Life Science Disciplines Research Articles

On-line correlative imaging of cryo-PALM and soft X-ray tomography for identification of subcellular structures.

Correlative imaging of fluorescence microscopy and soft X-ray microscopy plays a crucial role in exploring the relationship between structure and function in cellular biology. However, the current correlative imaging methods are limited either to off-line or low-resolution fluorescence imaging. In this study, we developed an integrated on-line cryogenic photoactivated localization microscopy (cryo-PALM) system at a soft X-ray microscopy station. This design eliminates some critical issues such as sample damage and complex post-correlation arising from transferring samples between different cryostages. Furthermore, we successfully achieved correlative imaging of cryopreserved near-native cells, with a resolution of about 50 nm of cryo-PALM. Therefore, the developed on-line correlation imaging platform provides a powerful tool for investigating the intricate relationship between structure and function in biological and molecular interactions, as well as in other life science disciplines.

Peer review trends in six fisheries science journals

BackgroundAs the production of scientific manuscripts and journal options both increase, the peer review process remains at the center of quality control. Recent advances in understanding reviewer biases and behaviors along with electronic manuscript handling records have allowed unprecedented investigations into the peer review process.MethodsWe examined a sample of six journals within the field of fisheries science (and all published by the American Fisheries Society) specifically looking for changes in reviewer invitation rates, review time, patterns of reviewer agreements, and rejection rates relative to different forms of blinding.ResultsData from 6,606 manuscripts from 2011–2021 showed significant increases in reviewer invitations. Specifically, four journals showed statistically significant increases in reviewer invitations while two showed no change. Review times changed relatively little (± 2 weeks), and we found no concerning patterns in reviewer agreement. However, we documented a consistently higher rejection rate—around 20% higher—of double-blinded manuscripts when compared to single-blinded manuscripts.ConclusionsOur findings likely represent broader trends across fisheries science publications, and possibly extend to other life science disciplines. Because peer review remains a primary tool for scientific quality control, authors and editors are encouraged to understand the process and evaluate its performance at whatever level can help in the creation of trusted science. Minimally, our findings can help the six journals we investigated to better understand and improve their peer review processes.

How do life sciences cite social sciences? Characterizing the volume and trajectory of citations

AbstractSocial sciences are increasingly recognized as significant for building a sustainable world since the social perspective can assist researchers in other fields in navigating public controversy and designing more responsible interaction mechanisms between the natural and social systems. However, the question arises: to what extent do natural sciences rely on social science research in their studies? Examining life science publications from seven PLoS journals, this paper attempts to characterize the volume and trajectory of citations from life sciences to social sciences. We explore three core questions: To what extent do life sciences cite social sciences? What actors in the life sciences are citing social sciences? Which actors in the social sciences are being cited? Our analysis estimates social sciences influence 15%–19% of life science publications, contributing to 1.1%–1.5% of references in 2018. Social science citers are found across peripheral and central topics of life science disciplines. Cited social science publications exhibit various levels of interdisciplinarity and achieve the greatest citation impact among peers. Citations to social sciences are prevalent in both theoretically and methodologically oriented sections. We show empirically the increasing impact of social sciences on the development of the life sciences.

Controlled experiment finds no detectable citation bump from Twitter promotion.

Multiple studies across a variety of scientific disciplines have shown that the number of times that a paper is shared on Twitter (now called X) is correlated with the number of citations that paper receives. However, these studies were not designed to answer whether tweeting about scientific papers causes an increase in citations, or whether they were simply highlighting that some papers have higher relevance, importance or quality and are therefore both tweeted about more and cited more. The authors of this study are leading science communicators on Twitter from several life science disciplines, with substantially higher follower counts than the average scientist, making us uniquely placed to address this question. We conducted a three-year-long controlled experiment, randomly selecting five articles published in the same month and journal, and randomly tweeting one while retaining the others as controls. This process was repeated for 10 articles from each of 11 journals, recording Altmetric scores, number of tweets, and citation counts before and after tweeting. Randomization tests revealed that tweeted articles were downloaded 2.6-3.9 times more often than controls immediately after tweeting, and retained significantly higher Altmetric scores (+81%) and number of tweets (+105%) three years after tweeting. However, while some tweeted papers were cited more than their respective control papers published in the same journal and month, the overall increase in citation counts after three years (+7% for Web of Science and +12% for Google Scholar) was not statistically significant (p > 0.15). Therefore while discussing science on social media has many professional and societal benefits (and has been a lot of fun), increasing the citation rate of a scientist's papers is likely not among them.

Techniques and applications of 3D bioprinting

3D bioprinting is an emerging technology that uses computer printing technology and unique bio-ink components to create artificial organs and biomedical objects. It is an interdisciplinary development technology integrating biology, chemistry, materials science, life science and other disciplines, and the technology behind biological 3D printing has improved in its development over the past few decades. Precisely printed biomaterials could benefit both tissue engineering and regenerative medicine. 3D bioprinting technology makes it possible to print tissues and organs, providing favorable conditions for organ transplantation and medical experiments. This paper mainly reviews the development of bioprinting technology and related concepts. According to the morphological change and chemical composition, the commonly used bioprinting materials (bio-inks) and their characteristics are described. The main methods of bioprinting are summarized, including traditional inkjet 3D bioprinting, extrusion 3D bioprinting, laser-assisted 3D bioprinting, photocuring 3D bioprinting and emerging 4D bioprinting and in situ bioprinting technologies. Finally, the paper introduces the development trend of bioprinting in the transplantation of skin, blood vessels and complex organs, as well as the precision research of tumors. In addition, current research challenges and prospects for future bioprinted 3D printing materials are discussed.

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.

Computer programming is a fundamental tool for life scientists, allowing them to carry out essential research tasks. However, despite various educational efforts, learning to write code can be a challenging endeavor for students and researchers in life-sciences disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising questions about whether these technologies can aid (or replace) life scientists' efforts to write code. Using 184 programming exercises from an introductory-bioinformatics course, we evaluated the extent to which one such tool-OpenAI's ChatGPT-could successfully complete programming tasks. ChatGPT solved 139 (75.5%) of the exercises on its first attempt. For the remaining exercises, we provided natural-language feedback to the model, prompting it to try different approaches. Within 7 or fewer attempts, ChatGPT solved 179 (97.3%) of the exercises. These findings have implications for life-sciences education and research. Instructors may need to adapt their pedagogical approaches and assessment techniques to account for these new capabilities that are available to the general public. For some programming tasks, researchers may be able to work in collaboration with machine-learning models to produce functional code.

Crucial but Neglected: Limited Availability of Animal Welfare Courses in Education of Wildlife Researchers.

Animal welfare is a subject of increasing scientific and ethical concern in today's society, crucial for the well-being of animals used in research and the integrity of scientific data. Equipping researchers in the life science disciplines with a science-based knowledge of animal welfare, behaviour, physiology, and health is, therefore, essential. Nevertheless, previous studies evaluating animal welfare education focused on veterinary, laboratory, or farm animal science. Consequently, the aim of this study was, for the very first time, to map the prevalence of animal welfare courses in the university education of ecologists, wildlife biologists, and conservation managers in Europe, Canada, the USA, Australia, and New Zealand. A comprehensive assessment of 1548 universities was conducted, resulting in the identification of 596 relevant programs at the bachelor's and master's levels. Analysis of the curricula revealed that only 1% of the programs offered a formal course on animal welfare, while 65% provided courses on animal behaviour, 59% on animal physiology, and 34% on animal health. However, the majority of these courses were listed as electives rather than mandatory components of the programs. These results underscore the need for universities to incorporate more formal and obligatory education in animal welfare in order to better prepare future ecologists, wildlife biologists, and conservation managers for the challenges of working with wildlife.

Recent Progress of Droplet Microfluidic Emulsification Based Synthesis of Functional Microparticles.

The remarkable control function over the functional material formation process enabled by droplet microfluidic emulsification approaches can lead to the efficient and one-step encapsulation of active substances in microparticles, with the microparticle characteristics well regulated. In comparison to the conventional fabrication methods, droplet microfluidic technology can not only construct microparticles with various shapes, but also provide excellent templates, which enrich and expand the application fields of microparticles. For instance, intersection with disciplines in pharmacy, life sciences, and others, modifying the structure of microspheres and appending functional materials can be completed in the preparation of microparticles. The as-prepared polymer particles have great potential in a wide range of applications for chemical analysis, heavy metal adsorption, and detection. This review systematically introduces the devices and basic principles of particle preparation using droplet microfluidic technology and discusses the research of functional microparticle formation with high monodispersity, involving a plethora of types including spherical, nonspherical, and Janus type, as well as core-shell, hole-shell, and controllable multicompartment particles. Moreover, this review paper also exhibits a critical analysis of the current status and existing challenges, and outlook of the future development in the emerging fields has been discussed.

Application of Nanotechnology in Malaria Research

Introduction In many ways, malaria is giving a challenge to researchers globally, day by day. But, the potential of nanotechnology/nanomedicine to work at the nanoscale has allowed us to target receptors/molecules of the parasite directly at a nanoscale level as well as the impetus to develop devious nanostructures that could solve the problems which previously impeded the conventional pharmacological approaches from being successful. Over the four decades, the slow but steady integration of life-sciences disciplines and nanotechnology has started transforming the way to detect and diagnose for the betterment of health1. This idea was first presented in 1974 by Professor Norio Taniguchi2, and it received the least attention concerning malaria. However, drug resistance, social demerits, and environmental concerns made malaria the exterminator and notorious disease that is known to all. The mainstay of current anti-plasmodial medication is chemotherapy, which comes with toxic severe side effects. Resistance among the parasite spp. that leads to treatment failure, insufficient knowledge of the biology and pathology of a parasite, complexity of life-cycle, dispersed locations of Plasmodium spp., and the difficulty in developing new antimalarial drugs as this development process is time-consuming and an expensive, poses a significant challenge when researchers are trying to create new antimalarial medications3. Therefore, researchers are trying to deliver drugs without toxicity and improve efficacy4 by employing nanotechnological approaches. It enhances its solubility profile, modifies the pharmacokinetic characteristics of the drug, prevents drug deterioration, and supports a continuous release of the drug at the intended site.

Physical Activity and Academic Burnout among Postgraduate Students of Life Science Disciplines

Physical Activity and Academic Burnout among Postgraduate Students of Life Science Disciplines

Integration and Design of Ideological and Political Points in Course of Plant Physiology

Plant physiology is one of the fundamental disciplines of life sciences, and is also a compulsory basic course for undergraduate and graduate students of biology-related majors in various colleges and universities, whose content is based on elucidating the laws and nature of plant life activities. Ideological and political education in all courses is a multi-dimensional educational reform that cultivates excellent builders and successors of socialism with Chinese characteristics in the context of the rapid development of higher education in the new era. On the example of plant physiology, we explore the design of ideological and political elements in important chapters based on the construction background of the course, and consider the problems encountered in the ideological and political education in the course, to show the view of education, mission and curriculum in the teaching of professional courses, thus providing reference for the integration of ideological and political education into the course of plant physiology.

Multisite assessment of reproducibility in high‐content cell migration imaging data

High‐content image‐based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high‐quality open‐access data sharing and meta‐analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta‐analysis of results from live‐cell microscopy, have not been systematically investigated. Here, using high‐content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta‐analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image‐based datasets of perturbation experiments. Thus, reproducible quantitative high‐content cell image analysis of perturbation effects and meta‐analysis depend on standardized procedures combined with batch correction.

Effect of serum lipid subfractions on nuclear magnetic resonance spectroscopy's ability to detect coronary atherosclerosis early

Nuclear magnetic resonance spectroscopy, also known as NMRS, is a cutting-edge method based on nuclear magnetic induction theory and quantum optics that has found extensive usage in the domains of chemical analysis, life science, and other disciplines. The method is quantitative and repeatable, making it particularly effective for detecting and analyzing tiny compounds in complicated solutions like blood and urine. With a high degree of standardization and automation, it can assess 114 hemo lipoprotein subfractions and particles in human serum/plasma in a targeted way (exact quantification) and produce precise and dependable detection findings. All processes may be tracked back to fulfill our requirements for non-targeted analysis, which is suited for biological fluid specimens and water-soluble specimens from tissue or cell extracts. The 114 lipoprotein subfractions and particles can be targeted using nuclear magnetic resonance spectroscopy (NMRS), which can detect the serum lipid profile in its entirety. The analysis of the serum lipid profile, the correlation between the levels of lipid subfractions and lipid particles and the degree of coronary stenosis, and the development of a coronary stenosis early warning system can therefore improve the current risk model on the inadequacy of the risk stratification of the patients. These studies are based on a cohort of individuals with varying degrees of coronary atherosclerosis. The development of a coronary artery stenosis early warning system might enhance the patient risk classification models already in use. To analyze the correlation of lipid subfractions and particle levels with cardiovascular events and therapeutic efficacy, to explore more effective biomarkers for lipid-lowering monitoring, and to evaluate the efficacy of classical Chinese medicinal preparations.

A road less travelled?: coherence and coverage of integrated science in Singapore

ABSTRACT Background Integrated science is a ubiquitous school subject that is an amalgamation of science disciplines; its teaching allows topics to be sequenced in any order and given various degrees of coverage and emphasis in the classroom. Ensuring canonical coherence, which is the logical organization of subject matter for effective instruction is therefore necessary for meaningful student learning to occur. Purpose We examine the coherence as well as closely related ideas of coverage and emphasis of the integrated science curriculum and textbooks from Singapore. Such an analysis has not been attempted before, which might shed light on strong student achievement reported from this region in this subject. Methods Coherence was determined by finding buttress topics and upper triangular patterns based on a list of standard science topics––these inter-related curricular features aid in conceptual learning of a subject. We also investigated questions about coverage and emphasis from the number of learning outcomes, topics in curriculum and textbooks, and page surface area of textbooks following past TIMSS research. Results Three buttress topics and two upper triangular patterns in life and physical science disciplines were found, but not among earth science topics. Two topics were strongly emphasised in the curriculum and textbooks––organs, tissues and physical properties of matter––and there was a close alignment between topics in the curriculum and textbooks. Integrated science here was relatively restricted compared to three other high-performing East-Asian regions, but there was a common strong emphasis on physical science topics. Conclusions Integrated science in Singapore has shown some evidence of coherence in its curriculum and textbooks that have also emphasised physical science topics. Because learning outcomes here were intentionally trimmed due to past general educational reforms, the findings lend tentative support to arguments stating that a reduced, but well-designed science curriculum has benefits for learners.

Lineage Landscape: a comprehensive database that records lineage commitment across species.

Commitment to specific cell lineages is critical for mammalian embryonic development. Lineage determination, differentiation, maintenance, and organogenesis result in diverse life forms composed of multiple cell types. To understand the formation and maintenance of living individuals, including human beings, a comprehensive database that integrates multi-omic information underlying lineage differentiation across multiple species is urgently needed. Here, we construct Lineage Landscape, a database that compiles, analyzes and visualizes transcriptomic and epigenomic information related to lineage development in a collection of species. This landscape draws together datasets that capture the ongoing changes in cell lineages from classic model organisms to human beings throughout embryonic, fetal, adult, and aged stages, providing comprehensive, open-access information that is useful to researchers of a broad spectrum of life science disciplines. Lineage Landscape contains single-cell gene expression and bulk transcriptomic, DNA methylation, histone modifications, and chromatin accessibility profiles. Using this database, users can explore genes of interest that exhibit dynamic expression patterns at the transcriptional or epigenetic levels at different stages of lineage development. Lineage Landscape currently includes over 6.6 million cells, 15 million differentially expressed genes and 36 million data entries across 10 species and 34 organs. Lineage Landscape is free to access, browse, search, and download at http://data.iscr.ac.cn/lineage/#/home.

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey.

Background: Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods: An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results: The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusion: The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.

E-Learning Materials in Earth and Life Science for Struggling Learners

The purpose of the study is to design and validate e-learning materials for a few selected Earth and Life Science disciplines. It concentrated on figuring out how the e-learning content would help increase the learners' conceptual comprehension and their perception of the intervention material's effectiveness. The area of investigation was limited to four (4) areas of investigation: 1) Determine the level of quality of the respondents on the use of the E – Learning Material in Earth and Life Science for Struggling Learners in terms of its objective, content and exercises, 2) Determine the level of acceptability of the respondents on the use of the E – Learning Material in Earth and Life Science for Struggling Learners in terms of its efficiency, usability and adaptability, 3) Know the mean score performance of the control and experimental group on the second quarter topic: matter in the use of E – Learning Material in Earth and Life Science in terms of Pre – Test and Post – Test, and 4) Determine if there is a significant difference between the pre-test performance and posttest performance of the control group and experimental group. It was founded on the level quality in terms of objectives, content, and exercises, it was determined that the e-learning material was highly acceptable to teachers and students as an intervention for the struggling learners. The e-learning material was successful in enhancing the students' competencies in Earth and Life Science disciplines as evidenced by the students' improved performance on the post-test. It was revealed that the e-learning material was highly acceptable to teachers and students as an intervention for the struggling learners in terms of acceptability based on its efficiency, usability and adaptability. According to the students' increased performance on the post-test, the e-learning material was effective in improving the students' competences in Earth and Life Science subjects. It was described that the mean score performance in the pretest of the control and experimental group were both average. While the mean score performance in the posttest of the control and experimental group were described as good. A significant improvement in the students' performance was revealed by the study. Based on the results of the pre-test and the post-test, there was a significant difference in the students' performance of the control and experimental group. Based from the findings of the study the author of this research concluded that there is a significant difference between the posttest mean score of the control and experimental group, hence, the null hypothesis stating that there is no significant difference is hereby rejected. The researcher recommends to change the research paradigm. Investigate the potential modifying impact of learners' academic abilities and parental support on the impact of employing science-related films as a motivating and cognitive teaching strategy during a certain grading period.

The modularity codes

The hypothesis presented here is that codes as described by Marcello Barbieri are the fundamental principle behind biological modularity. Modularity has been studied in different life science disciplines, especially in the fields of evolution and development, as well as in network biology, yet there is still no consensus on how modularity evolved itself. Modularity is basically the functional integrity of multiple molecular players involved in a common process. Codes as defined by Barbieri describe a tripartite relation involving an adapter molecule connecting two other independent types of molecules to each other in an arbitrary, but semantic manner. This form of interaction goes beyond predictable mere physical or chemical one-to-one interactions and always relates three molecules to each other. A code of three topologically related molecules interacting in a defined order may be considered a minimal module on its own, but when one regards a set of multiple, overlapping tripartite, coded interactions, this paves the way towards logically and functionally consistent coherence of multiple participants of a certain, modular process. A theoretical outline of how to identify and describe such modular structures is given.

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey.

Background Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusions The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.

The Research‐Intensive Community Model has the Necessary Properties for Successful Propagation at Research‐Extensive Universities

Novel research education models often fail to propagate widely because they typically only include two of four necessary properties to successfully propagate and maintain their impacts: scalability, adaptability, sustainability, and inclusivity. Furthermore, research education models typically address the unmet needs of one stakeholder at a time. First, undergraduates need greater access to limited research opportunities at research‐extensive universities. Second, graduate students and postdoctoral scholars need mentoring and management experience to prepare for leadership roles in the next stage of their careers. Third, faculty need to maximize research productivity and recruit future graduate students with sufficient preparation. Fourth, administrators need to stretch their limited resources to support the competing institutional missions of research and education. The Research‐Intensive Community (RIC) model developed at Texas A&M University has the properties that are both necessary and sufficient to propagate broadly at research‐extensive universities because it turns the competing needs of diverse stakeholders into opportunities. Briefly, instead of a traditional 1‐on‐1 research apprenticeship, research is performed by a diverse undergraduate research team led by a graduate student or postdoctoral scholar. Research teams are productive because they leverage each undergraduate’s unique assets (talents, skills, perspectives, and experiences) to advance the research of the graduate student or postdoctoral scholar. Team leaders meet monthly to discuss best practices for leadership and mentoring that increase their own research productivity through effective team management. Because team leaders are empowered to run their team by their faculty mentors, economies of scale are leveraged to efficiently centralize program marketing, participant registration, project advertisement, and program evaluation. Since 2016, the Aggie Research Program (ARP) has implemented the RIC model to cultivate mutually beneficial relationships to meet the diverse needs of diverse stakeholders. As the ARP has grown, team leader meetings have become a nexus for specific research leadership programs that are either interdisciplinary or focused on specific life science disciplines. The ARP exhibits the necessary and sufficient properties for successful propagation: 1) Scalability: participation has grown 30% each of the first 5 years to currently serve over 800 participants/year 2) Adaptability: research teams are distributed across diverse disciplines in 12 colleges. 3) Sustainability: administrative costs are limited to $50,000/year. 4) Inclusivity: 41% of participants belong to underrepresented groups (financially disadvantaged, first‐generation, disabled and underrepresented minorities), which matches the demographics of the undergraduate student population at Texas A&M University.