bluuebunny/crossref_metadata_2025_split huggingface dataset:
A biological growth model using continued fraction of straight lines
Authors: S Shruti I , S Vijay Prakash 
Published: January 2025

AbstractS-shaped curves are ubiquitous in biology especially when it comes to growth of a population or even an individual. Growth models such as the classical Verhulst-Pearl logistic growth equation and its extensions effectively model such S-shaped growth curves. Most of these models are parametrised by three or more parameters. In this work, continued fraction of straight lines has been applied to model S-shaped curves of biological growth through the use of only two parametersaandm. Here,mis the maximum growth rate andais the parameter restricting the growth rate. The parametersaandmhelp to better interpret the data when compared to the logistic growth model sincemrepresents factors promoting growth whilearepresents the constraints on growth. This model is effective for modeling both population as well as individual growth, especially around the phase of rapid growth.
Soluble Immune Checkpoint Protein and Lipid Network Associations with All-Cause Mortality Risk: Trans-Omics for Precision Medicine (TOPMed) Program
Authors: Rodriguez Annabelle , Yang Chaojie , Gan Wenqi , Karlinsey Keaton , Zhou Beiyan , Rich Stephen S. , Taylor Kent D. , Guo Xiuqing , Rotter Jerome I. , Johnson W. Craig , Cornell Elaine , Tracy Russell P. , Durda J. Peter , Gerszten Robert E. , Clish Clary B. , Blackwell Thomas , Papanicolaou George J. , Lin Honghuang , Raffield Laura M. , Vargas Jose D. , Vasan Ramachandran , Manichaikul Ani 
Published: January 2025

AbstractAdverse cardiovascular events are emerging with the use of immune checkpoint therapies in oncology. Using datasets in the Trans-Omics for Precision Medicine program (Multi-Ethnic Study of Atherosclerosis, Jackson Heart Study [JHS], and Framingham Heart Study), we examined the association of immune checkpoint plasma proteins with each other, their associated protein network with high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C), and the association of HDL-C- and LDL-C-associated protein networks with all-cause mortality risk. Plasma levels of LAG3 and HAVCR2 showed statistically significant associations with mortality risk. Colocalization analysis using genome wide-association studies of HDL-C or LDL-C and protein quantitative trait loci from JHS and the Atherosclerosis Risk in Communities identified TFF3 rs60467699 and CD36 rs3211938 variants as significantly colocalized with HDL-C; in contrast, none colocalized with LDL-C. The measurement of plasma LAG3, HAVCR2, and associated proteins plus targeted genotyping may identify patients at increased mortality risk.
Performance management and development system in South Africa, a necessary evil. Qualitative study
Authors: Ibeziako Ozo J 
Published: January 2025

AbstractPerformance management, primarily developmental-oriented, improves individual and organisational performance as key enablers of improved services. Accomplishing performance management’s objectives are critical in the current global challenges of the shortage of healthcare workers and providing equitable, quality healthcare for all. The weakened South African district-based primary healthcare system is strongly linked to poor leadership and governance. This study aims to understand how doctors in primary health care experience the performance management and development system. The objectives explored what medical officers know about it and their experiences. Emerging themes could provide insights into improving its implementation. The study used a qualitative, interpretive phenomenological research design. Data was collected through Focus Group Discussions with semi-structured interview guide. Stratified purposive sampling was used, and thematic analysis was performed. The overarching theme was Performance Management and Development System, a necessary evil with benefits and challenges. The subthemes included understanding its multiple components, understanding clinic systems to improve service outcomes, promoting employee-supervisor interactions and interconnectedness, creating a performance and learning culture, and personal and professional growth. Effective and efficient implementation of the Performance Management and Development System at the coalface demands that managers and supervisors drive this process in an informed and strategic manner. Managers and supervisors entrusted with clinical governance should invest time in personal development to understand the process and creatively consider a fit-for-purpose implementation tool.
“Our kids are our future”: Barriers and facilitators to vaccine uptake and timeliness among Aboriginal children aged under five years in Boorloo (Perth), Western Australia
Authors: Puca Carla , Wood-Kenney Paige , Nelson Naomi , Hansen Jordan , Mathews Judy , van der Helder Erin , Kickett Justin , Robinson Melanie , Attwell Katie , Phillips Anastasia , Swift Valerie , Blyth Christopher C. , Carlson Samantha J. 
Published: January 2025

AbstractIntroductionRates of several vaccine preventable diseases, and associated hospitalisation, are higher among Aboriginal and/or Torres Strait Islander children than non-Indigenous children. Western Australia has among the lowest childhood vaccine coverage in Australia, particularly among Aboriginal and/or Torres Strait Islander children. Delayed vaccination is also more common in this population. This project aimed to understand the barriers and facilitators to vaccine uptake and timeliness among Aboriginal and/or Torres Strait Islander children aged under five years in Boorloo (Perth).MethodsThe Tailoring Immunisation Programs method was used to determine the barriers and facilitators to vaccination. Between March – November 2023, in-depth interviews were conducted with 18 parents/carers of Aboriginal and/or Torres Strait Islander children in Boorloo who were currently or previously overdue for one or more childhood vaccines. Qualitative data were analysed in NVivo 14 using deductive and inductive coding following the Capability-Opportunity-Motivation-Behaviour model.ResultsThe majority of participants believed vaccines are safe, effective and supported vaccination as a means to strengthen the next generation of Aboriginal and/or Torres Strait Islander children. Barriers to on-time vaccination related to access and ineffective reminder systems. Participants expressed limited knowledge about additional vaccines recommended for Aboriginal and/or Torres Strait Islander children under Australia’s National Immunisation Program.ConclusionAn increase in vaccine coverage and timeliness will optimise protection and decrease the burden of disease in Aboriginal and/or Torres Strait Islander children in Boorloo. This can be supported by policy interventions to better cater for the needs of families, including addressing transport challenges, being mindful of the wider network of kin and care relationships, ensuring the funding of Aboriginal health services, and co-designing culturally appropriate resources. The federal government should use the Centrelink system to notify all eligible families of pending vaccines due.
Protein Structure Description with ρ, θ and ϕ: A Case Study with Caenopore-5
Authors: Li Wei 
Published: January 2025

AbstractSince its establishment in 1971, the Protein Data Bank (PDB) has been using Cartesian coordinate system (CCS) as the standard framework for protein structure description withx, y, z. Despite the interconvertibility of CCS and spherical coordinate systems (SCS, ρ, θ and ϕ), CCS remains to date the default and the only framework for protein structure description in PDB. Recent advances in protein structure prediction (e.g., AlphaFold) revolutionized the field by integrating deep learning algorithms with experimental structural data, achieving unprecedented accuracy of protein structure prediction and relying on Cartesian representation of protein structures to extract geometric features, such as inter-residue distances and dihedral angles, which are essential for building and visualizing protein structures withx, y, z. To this end, questions remain about the potential for further improvement in the performance of protein structure prediction, i.e., what is going to drive the next stage of its continued development with improved accuracy and efficiency. Therefore, this article introduces an alternative coordinate system for protein structure description and feature extraction. Using Caenopore-5 as an example, this article redefines protein backbone structures using atomic bonding networks (ABN) within the SCS framework (ABN-SCS), leading to the extraction of a set of spherical parameters (ρ, θ and ϕ) from the NMR ensemble of Caenopore-5, encompassing 477 covalent bonds and 80 peptide bonds within its backbone for each structural model in its NMR ensemble. Overall, this work offers an alternative spherical framework (ABN-SCS), i.e., a new language (ρ, θ, ϕ), for protein structure description and ABN-SCS-based extraction of spherical geometric features for protein structure prediction, aiming to contribute a little bit to its performance and application in drug discovery and design.
Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells
Authors: Kowar Alexander , Becker Jonas P. , Del Pizzo Rossella , Tang Zhiwei , Champagne Julien , Körner Pierre-René , Navarro Jasmine Montenegro , Tilghman Fiona Megan , Sakeer Hanan , Riemer Angelika B. , Agami Reuven , Loayza-Puch Fabricio 
Published: January 2025

AbstractMitosis is a critical phase of the cell cycle and a vulnerable point where cancer cells can be effectively disrupted, leading to cell death and inhibition of tumor growth. However, challenges such as drug resistance remain significant in clinical applications. During mitosis, mRNA translation is generally downregulated, while non-canonical translation of specific transcripts proceeds. Here, we demonstrate that mitotic cancer cells redistribute ribosomes toward the 5’ untranslated region (5’ UTR) and the start of the coding sequence (CDS), enhancing the translation of thousands of upstream open reading frames (uORFs) and upstream overlapping open reading frames (uoORFs). This mitotic induction of uORF/uoORF enriches the presentation of immunopeptides at the surface of cancer cells following treatment with mitotic inhibitors. Functional assays indicate the potential of such neoepitopes to provoke cancer-cell killing by T cells. Altogether, our findings highlight the therapeutic potential of targeting uORF/uoORF-derived neoepitopes in combination with mitotic inhibitors to enhance immune recognition and tumor cell elimination.
SLFN11-mediated tRNA regulation induces cell death by disrupting proteostasis in response to DNA-damaging agents
Authors: Iimori Yuki , Morita Teppei , Masuda Takeshi , Kitajima Shojiro , Kono Nobuaki , Kageyama Shun , Galipon Josephine , Sasaki Atsuo T. , Kanai Akio 
Published: January 2025

ABSTRACTDNA-damaging agents (DDAs) have long been used in cancer therapy. However, the precise mechanisms by which DDAs induce cell death are not fully understood and drug resistance remains a major clinical challenge. Schlafen 11 (SLFN11) was identified as the gene most strongly correlated with the sensitivity to DDAs based on mRNA expression levels. SLFN11 sensitizes cancer cells to DDAs by cleaving and downregulating tRNALeu(TAA). Elucidating the detailed mechanism by which SLFN11 induces cell death is expected to provide insights into overcoming drug resistance. Here, we show that, upon administration of DDAs, SLFN11 cleaves tRNALeu(TAA), leading to ER stress and subsequent cell death regulated by inositol-requiring enzyme 1 alpha (IRE1α). These responses were significantly alleviated by SLFN11 knockout or transfection of tRNALeu(TAA). Our proteomic analysis suggests that tRNALeu(TAA) influences proteins essential for maintaining proteostasis, especially those involved in ubiquitin-dependent proteolysis. Additionally, we identified the cleavage sites of tRNALeu(TAA) generated by SLFN11 in cells, and revealed that tRNA fragments contribute to ER stress and cell death. These findings suggest that SLFN11 plays a crucial role in proteostasis by regulating tRNAs, and thus determines cell fate under DDA treatment. Consequently, targeting SLFN11-mediated tRNA regulation could offer a novel approach to improve cancer therapy.GRAPHICAL ABSTRACT
Unveiling Hidden Threats: Introduction of a Routine Workflow for Label-Free and Non-destructive Detection of Microplastics in Human FFPE Tissue Sections
Authors: Gruber Elisabeth S. , Karl Verena , Duswald Kristina , Bhamidipalli Mukund S. , Schlederer Michaela , Limberger Tanja , Teleky Béla , Kenner Lukas , Brandstetter Markus 
Published: January 2025

ABSTRACTMicroplastic (MP) pollution has emerged as a significant environmental and health concern. This study aimed at developing a novel method for detecting MP particles in deparaffinized formalin-fixed paraffin-embedded (FFPE) routine tissue sections of human colon samples. By utilizing mid-infrared photothermal (MIP) microscopy, also known as optical photothermal infrared (OPTIR) spectroscopy, we here aimed to establish a work-flow representing a non-destructive infrared spectroscopic approach for distinct identification and localization of polymers in FFPE colon tissue sections by respecting standardized protocols well integrated into clinical routine. After OPTIR analysis, samples were processed to H&E staining for histopathological analysis at defined regions of interest. By using OPTIR spectroscopy, we succeeded in localizing polyethylene (PE), polystyrene (PS), and polyethylene terephthalate (PET) MPs in distinct regions of interest (21 PE particles, 1 PS particle, 1 PET fiber) and clearly identifying the embedded polymers in the respective colon tissue sections. Subsequent H&E analysis confirmed characteristic histopathological features of inflammation spatially associated with the respective MP polymers. We present here for the first time a diagnostic workflow that has the potential to enhance our understanding of MP accumulation in routine organ tissue slides and allows for exploration of its implications for human health. The observed morphological H&E features in proximity to the identified MPs could possibly indicate a link between MP exposure and colon inflammation.
AI in ECG-Based Electrolyte Imbalance Prediction: A Systematic Review and Meta Analysis
Authors: Dasdelen Muhammed Furkan , Almas Furkan , Dasdelen Zehra Betul , Balci Yapalak Ayse Nur , Marr Carsten 
Published: January 2025

BackgroundElectrolyte imbalances significantly affect heart function, making electrocardiography (ECG) a crucial non-invasive tool. This study systematically reviewed and meta-analyzed AI models’ diagnostic accuracy for detecting these imbalances from ECG, aiming to enhance early detection and improve cardiac care.MethodsWe searched 9 databases and reference lists. Two reviewers assessed bias via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). Test performance data were extracted into 2×2 tables and pooled estimates of specificity, sensitivity, and diagnostic odds ratio (DOR) were calculated using a bivariate random-effects model, presented in forest plots and summary receiver operating characteristic curves. We explored heterogeneity by meta-regression, examining internal/external datasets and the number of leads.Results21 studies addressing potassium, calcium, and sodium were included. A meta-analysis was conducted only on potassium imbalances (10 studies), covering over 600,000 ECGs from five countries, mostly 12-lead. Among eight studies focused on hyperkalemia, pooled sensitivity, specificity, and DOR were 0.856 (95% CI: 0.829–0.879), 0.788 (0.744–0.826), and 21.8 (17.8–26.7). For hypokalemia (six studies), pooled sensitivity, specificity, and DOR were 0.824 (0.785– 0.856), 0.724 (0.668–0.774), and 12.27 (9.15–16.47). QUADAS-2 assessment showed a 52% high risk of bias in patient selection, mainly due to inadequate sampling details and case-control approaches.ConclusionAI models can detect ECG-based electrolyte abnormalities, particularly hyperkalemia, and valuable in ICU settings requiring frequent electrolyte assessments and in home monitoring for patients with end-stage renal disease. However, larger retrospective and prospective studies across diverse clinical settings, hospitals, ethnic groups, countries, and regions are warranted.
Deciphering the zebrafish hepatic duct heterogeneity and cell plasticity using lineage tracing and single-cell transcriptomics
Authors: Mi Jiarui , Ren Lipeng , Liu Ka-Cheuk , Buttò Lorenzo , Colquhoun Daniel , Andersson Olov 
Published: January 2025

AbstractDespite the liver’s recognized regenerative potential, the role of the hepatic ductal cells (a.k.a. biliary epithelial cells), its heterogeneity, and functionality remain incompletely understood in this process. This study provides a comprehensive examination of the molecular and cellular mechanisms underpinning liver ductal development and liver regeneration in zebrafish, with a spotlight on the functional roles ofherfamily genes in these processes. Using state-of-the-art knock-in zebrafish models and single-cell transcriptomics we reveal the differential expression patterns of the differenthergenes, of whichher2,her6, andher9, were identified as specific molecular signatures for distinguishing different ductal cell types with unique morphology and spatial distribution. Particularly,her9serves as a pan-ductal marker and shows responsiveness to the synergistic effect of Notch and BMP signaling. By analyzing multiple single-cell RNA-seq datasets, we identify numerous ductal markers which are functional proteins for ductal integrity, and most notably CRISPR mutagenesis demonstrates thather9is essential for hepatocyte recovery. Using multiple transgenic and knock-in zebrafish lines and genetic fate mapping, we provide a detailed characterization of the ductal remodeling process under development and extreme loss of intra-hepatic duct, highlighting the remarkable ductal cell plasticity. Single-cell transcriptomics of lineage-tracedher9-expressing liver ducts in static and regenerative states uncover distinct cell clusters with unique molecular signatures and morphology, reflecting the liver’s regenerative dynamics and highlight relevant key biological processes that could be leveraged to expedite liver regeneration.
Metatranscriptomics sheds light on “who is doing what” in the coralPorites lutea
Authors: Tandon Kshitij , Hu Juntong , Ricci Francesco , Blackall Linda Louise , Medina Mónica , Kühl Michael , Verbruggen Heroen 
Published: January 2025

AbstractGlobal decline of coral reefs due to climate change calls for effective, nature-based strategies to protect these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions of key inhabitants within coral holobionts. Using a metatranscriptomics approach, we investigated the transcriptionally active microbiome of the healthy stony coralPorites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. We show distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides the first transcriptomic evidence of the ability ofOstreobiumto transfer fixed carbon to other members of the holobiont and the coral host. Additionally, we identified critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour several distinct microbiomes with a wide array of functions.
Comprehensive Infectome Analysis Reveals Diverse Infectious Agents with Zoonotic Potential in Wildlife
Authors: Hou Xin , Wang Jing , Wang Da-Xi , Chen Ye , Li Xin-Xin , Wu Wei-Chen , Le Shi-Jia , Mei Shi-Qiang , Liu Han-Lin , Feng Yun , Yang Li-Fen , Shi Pei-Bo , Ren Zi-Rui , Yang Lin , He Hai-Jian , Song Wan-Jie , Chen Jie , Zhu Meng-Meng , Jiang Zhi-Wen , Li Xing-Mei , Li Mei-Rong , Guo Deyin , Holmes Edward C. , Deng Zi-Qing , Shi Mang 
Published: January 2025

AbstractUnderstanding wildlife-pathogen interactions is crucial for mitigating zoonotic risk. Through meta-transcriptomic sequencing we profiled the infectomes of 1,922 samples from 67 mammalian species across China, uncovering a remarkable diversity of viral, bacterial, fungal, and parasitic pathogens. Of the 195 pathogens identified, 62 were novel, including a bi- segmented coronavirus in diseased lesser pandas, which we propose represents a new genus – Zetacoronavirus. The orders Carnivora and Rodentia exhibited the highest pathogen diversity and were implicated in numerous host-jumping events. Comparative analysis of diseased versus healthy animals revealed a trend of higher pathogen loads in the former, with possible differences in tissue tropisms. In total, 48 zoonotic and 17 epizootic pathogens were identified, with frequent cross-species transmission, emphasizing the potential for emerging public health threats. This study highlights the urgent need for wildlife pathogen surveillance to inform proactive disease management strategies.
Age-dependent alterations in the head-direction signal in a rat model of Fragile X Syndrome
Authors: Moore Noah , Duszkiewicz Adrian J. , Asiminas Antonis , Dudchenko Paul A. , Peyrache Adrien , Wood Emma R. 
Published: January 2025

AbstractFragile X Syndrome (FXS) is a common monogenic cause of autism spectrum disorder and intellectual disability (ASD/ID), but the neural mechanisms underlying its symptoms remain unclear. Here, we investigate the development of the head-direction (HD) system in a rat model of FXS (Fmr1-/yrats). Using high-density silicon probes, we recorded neuronal activity in the postsubiculum (PoSub), a cortical hub of the HD system, during exploration and sleep in juvenile and adultFmr1-/yand wild-type (WT) rats. JuvenileFmr1-/yrats exhibited enhanced HD tuning characterized by sharper directional tuning curves and improved stability of the HD signal in relation to the external environment. This enhancement was intrinsic to the HD circuit and persisted across behavioral and sleep states. However, by adulthood, HD tuning inFmr1-/yrats became unstable, with increased drift in the allocentric reference frame despite intact intrinsic HD dynamics. These findings reveal a transient enhancement of spatial coding in the HD system of juvenileFmr1-/yrats, followed by a degradation in adulthood, providing insights into network-level dysfunctions in FXS and their developmental trajectories. Overall, our work establishes the HD system as a valuable and tractable model for studying neurodevelopmental disorders.