identity, power, privilege and positionality and has successfully shifted educators mindsets and abilities. A central question is whether local LCs across contexts maintain equity-minded core practices and achieve inclusive, reflective practitioner outcomes. Our mixed methods analysis of LC participant (n = 165) and facilitator (n = 83) matching survey data spanning five course offerings over two years directly explores the relationship between the learning environments created by facilitators and their participant experiences. Findings demonstrate high fidelity of implementation to training by facilitators that resulted in consistent LC experiences of participants, especially around building a community, sense of belonging and positive peer engagement. Participants overall speak to the importance of facilitated LCs as an inclusive space where they can critically engage with one another as they reflect on, discuss, and ultimately improve their inclusive teaching practices.

scientific communication and education↗

bioRxiv2020

Introducing undergraduate students to reverse genetics in the laboratory: a case study of a project-oriented learning (POL) system in Taishan Medical University, China

Biochemistry and molecular biology have become increasingly reliant on experimental experience, because they are difficult subjects to understand from a theoretical approach. The Innovation and Entrepreneurship Training Program was established by the China Ministry of Education to foster the scientific interests and experiences of undergraduate students. Here, we reported on an innovative project-oriented learning (POL) system directed by Taishan Medical University (Named Shandong First Medical University & Shandong Academy of Sciences since February 2019) China, which fused innovative project with biochemical course concepts. This study takes reverse genetics, which is considered to be difficult to understand through course-only learning, as an example. To help undergraduate students understand the principle of reverse genetics, the project involved producing hepatitis C virus in vitro. Furthermore, to give them a comprehensive scientific experience based on their knowledge from textbook, extensive mentorship was provided through the project, including theoretical guidance and technical support for experiments. Assessment showed a comprehensive improvement after participating in these programs. In conclusion, this POL system was a good model that enabled undergraduates to learn more during courses. It also provided a chance to experience hands-on sciences, which might motivate them to pursue a career in science.View Full Text

scientific communication and education↗

bioRxiv2022

Translating DNA origami Nanotechnology to Middle School, High School, and Undergraduate Laboratories

DNA origami is a rapidly emerging nanotechnology that enables researchers to create nanostructures with unprecedented geometric precision that have tremendous potential to advance a variety of fields including molecular sensing, robotics, and nanomedicine. Hence, many students could benefit from exposure to basic knowledge of DNA origami nanotechnology. However, due to the complexity of design, cost of materials, and cost of equipment, experiments with DNA origami have been limited mainly to research institutions in graduate level laboratories with significant prior expertise and well- equipped laboratories. This work focuses on overcoming critical barriers to translating DNA origami methods to educational laboratory settings. In particular, we present a streamlined protocol for fabrication and analysis of DNA origami nanostructures that can be carried out within a 2-hour laboratory course using low-cost equipment, much of which is readily available in educational laboratories and science classrooms. We focus this educational experiment module on a DNA origami nanorod structure that was previously developed for drug delivery applications. In addition to fabricating nanostructures, we demonstrate a protocol for students to analyze structures via gel electrophoresis using classroom-ready gel equipment. These results establish a basis to expose students to DNA origami nanotechnology and can enable or reinforce valuable learning milestones in fields such as biomaterials, biological engineering, and nanomedicine. Furthermore, introducing students to DNA nanotechnology and related fields can also have the potential to increase interest and future involvement by young students. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/508130v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@137f058org.highwire.dtl.DTLVardef@1843271org.highwire.dtl.DTLVardef@bc9b4org.highwire.dtl.DTLVardef@1e779af_HPS_FORMAT_FIGEXP M_FIG C_FIG

scientific communication and education↗

bioRxiv2022

Bioschemas Training Profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources

Stand-alone life science training events and e-learning solutions are amongst the most sought-after modes of training because they address both point-of-need learning and the limited timeframes available for upskilling. Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for Internet searches in a consistent way. This absence of mark-up standards to facilitate discovery, re-use and aggregation of training resources limits their usefulness and knowledge-translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the three Bioschemas Training profiles: TrainingMaterial, Course and CourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals learning needs, and the discovery and re-use of training and instructional materials.

scientific communication and education↗