Life Sciences Research Articles

Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models.

Fine-tuning pretrained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing parameter-efficient fine-tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is nontrivial due to the different training strategies and data forms. To address this gap, we introduce SES-Adapter, a simple, efficient, and scalable adapter method for enhancing the representation learning of PLMs. SES-Adapter incorporates PLM embeddings with structural sequence embeddings to create structure-aware representations. We show that the proposed method is compatible with different PLM architectures and across diverse tasks. Extensive evaluations are conducted on 2 types of folding structures with notable quality differences, 9 state-of-the-art baselines, and 9 benchmark data sets across distinct downstream tasks. Results show that compared to vanilla PLMs, SES-Adapter improves downstream task performance by a maximum of 11% and an average of 3%, with significantly accelerated convergence speed by a maximum of 1034% and an average of 362%, the training efficiency is also improved by approximately 2 times. Moreover, positive optimization is observed even with low-quality predicted structures. The source code for SES-Adapter is available at https://github.com/tyang816/SES-Adapter.

Occupational inequalities in mortality from cardiovascular disease, 2020-2021.

In recent years previous declines in cardiovascular disease (CVD) have stalled. There are occupational risk factors for CVD mortality. This study seeks to examine inequalities in CVD mortality for working-age adults in the United States by occupation. Death certificate data for CVD deaths were obtained from the National Center for Health Statistics. Occupation data from these death certificates were coded to major occupation groups. Using information about the number of workers employed in these occupations obtained from the American Community Survey, we calculated mortality rates and rate ratios (RRs), adjusted for covariates associated with CVD mortality. After adjusting for age, sex, race/ethnicity, and educational attainment, workers in 11 occupations had significantly elevated RRs: food preparation and serving; construction and extraction; arts, design, entertainment, sports, and media; life, physical, and social science; farming, fishing, and forestry; legal; protective services; building and grounds cleaning and maintenance; healthcare practitioners and technical; personal care and service; and community and social services. Occupation appears to be a significant predictor of CVD mortality. Further research is needed to assess how occupational risk factors contribute to changing trends for CVD mortality. Interventions are needed to address workplace risk factors for CVD.

Moral sensitivity, moral courage, and ethical behaviour among clinical nurses.

Background: Ethical behaviour in nursing practice is integral to establishing a harmonious nurse-patient relationship and improving the quality of care. A multitude of factors shapes such behaviour. Therefore, it is crucial to understand the interplay between these factors. Research objectives: This study aimed to explore the mechanisms underlying the influence of moral sensitivity on nurses' ethical behaviour and clarify the mediating role of moral courage. Research design: This cross-sectional quantitative study was conducted between July and August 2023. Participants and Research Context: The sample comprised 465 clinical nurses from three tertiary hospitals in Zhengzhou City, Henan Province, China. Data were collected using the Chinese version of the Moral Sensitivity Questionnaire-Revised Version, Nurses' Moral Courage Scale, and Ethical Behaviour Scale for Nurses. Data analysis was performed with SPSS 26.0 and AMOS 24.0, using descriptive statistics, Pearson correlation analysis, structural equation modelling, and bootstrapping methods. Ethical considerations: This study was approved by the Ethical Review Committee of Life Sciences of Zhengzhou University, China. Results: The participants were predominantly female (95.1%), with a mean age of 31.9 years. Moral courage and moral sensitivity were positively correlated with ethical behaviour. Moral sensitivity was positively associated with moral courage. Moral courage partially mediates the relationship between moral sensitivity and ethical behaviour. The indirect effect of nurses' moral sensitivity on ethical behaviour was quantified through moral courage (indirect effect = 0.290). Conclusion: Moral courage intermediates nurses' moral sensitivity and ethical behaviour. This conclusion provides nursing administrators with the insight that improving clinical nurses' moral sensitivity and courage can contribute to ensuring appropriate ethical behaviour.

Early detection of abiotic stress in plants through SNARE proteins using hybrid feature fusion model

Agriculture is the main source of livelihood for most of the population across the globe. Plants are often considered life savers for humanity, having evolved complex adaptations to cope with adverse environmental conditions. Protecting agricultural produce from devastating conditions such as stress is essential for the sustainable development of the nation. Plants respond to various environmental stressors such as drought, salinity, heat, cold, etc. Abiotic stress can significantly impact crop yield and development posing a major threat to agriculture. SNARE proteins play a major role in pathological processes as they are vital proteins in the life sciences. These proteins act as key players in stress responses. Feature extraction is essential for visualizing the underlying structure of the SNARE proteins in analyzing the root cause of abiotic stress in plants. To address this issue, we developed a hybrid model to capture the hidden structures of the SNAREs. A feature fusion technique has been devised by combining the potential strengths of convolutional neural networks (CNN) with a high dimensional radial basis function (RBF) network. Additionally, we employ a bi-directional long short-term memory (Bi-LSTM) network to classify the presence of SNARE proteins. Our feature fusion model successfully identified abiotic stress in plants with an accuracy of 74.6%. When compared with various existing frameworks, our model demonstrates superior classification results.

Must we lose our biological connection to nature to endure changing times?

AbstractEarth has >8 billion people. Scholarly publications number nearly 7 million annually with >1 million in the life and biomedical sciences, and ≥52 professional journals specializing in conservation, ecology, or related disciplines. The challenges of applying ecological data to conservation and wildlife management can easily become overwhelming. Herein we offer reflective perspectives about the changing face of applied knowledge and engagement from our personal employment histories as ecologists working in agency, university, and non‐governmental organization (NGO) biologist positions. We suggest natural history will always be nature's glue, but knowledge steeped mostly in muddy boots and field biology are no longer the soup du jour of our profession. In many ways, new technologies have changed data collection and the scientific questions asked. Arguably, such change is not welcomed by all, but a change in overlap across decades is needed to sustain and improve upon how the planet's biological diversity can coexist with increasingly difficult human conditions. Given that 80% of the people in the United States live in urban areas, with similar numbers internationally, a future possibility may be an even greater divide between wild nature, ecological services, and enjoyment in the field. This is disturbing. Despite fundamental scientific insights that help understand critical components of the natural world, once society loses touch with nature, what will remain?

Disseminated Infection with Aspergillus fumigatus in a Scarlet Macaw Parrot (Ara macao)—A Case Report

A 3-year-old male scarlet macaw parrot (Ara macao) was presented to the Exotic Animal Clinic at the Faculty of Veterinary Medicine, Iași University of Life Sciences (Iași, Romania) for its postmortem examination. According to the owner, the parrot had been raised only in captivity and after 5 days of inappetence, lethargy, and mild respiratory clinical signs, the parrot died. The post mortem examination revealed various-sized granulomas and caseous plaques in the lungs, air sacs, spleen, intestinal serosa, and liver. Microscopically, the granulomas were characterized by a necrotic center and the infiltration of numerous multinucleated giant cells and epithelioid-like cells and by the presence of hyphae typical of Aspergillus spp. Moreover, in the liver tissue, a diffuse inflammation, with numerous fungal hyphae, was noted. The fungal culture and the PCR assay allowed for the isolation and identification of Aspergillus fumigatus from the lung and liver samples. The macroscopical lesions and the histopathological findings, with the fungal isolation and molecular confirmation of Aspergillus fumigatus by nested PCR, provided the basis for the diagnosis of disseminated aspergillosis. To the authors’ best knowledge, this is the first report of disseminated infection caused by Aspergillus fumigatus in a scarlet macaw parrot (Ara macao).

Surface Microfabrication of Lactic Acid–Glycolic Acid Copolymers Using a Gas-Permeable Porous Mold

We attempted to perform surface microfabrication of the bioabsorbable material lactic acid–glycolic acid copolymer (LG-80) using a micro-imprint lithography technique with a gas-permeable porous mold at less than 5 °C. As a result, high-resolution surface micromachining with a height of 1.26 μm and a pitch of 2.97 μm was achieved using a convex sapphire mold with a height of 1.3 μm and a pitch of 3 μm. After processing, the LG-80 exhibited high water repellency, and FT-IR analysis of the surface showed no significant change in its chemical structure, confirming that the surface microfabrication was successful, while retaining the properties of the material. This demonstrated new possibilities for surface microfabrication technology for bioabsorbable materials, which are expected to be applied in the medical and life science fields in products such as surgical implants, tissue regeneration materials, and cell culture scaffold materials. In particular, the use of micro-imprint lithography enables low-cost and high-precision processing, which will be a major step toward the practical application of bioabsorbable materials.

A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology

Equitable and accessible education in life sciences, bioengineering, and synthetic biology is crucial for training the next generation of scientists, fostering transparency in public decision-making, and ensuring biotechnology can benefit a wide-ranging population. As a groundbreaking technology for genome engineering, CRISPR has transformed research and therapeutics. However, hands-on exposure to this technology in educational settings remains limited due to the extensive resources required for CRISPR experiments. Here, we develop CRISPRkit, an affordable kit designed for gene editing and regulation in high school education. CRISPRkit eliminates the need for specialized equipment, prioritizes biosafety, and utilizes cost-effective reagents. By integrating CRISPRi gene regulation, colorful chromoproteins, cell-free transcription-translation systems, smartphone-based quantification, and an in-house automated algorithm (CRISPectra), our kit offers an inexpensive (~$2) and user-friendly approach to performing and analyzing CRISPR experiments, without the need for a traditional laboratory setup. Experiments conducted by high school students in classroom settings highlight the kit’s utility for reliable CRISPRkit experiments. Furthermore, CRISPRkit provides a modular and expandable platform for genome engineering, and we demonstrate its applications for controlling fluorescent proteins and metabolic pathways such as melanin production. We envision CRISPRkit will facilitate biotechnology education for communities of diverse socioeconomic and geographic backgrounds.

Toothbrushing programme in Saudi Arabia ‘TOPS’: a study protocol for a cluster randomised controlled trial in kindergartens, Riyadh

IntroductionDental caries among children is a major global health problem and is a particular public health challenge in Saudi Arabia. Dental caries cause pain, infection and negatively impact quality of...

A methodological approach to age estimation of the intra-puparial period of the forensically relevant blow fly Calliphora vicina via Fourier transform infrared spectroscopy.

Estimating the age of immature blow flies is of great importance for forensic entomology. However, no gold-standard technique for an accurate determination of the intra-puparial age has yet been established. Fourier transform infrared (FTIR) spectroscopy is a method to (bio-)chemically characterise material based on the absorbance of electromagnetic energy by functional groups of molecules. In recent years, it also has become a powerful tool in forensic and life sciences, as it is a fast and cost-effective way to characterise all kinds of material and biological traces. This study is the first to collect developmental reference data on the changes in absorption spectra during the intra-puparial period of the forensically important blow fly Calliphora vicina Robineau-Desvoidy (Diptera: Calliphoridae). Calliphora vicina was reared at constant 20°C and 25°C and specimens were killed every other day throughout their intra-puparial development. In order to investigate which part yields the highest detectable differences in absorption spectra throughout the intra-puparial development, each specimen was divided into two different subsamples: the pupal body and the former cuticle of the third instar, that is, the puparium. Absorption spectra were collected with a FTIR spectrometer coupled to an attenuated total reflection (ATR) unit. Classification accuracies of different wavenumber regions with two machine learning models, i.e., random forests (RF) and support vector machines (SVMs), were tested. The best age predictions for both temperature settings and machine learning models were obtained by using the full spectral range from 3700 to 600 cm-1. While SVMs resulted in better accuracies for C. vicina reared at 20°C, RFs performed almost as good as SVMs for data obtained from 25°C. In terms of sample type, the pupal body gave smoother spectra and usually better classification accuracies than the puparia. This study shows that FTIR spectroscopy is a promising technique in forensic entomology to support the estimation of the minimum post-mortem interval (PMImin), by estimating the age of a given insect specimen.

Building Research Communities for Life Science Transfer Students: Improving Retention and Student Outcomes

Building Research Communities for Life Science Transfer Students: Improving Retention and Student Outcomes

The life sciences and the history of analytic philosophy.

Comparative to the commonplace focus onto developments in mathematics and physics, the life sciences appear to have received relatively sparse attention within the early history of analytic philosophy. This paper addresses two related aspects of this phenomenon. On the one hand, it asks: to the extent that the significance of the life sciences was indeed downplayed by early analytic philosophers, why was this the case? An answer to this question may be found in Bertrand Russell's 1914 discussions of the relation between biology and philosophy. Contrary to received views of the history of analytic philosophy, Russell presented his own 'logical atomism' in opposition not only to British Idealism, but also to 'evolutionism'. On the other hand, I will question whether this purported neglect of the life sciences does indeed accurately characterise the history of analytic philosophy. In answering this, I turn first to Susan Stebbing's criticisms of Russell's overlooking of biology, her influence on J.H. Woodger, and her critical discussion of T.H. Huxley's and C.H. Waddington's application of evolutionary views to philosophical questions. I then discuss the case of Moritz Schlick, whose evolutionist philosophy has been overlooked within recent debates concerning Logical Empiricism's relation to the philosophy of biology.

Artistic mutilation of genitalia: an interpretive analysis of representations of genitalia in Indian school science textbooks

ABSTRACT Visual representations (and their censorship) are carriers of messages and are powerful tools to invoke discourses. Visuals are not just supplements to written text; rather, these can be read independently as the primary text and are crucial to scientific communication, particularly in life sciences. This paper aims to investigate various textbook depictions of genitalia and examine how ideologies are manifested through visuals in relation to the human body. Here we try to unpack the visual representations of genitalia in different discursive spaces within Indian science textbooks from 6th to 12th grade. We position our study within the hermeneutic methodological landscape and apply the socio-semiotic analytic framework developed by Serafini [Serafini, Frank. 2010. “Reading Multimodal Texts: Perceptual, Structural and Ideological Perspectives.” Children's Literature in Education 41 (2): 85–104. https://doi.org/10.1007/s10583-010-9100-5], consisting of three analytic perspectives: perceptual, structural, and ideological, to interpret the visual images of genitalia and the ideological matrix that produced these images. Our analysis of textbooks' portrayal reveals a tendency to censor or obscure genital depictions. The paper discusses the potential effects of these representations on students' health and relationships with their bodies and argues that they must engage in dialogue with discourses challenging normative understandings of the body and remain open to change.

Cover Picture: Engineering in Life Sciences 8'24

Cover Picture: Engineering in Life Sciences 8'24

Pembelajaran Distribusi Gamma dalam Masalah Biomedis: Tinjauan pada Pengaruh Dosis Beracun pada Tikus

Purpose: The objective of this study is to examine the use of the Gamma function in the Gamma distribution and its application in analyzing the effect of toxic doses on rats. Methodology: The methodology employed in this study utilizes a non-standard Gamma distribution, with a continuous random variable X that has parameters α and β. The research methods employed in this study include a literature review and a case study. Findings: The results of the calculations indicated that the mean time to death for the rats was 50 weeks, with a standard deviation of 22.36 weeks. Significance: It was also found that the probability of rats surviving for more than 60 days was less than 60%. Based on these findings, the study offers recommendations for the teaching of mathematics, particularly in the context of understanding probability distributions and their applications in biological and toxicological contexts. This study underscores the significance of grasping the Gamma distribution in anticipating and interpreting data in the life sciences, as well as the capacity of mathematical concepts to be operationalized in genuine settings.

Life sciences teachers’ integration of indigenous knowledge: A vision for making science classrooms culturally responsive

This article presents findings from a qualitative study exploring factors influencing life sciences teachers’ integration of indigenous knowledge (IK) across various topics in grades 10-12, as mandated by the curriculum and assessment policy statement in South Africa. Despite this mandate aiming to enhance accessibility and comprehension, many teachers struggle to integrate IK meaningfully. Through in-depth interviews and lesson observations with five teachers in Gauteng Province, the study reveals challenges such as inadequate training, limited support structures, and negative attitudes towards IK. Observations highlight deficiencies in pedagogical content knowledge related to IK integration. The study suggests intensified teacher training and future research focusing on textbook content and leveraging information and communication technologies to digitize IK and make its integration more meaningful and interesting. This will enhance educational experiences for both the teachers and learners in life sciences classrooms.

Molecular Differences With Therapeutic Implications in Early-Onset Compared With Average-Onset Biliary Tract Cancers.

Early-onset biliary tract cancer (eoBTC) is among the fast-growing subset of early-onset cancers, yet little is known about its biology. We sought to identify novel molecular characteristics of eoBTC in relation to average-onset BTC (aoBTC) using a real-world multiomics data set. The study comprised patients with BTC whose tumors underwent molecular analyses at Caris Life Sciences and were categorized by age (<50 years for eoBTC, ≥50 years for aoBTC). P values were adjusted for multiple testing and considered significant at Q < 0.05 (molecular comparisons) or Q < 0.25 (Gene Set Enrichment Analysis [GSEA]). Insurance claims data were used for survival analysis. The study included 5,587 patients with BTC (453 eoBTC, median age = 44 years and 5,134 aoBTC, median age = 68 years). FGFR2 fusion (15.7% in eoBTC v 5.9% in aoBTC) and NIPBL fusion (1.1% v 0%) were significantly more prevalent in eoBTC (both Q < 0.001). The interferon gamma-IFG score (fold change [FC], 1.1; Q = 0.01) and T-cell inflammation score (FC, 17.3; Q = 0.03) were significantly higher in aoBTC. On GSEA, angiogenesis was enriched in eoBTC (normalized enrichment score [NES] = 1.51; Q = 0.16), whereas IFG (NES = -1.58; Q = 0.06) and inflammatory response (NES = -1.46; Q = 0.18) were enriched in aoBTC. The median overall survival (OS) was 16.5 (eoBTC) versus 13.3 months (aoBTC), hazard ratio = 0.86, P = .004. The median OS by FGFR2 fusion (with fusion v without) was 21.7 versus 15.0 months (P = .47) for eoBTC and 18.6 versus 12.2 months (P < .001) for aoBTC. We identified crucial differences including higher prevalence of FGFR2 fusions in eoBTC and variations in immunotherapy-related markers. Better outcomes in eoBTC were affected by the FGFR2 fusion status. Our findings underscore the need for ensuring access to next-generation sequencing testing, including prompt identification of actionable targets.

A review on molecular scissoring with CRISPR/Cas9 genome editing technology.

Genome editing is a technology to make specific changes in the DNA of a cell or an organism. It has significantly altered the landscape of life sciences, facilitating the establishment of exceedingly customized genetic modifications. Among various genome editing technologies, the CRISPR/Cas9 system, a specific endonuclease induces a double stranded DNA break and enabling modifications to the genome, has surfaced as a formidable and adaptable instrument. Its significance cannot be overstated, as it not only allows for the manipulation of genomes in model organisms but also holds great potential for revolutionary advances in medicine, particularly in treating genetic diseases. This review paper explores the remarkable journey of CRISPR/Cas9, its natural function, mechanisms, and transformative impact on genome editing and finally the use of artificial intelligence and other intelligent manufacturing tools used. The introduction provides the background on genome editing, emphasizing the emergence and significance of CRISPR/Cas9. Subsequent sections comprehensively elucidate its natural function, disease modeling, agriculture, and biotechnology, address therapeutic applications, and ongoing clinical trials while also discussing prospects and ethical implications. We summarized the key findings, indicating that CRISPR/Cas9 has empowered the creation of disease-specific animal models. This provides invaluable insights into pathogenic mechanisms and opens new avenues for drug discovery, reaffirming the transformative impact of CRISPR/Cas9 on genome editing. Finally we discussed the importance of continued research and collaboration for comprehensive utilization of the inherent capabilities of this molecular precision tool in shaping forthcoming advancements.

Mathematics in medical and life sciences: special issue on applications of AI in computational modelling in medical and life sciences

Mathematics in medical and life sciences: special issue on applications of AI in computational modelling in medical and life sciences

Ultrafast Metaphotonic PCR Chip with Near-Perfect Absorber.

Polymerase chain reaction (PCR) is the gold standard for nucleic acid amplification and quantification in diverse fields such as life sciences, global health, medicine, agricultural science, forensic science, and environmental science for global sustainability. However, implementing a cost-effective PCR remains challenging for rapid preventive medical action to the widespread pandemic diseases due to the absence of highly efficient and low-cost PCR chip-based POC molecular diagnostics. Here, this work reports an ultrafast metaphotonic PCR chip as a solution of a cost-effective and low-power-consumption POC device for the emerging global challenge of sustainable healthcare. This work designs a near-perfect photonic meta-absorber using ring-shaped titanium nitride to maximize the photothermal effect and realize rapid heating and cooling cycles during the PCR process. This work fabricates a large-area photonic meta-absorber on a 6-inch wafer cost-effectively using simple colloidal lithography. In addition, this work demonstrates 30 thermocycles from 65 (annealing temperature) to 95°C (denaturation temperature) within 3min 15s, achieving an average 16.66°Cs-1 heating rate and 7.77°Cs-1 cooling rate during thermocycling, succeeding rapid metaphotonic PCR. This work believes a metaphotonic PCR chip can be used to create a low-cost, ultrafast molecular diagnostic chip with a meta-absorber.