Life Sciences Research Articles

A group-forming course content-focused icebreaker for life science classrooms.

Collaboration and communication are important competencies for undergraduate life science education, as noted in the Vision and Change in Undergraduate Biology Education report. However, initiating collaboration and communication in the classroom can be an anxiety-inducing experience for many students. In contrast to traditional-style icebreakers, we introduce a course content-focused icebreaker activity that served as a group-forming undertaking on the first day of class. We developed four sets of handouts (icebreaker tickets), each having a common course theme (e.g., microbiology, cell biology, physiological system infections/disorders, virology). Students were randomly provided with a ticket at the beginning of the course, and they worked to establish groups with their peers, based on their own interpretation of the ticket's content and rationalization of a grouping scheme. Student feedback and engagement data collected from implementation at three independent institutions were largely positive, where students reported the activity to be an effective tool for building a course content-focused community of learners. The icebreaker tickets and instructor's notes disseminated in this manuscript can be adapted to fit educators' course goals and help set the tone for the first day of the class and beyond that fosters communication and collaboration among students.

Discovering fully semantic representations via centroid- and orientation-aware feature learning

Abstract Learning meaningful representations of images in scientific domains that are robust to variations in centroids and orientations remains an important challenge. Here we introduce centroid- and orientation-aware disentangling autoencoder (CODAE), an encoder–decoder-based neural network that learns meaningful content of objects in a latent space. Specifically, a combination of a translation- and rotation-equivariant encoder, Euler encoding and an image moment loss enables CODAE to extract features invariant to positions and orientations of objects of interest from randomly translated and rotated images. We evaluate this approach on several publicly available scientific datasets, including protein images from life sciences, four-dimensional scanning transmission electron microscopy data from material science and galaxy images from astronomy. The evaluation shows that CODAE learns centroids, orientations and their invariant features and outputs, as well as aligned reconstructions and the exact view reconstructions of the input images with high quality.

Three-Dimensional Reconstruction-Characterization of Polymeric Membranes: A Review.

Polymeric membranes serve as vital separation materials in diverse energy and environmental applications. A comprehensive understanding of three-dimensional (3D) structures of membranes is critical to performance evaluation and future design. Such quantitative 3D structural information is beyond the limit of most employed conventional two-dimentional characterization techniques such as scanning electron microscopy. In this review, we summarize eight types of 3D reconstruction-characterization techniques for membrane materials. Originated from life and materials science, these techniques have been optimized to reveal the 3D structures of membrane materials in the separation field. We systematically introduce the theories of each technique, summarize the sample preparation procedures developed for membrane materials, and demonstrate step-by-step data processing, including 3D model reconstruction and subsequent characterization. Representative case studies are introduced to show the progress of this field and how technical challenges have been overcome over the years. In the end, we share our perspectives and believe that this review can serve as a useful reference for 3D reconstruction-characterization techniques developed for membrane materials.

A new era of learning: exploring science teachers’ perceptions of virtual lab in rural schools

Abstract Virtual learning technologies have become integral in education globally, with developed countries leading in implementation. In contrast, Global South countries like South Africa are only beginning to conceptualise Virtual Laboratory (VL) integration, with limited practical implementation. This study underscores the importance of understanding teachers’ perceptions of VL before deployment to minimise the risk of underuse or abandonment. Guided by the Technology Acceptance Model Davis (MIS Quarterly 13(3):319–340, 1989), this research employed a sequential explanatory mixed-methods approach. In Phase 1, 186 Life Sciences teachers from South Africa’s Eastern Cape province participated in a survey and semi-structured interviews with four teachers in Phase 2. Data were analysed using descriptive statistics and thematic analysis. Findings reveal that teachers perceive VL positively and see potential benefits for rural education. The study also signals that intent alone may not lead to full adoption. This study contributes unique insights from rural teachers often absent in the broader technology adoption dialogue.

Governing Dual-Use Research of Concern in the Life Sciences: United States and Canada Policy Comparative Analysis and Recommendations

Governing Dual-Use Research of Concern in the Life Sciences: United States and Canada Policy Comparative Analysis and Recommendations

LitSumm: large language models for literature summarization of noncoding RNAs.

Curation of literature in life sciences is a growing challenge. The continued increase in the rate of publication, coupled with the relatively fixed number of curators worldwide, presents a major challenge to developers of biomedical knowledgebases. Very few knowledgebases have resources to scale to the whole relevant literature and all have to prioritize their efforts. In this work, we take a first step to alleviating the lack of curator time in RNA science by generating summaries of literature for noncoding RNAs using large language models (LLMs). We demonstrate that high-quality, factually accurate summaries with accurate references can be automatically generated from the literature using a commercial LLM and a chain of prompts and checks. Manual assessment was carried out for a subset of summaries, with the majority being rated extremely high quality. We apply our tool to a selection of >4600 ncRNAs and make the generated summaries available via the RNAcentral resource. We conclude that automated literature summarization is feasible with the current generation of LLMs, provided that careful prompting and automated checking are applied. Database URL: https://rnacentral.org/.

Modern Approaches for Asymmetric Construction of CF3‐All Carbon Quaternary Stereocenters from Prochiral Trifluoromethyl Alkenes

AbstractAt present, the research of organofluorine chemistry is a leading and rapidly emerging area of life sciences. Organofluorine molecules have drawn much attention by displaying a wide variety of applications in agrochemicals, medicines, fire extinguishers, and blowing agents. In the present review, the great advances made in the last decade for the asymmetric construction of quaternary stereocenters bearing trifluoromethyl group from the corresponding prochiral‐trifluoromethylated substrates are discussed. A variety of catalytic frameworks have been designed in this field for asymmetric induction. The main prochiral‐trifluoromethyl substrates chosen for this review are β‐CF3‐β‐substituted nitro alkenes and α, β‐ unsaturated trifluoromethyl ketones. Moreover, this review describes the further utilization of obtained CF3‐quaternary centres to access the important organofluorine molecules.

Virtual labs in life sciences education: A case study of grade 10 learners in selected South African rural schools

This study investigated the effectiveness of virtual reality lab activities in enhancing grade 10 learners’ understanding of life sciences concepts and science process skills. A quasi-experimental design was employed, with a control group using traditional teaching methods and an experimental group using virtual reality lab activities. The results showed significant improvements in the experimental group’s understanding of life sciences concepts and science process skills, including making observations, interpretation, measurement, recording data, and planning an investigation. The virtual reality lab activities were found to be effective in enhancing learners’ understanding and skills, with significant differences observed between the control and experimental groups. The study’s findings suggest that virtual reality lab activities can be a valuable tool for teaching life sciences and promoting science process skills and have implications for the integration of technology in science education.

Management of Myasthenia Gravis through Herbomineral Drug - A Case Study

Ayurveda is an oldest traditional medicine system that believes on natural and holistic approach of treatment for various diseases. It is the science of healthy life. Myasthenia gravis is a chronic autoimmune neuromuscular disease that causes weakness in the skeletal muscles, which are responsible for breathing and moving parts of the body including the arms and legs. Myasthenia gravis affects approximately 2 out of every 100000 people and can occur at any age of 18 and 25 years. In Ayurveda, the symptoms of myasthenia gravis closely resemble with Vata Vyadhi. As per Ayurvedic perspective, dysregulation of the immune function occurs on account of either Ojovyapat or Ojovisramsa the dearrangement or displacement of Ojas resulting from inherent disposition, nutritional inadequacy, digestive or eliminative, vitiation of the Doshas by tissues destructions and metabolic disruption, unresolved psychological trauma or protected somatic stress, or environment or Karmic factors may lead to develop myasthenia gravis. Ojas disorders still they have no satisfactory management. Myasthenia gravis is mainly due to Srotorodha and Agnidusti. Agnidusti leads to formation of Samavastha in the body which provide hinderance in the functioning of body. A case study of Myasthenia gravis was studied and managed accordingly symptomatic improvement was noted after 21 days of treatment.

The effect of Guizot’s thought on Japan in the end of Edo period ‐ how his essay on civilization had come to Japan globally

Professor Atsuko Kawata, Faculty of Contemporary Life Sciences, Tokyo Kasei Gakuin University, Japan, is exploring the nation’s (public) power impacts of different individuals on a country’s citizens, including how they affect societal structures and gender roles, especially through educational system. During her PhD studies, Kawata discovered Naito Masu; a pioneer of women’s education in Yamanashi Prefecture in the Meiji period. A woman occupying a leading role in education was unusual for the time, which fascinated Kawata. Masu challenged the beliefs of the time, which were that Japanese women didn’t need knowledge or education, and set about championing for change. During her research on Masu, Kawata also discovered that in the Meiji period people believed that neither state nor religious power should subordinate the inner self of human beings. This sparked an interest in uncovering how this belief entered society and this led to Kawata’s current research on unpicking the gender structure that has come about since the Meiji period in modern Japan and the influence of French politics and governance. Kawata looked at the introduction of French law at the beginning of the Meiji period. She also began investigating the influence of French Minister of Public Education François Guizot â–“ and his desire to civilise Asia ‐ on Japan. She is exploring the impact of his thought, including his beliefs about civilisation, which influenced on the concepts of ‘Oyake’(public) and ‘Watakushi’(private), in Japan.

Optical widefield nuclear magnetic resonance microscopy

Microscopy enables detailed visualization and understanding of minute structures or processes. While cameras have significantly advanced optical, infrared, and electron microscopy, imaging nuclear magnetic resonance (NMR) signals on a camera has remained elusive. Here, we employ nitrogen-vacancy centers in diamond as a quantum sensor, which converts NMR signals into optical signals that are subsequently captured by a high-speed camera. Unlike traditional magnetic resonance imaging, our method records the NMR signal over a wide field of view in real space. We demonstrate that our optical widefield NMR microscopy can image NMR signals in microfluidic structures with a ~10 μm resolution across a ~235 × 150 μm2 area. Crucially, each camera pixel records an NMR spectrum providing multicomponent information about the signal’s amplitude, phase, local magnetic field strengths, and gradients. The fusion of optical microscopy and NMR techniques enables multifaceted imaging applications in the physical and life sciences.

ESTraS, an easy and simple tracking system for assessing rodent behavior

Animal behavior analysis software has become an essential tool in the life sciences. However, the currently available tools have some significant shortcomings that limit their use by individuals without programming skills, access to higher informatics resources, or the capability to invest large sums of money. We have developed and validated an easy-to-use and straightforward tracking system named ESTraS to address this issue. This freeware software allows researchers to track and analyze rodent behaviors, offering additional options such as trajectory and angle analysis. Through ESTraS, researchers can utilize unsupervised clustering techniques, such as k-means or hierarchical clustering, to further explore the obtained results. This clustering enables the classification of results based on observed similarities among subjects. The data of this manuscript shows that ESTraS can prove to be extremely valuable, not only by providing essential behavioral analysis tools but also by offering specific data analysis options with just one click.

Front Cover

Journal of Biophotonics focuses on the interdisciplinary field of biophotonics, publishing cutting‐edge research on interactions between light and biological material. The journal covers photonics research in areas such as life sciences, medicine and biomedicine, environmental science, nutrition, biology, physics, and chemistry, ranging from fundamental research to the latest clinical applications. image

Resisting Newton in provincial France, 1750s-1770s: Opposition from the margins to the Parisian academic community.

In the eighteenth century, the requirements for participation in scientific life were progressively narrowed, leading to a gradual closure of the community of the learned. This shift was influenced by the dissemination of Newton's natural philosophy across Europe, which catalysed the rejection of previously dominant principles and methods, while heralding the adoption of a new approach, based on mathematics and experimentalism. This paper examines various forms of resistance to the emergence of a community of Newtonian savants in post-1750 France, focusing on institutions and authors located at its margins. First, I analyse the relationship between provincial and central academies through the case study of the Académie des Belles-Lettres de Caen. Here, the persistent opposition to Newton was partly due to cultural conservatism but was also a form of resistance to the centralisation and concentration of expertise, and the resulting homogenisation of practices, promoted by the Paris Academy. Secondly, I examine the opposition to Newton by some authors working outside the academic milieu, who contributed to the "provincialisation" of knowledge by addressing a provincial public in their writings. Their aim was not only to engage in a dialogue with the savants of the authoritative institutions, which was almost impossible at the time, but also to appear as polemicists on the public stage, attracting a readership thirsty for scientific perspectives alternative to those considered mainstream.

The sounds of music: Tracing memories and pathways through research and resistance.

Jheannelle Johnson is a winner of the fifth annual Rising Black Scientists Awards for a scholar in the life and health sciences. We asked emerging Black scientists to tell us about their scientific vision and goals, experiences that sparked their interest in science, how they want to contribute to a more inclusive scientific community, and how these all fit together on their journey. This is her story.

Retooling science: Transforming tools into instruments of equity as a Black physician-scientist.

Victor Ekuta is a winner of the fifth annual Rising Black Scientists Awards for a scholar in the life and health sciences. We asked emerging Black scientists to tell us about their scientific vision and goals, the experiences that sparked their interest in science, how they want to contribute to a more inclusive scientific community, and how these all fit together on their journey. This is his story.

Investigating the clinical and molecular characteristics of class II and III BRAF mutations and their response to anti-EGFR therapy in MSS CRC: A comprehensive analysis.

274 Background: BRAF mutations (mts) are a heterogeneous group of molecular alterations seen in colorectal cancer (CRC). Class I BRAF mts (V600) are known to be associated with aggressive biology to CRC, but the knowledge of clinical characteristics of class II and III BRAF mts is limited. In this large cohort analysis, we evaluated the clinical and molecular features of class II and III BRAF mts and performed comparative analyses for their impact on survival outcomes. Methods: A total of 24402 MSS CRC samples were profiled by NGS (592-gene, NextSeq; WES, WTS NovaSeq) (Caris Life Sciences, Phoenix, AZ). BRAF mts were detected by NGS and classified using published literature (1). MAPK pathway activity score (MPAS) was calculated using RNA expression data. Real-world overall survival (OS) was obtained from insurance claims and calculated from tissue collection to last contact, while post-treatment survival from first treatment to last contact. KM estimates were calculated for defined patient cohorts. Significance was determined as P<0.05. Results: A total of 1270, 134, and 327 patients with class I, II, and III BRAF mts were identified. BRAF mts overall and class I BRAF mts were significantly less common among younger pts (age<50) compared to patients ≥ 50 (4.7% vs. 7.4 %; P< 0.001 and 3.2% vs. 5.7%, respectively, P<0.001). Class I BRAF mts were enriched with consensus molecular subtype 1 (CMS1) (class I, II, and III: 46% vs. 14% vs. 18% respectively) while class II and III mts had more CMS2 subtype compared to class I (2%, 30% and 29%, p<0.05). Higher MPAS scores were noted among patients with class I BRAF mts than those with class II and III mts (1.73 versus 0.38 vs 0.79). Class I BRAF mts and KRAS mts were nearly mutually exclusive (0.5%), while KRAS mts were relatively common among class II and III mts (12.8% and 27.4%, respectively). Median OS for patients with wild-type BRAF , class I, II, and III BRAF mts were significantly different (29.8, 17.3, 21.8, and 24.6 months, respectively, p<0.01). Similar OS was seen among patients who did not receive anti-EGFR therapy (28.3, 15.2, 20.7- and 21.9 months P<0.001). Patients with class III mts had significantly better OS compared to patients with class I mts (HR=1.28 CI: 1.09-1.48 p=0.002), and while no significant difference was noted for patients with class II vs class I mts, numerically more favorable outcomes were noted (mOS 21.8 vs 17.3 months P=0.133). Among treated with anti-EGFR, patients with class II and III BRAF mts had numerically better post-anti-EGFR survival compared to class I mts; however, this was not statistically significant (21.2 vs 14.2 vs. 10.4 respectively P=0.3). Conclusions: Class II and III BRAF mts represent a distinct biological subgroup of MSS CRC with distinct prognoses. Class II and III BRAF mts are associated with improved survival outcomes compared to patients with class I mts. 1. Sahin et al. JCO OP 2021.

Composition-dependent MRM transitions and structure-indicative elution segments (CMTSES)-based LC-MS strategy for disaccharide profiling and isomer differentiation.

Carbohydrates exhibit diverse functions and extensive biological activities and are notable in the field of life sciences. However, their inherent diversity and complexity-steaming from variations in isomeric monomers, glycosidic bonds, configurations, etc.-present considerable challenges in structural analysis. Considering these challenges, the disaccharide building blocks with simpler structures could provide more structural information. Although various approaches have been explored, sufficient standards or specialized equipment are required to differentiate and characterize isomers. Therefore, a strategy that addresses these challenges is urgently needed. A Composition-dependent MRM Transitions and Structure-indicative Elution Segments (CMTSES)-based liquid chromatography-triple quadrupole mass spectrometry (LC-QQQ-MS) strategy was developed to comprehensively profile disaccharide units and differentiate isomers. First, the composition-related precursor and structure-specific product ions of disaccharides were generated by QQQ-MS. Thereout, MRM transitions were proposed to enable the comprehensive profiling of disaccharides and rapid annotation of their compositions and saccharide types at both termini. Next, the linkage, composition, and configuration isomers of disaccharides were effectively differentiated and presented characteristic LC elution. Furthermore, low-cost and available "location references" (mannose, galactose, and isomaltose) were sought to define structure-indicative elution segments for the identification of isomeric hexose disaccharides. Building on this foundation, the novel CMTSES-based LC-MS strategy was designed, and its feasibility was further verified by successfully differentiating and identifying mixed homogenous and/or heterogenous disaccharide isomers in real samples. Sufficient structural information was obtained even for those consisting of diversified monomer types. This strategy comprehensively profiles both major and minor disaccharides and effectively differentiates multiple types of isomers. The use of readily available "location references" facilitated the identification of isomeric hexose disaccharide with reduced dependence on standards, thereby broadening the applicability of this strategy. However, the characterization of disaccharides with other compositions is challenging. Further in-depth investigations into intramolecular hydrogen bond simulation should provide solutions. Additionally, CMTSES-based LC-MS strategy is promising to analyze complex structures and samples.

Histological and genetic features and therapeutic responses of lung cancers explored via the global analysis of their metabolome profile.

Lung cancer is the deadliest disease globally, with more than 120,000 diagnosed cases and more than 75,000 deaths annually in Japan. Several treatment options for advanced lung cancer are available, and the discovery of biomarkers will be useful for personalized medicine. Using metabolome analysis, we aimed to identify biomarkers for diagnosis and treatment response by examining the changes in metabolites associated with lung cancer progression. Plasma samples from patients with recurrent or metastatic non-small cell lung carcinomas diagnosed at Tohoku University Hospital between 2019 and 2024 were used in this study. Metabolomic analysis was performed using the Biocrates Life Sciences MxP Quant 500 kit. Multivariate, principal component, and orthogonal partial least squares discriminant analyses were performed. The triglyceride and phosphatidylcholine concentrations were higher in the patients with early than in those with advanced lung adenocarcinomas. However, the cholesterol ester concentrations were higher for the patients with advanced lung cancer. The concentrations of hexosylceramide were higher in patients with early lung adenocarcinoma than in those with squamous cell carcinoma. Relative to epidermal growth factor receptor (EGFR)-mutation negative cases, the EGFR-mutation positive cases showed marked differences between the ceramide and triglyceride concentrations. For the best therapeutic effect of EGFR-TKI treatment, the hexosylceramide (HexCer) (d18:1/24:0), ceramide (Cer) (d18:2/22:0), and ceramide (Cer) (d18:2/24:0) concentrations were higher for the stable and progressive disease groups. The concentrations of phosphatidylcholine (PC) ae C42:2, sphingomyelin (SM) C24:1, and lysophosphatidylcholine (lysoPC) a C18:2 were higher in the partial response group treated with immune checkpoint inhibitors and chemotherapy. Metabolomic analysis may be useful for the diagnosis and treatment of lung cancer and may provide clues for new therapeutic strategies. PC ae C42:2, SM C24:1, and lysoPC a C18:2 can serve as predictive biomarkers for monitoring the therapeutic effects of the combination of immune checkpoint inhibitors and chemotherapy.

Elucidating the Memory Effects of Magnetic Water Treatment via Precipitated Phase Changes of Calcium Carbonate

Research on the effects of magnetic fields on water and aqueous solutions has produced various findings, such as the suppression of scale formation in pipes and boilers, inhibition of metal corrosion, enhancement of concrete strength, and changes in properties like viscosity and electrical conductivity. However, the challenges in quantifying these effects, the issues with reproducibility affected by trace elements in the water used in the experiments, and the involvement of complex parameters and mechanisms have led to ongoing debates, with some questioning the very existence of magnetic field effects. The “memory effect”, where the impact of magnetic exposure persists for a certain period, further complicates explanations of these phenomena. To fully elucidate and enable practical applications of these effects, further research is essential. In this study, we aimed to investigate the magnetic field effects on water, including memory effects, where the quantification and elucidation potentially lead to various applications, including environmentally friendly solutions on scale suppression and life science issues. The results revealed that the vaterite phase precipitation ratio significantly increased in magnetically treated water, reaching up to 51%, from 26% without the treatment, which is high reproducibility; furthermore, a reduction in mean particle size was observed when using magnetically treated water, suggesting that it may help prevent scaling. Furthermore, when solutions of calcium carbonate, calcium chloride, and sodium bicarbonate were individually subjected to magnetic treatment, the most notable increase in the vaterite phase precipitation ratio was observed when calcium chloride and sodium bicarbonate solutions were magnetically treated separately and then reacted to precipitate calcium carbonate.