bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial mutations in the nuclear gene encoding mitochondrial RNA polymerase restore pollen fertility in cytoplasmic male sterile tomato
Authors: Kuwabara Kosuke , Nakajima Rika , Van Bosstraeten Alexis Gaetan , Ezura Kentaro , Toriyama Kinya , Ariizumi Tohru , Shirasawa Kenta 
Published: February 2025

AbstractCytoplasmic male sterility (CMS) and restorer of fertility (Rf) are important traits in F1hybrid breeding. However, the CMS/Rfsystem has not been used in tomatoes because of the limited resources ofRflines. In this study, we performed mutagenesis in tomato CMS seeds and successfully obtained 13 suppressor mutants with pollen fertility. Using bulked segregant analysis and whole-genome sequencing for each suppressor mutant, we detected mutations associated with fertility restoration in the nuclear-encoded gene for the mitochondrial RNA polymerase termedSlRPOTmin four independent mutants created through mutagenesis. Furthermore, we found that the loss of function ofSlRPOTmwas associated with fertility restoration in the tomato CMS line. Expression analysis oforf137, a tomato CMS-causing gene, revealed that reduced expression oforf137was associated with fertility restoration in tomato CMS. In addition, F1plants carrying mutations inSlRPOTmwere generated, and tomato fruit formation was comparable to that of normal F1plants. This study demonstrates for the first time that the loss of function of mitochondrial RNA polymerase contributes to fertility restoration in CMS lines. Furthermore, it is possible to replace various tomato varieties withRflines using genome editing technology, which will promote tomato F1breeding in the future.
Investigate Channel Rectifications and Neural Dynamics by An Electrodiffusive Gauss-Nernst-Planck Approach
Authors: Liu Zichao , Li Yinyun 
Published: February 2025

AbstractElectrodiffusion plays a crucial role in modulating ion channel conductivity and neural firing dynamics within the nervous system. However, its influence on neural function remains underexplored. In this work, we introduce a novel Gauss-Nernst-Planck (GNP) approach to investigate how electrodiffusive dynamics influence ion channel rectification and neural activity. For the first time, we demonstrate that membrane conductivity is determined by both ion permeability and the harmonic mean of intramembrane ion concentration, bridging the gap between the permeability-based Goldman-Hodgkin-Katz (GHK) model and conductance-based models. We characterize the rectification properties ofGABAA,AMPA, and leaky channels by estimating their single-channel permeabilities and conductance. By integrating these rectifying channels into neurodynamic models, our GNP neurodynamic model reveals how electrodiffusive dynamics fundamentally shape neural firing by modulating membrane conductance and the interplay between passive and active ion transport-mechanisms that are often overlooked in conventional conductance-based neurodynamic models. This study provides a fundamental mechanistic understanding of electrodiffusion regulation in neural activity and establishes a robust framework for future research in neurophysiology.
Kidney cortex macrophages prevent the formation of mineral stones by reabsorbing phosphate from the urine
Authors: Wang Yuxi , Weng Yuancheng , Ding Xukai , Chen Ningting , Wang Qiang , Lu Zelin , Gao Ziqi , Chen Jianghua , Han Fei , Shen Xiao Z 
Published: February 2025

AbstractEmerging evidence showed that even in the same organ, macrophages distributed in disparate microanatomic niches execute different physiological functions. In the kidney, a recent report demonstrated that resident macrophages in the medulla were responsibe for removing sedimentary particles from urine to prevent tubule obstruction. In this study, we found that resident macrophages in the kidney cortex distinguishably highly expressed phosphate transporter SLC34A1 relative to other tissue macrophages including their counterparts in kidney medulla. The cortex juxtatubular macrophages formed transepithelial protrusions and could reabsorb phosphate from the urine via SLC34A1. As such, depletingSlc34a1from kidney macrophages increased phosphate urine output. Moreover, loss of SLC34A1 expression from kidney macrophages led to a rampant formation of intratubular calcium phosphate (CaP) microcrystals, which when in a challenge of oxalate over-exposure, accelerated the formation of kidney mineral stones. Physiologically, cortex macrophages would upregulate SLC34A1 expression in response to the overpresence of environmental CaP crystals, which could enhance phosphate reabsorption as a preventing strategy to preclude mineral stone formation in the downstream renal tubule system.
The distribution of connective tissue in humans – Reconstruction and classification
Authors: Stark Heiko , Sartori Julian 
Published: February 2025

ABSTRACTThis study aimed to measure human connective tissue distribution and characterise material properties. We used, therefore, the existing data sets of a male and female body donor from the Visible Human Project (VHP). In the first step, collagen-containing structures were segmented and reconstructed using digital image processing. In addition, several properties were characterised and analysed using computational methods. The percentage of fibrous components within the whole body was highest in the thigh. The results of the local orientation tensors showed that individual fascicles and subtendons can be resolved when isolated but not within compact regions of connective tissues.
Enhanced C/EBPα function extends healthspan and lifespan in the African turquoise killifish
Authors: Müller Christine , Muck Joscha S. , Kortman Gertrud , Hartung Josephine , Berezikov Eugene , Calkhoven Cornelis F. 
Published: February 2025

ABSTRACTThe transcription factor CCAAT/enhancer binding protein alpha (C/EBPα) regulates cell differentiation, proliferation, and function in various tissues, including the liver, adipose tissue, skin, lung, and hematopoietic system. Studies in rats, mice, humans, and chickens have shown that CEBPA mRNA undergoes alternative translation initiation, producing three C/EBPα protein isoforms. Two of these isoforms act as full-length transcription factors with N-terminal transactivation domains and a C-terminal dimerization and DNA-binding domains. The third isoform is an N-terminally truncated variant, translated from a downstream AUG codon. It competes with full-length isoforms for DNA binding, thereby antagonizing their activity. Expression of the truncated C/EBPα isoform depends on the initial translation of a short upstream open reading frame (uORF) in CEBPA mRNA and subsequent re-initiation at a downstream AUG codon, a process stimulated by mTORC1 signaling. We investigated whether the ortholog of the CEBPA gene in the evolutionarily distant, short-lived African turquoise killifish (Nothobranchius furzeri) is regulated by similar mechanisms. Our findings reveal that the uORF- mediated regulation of C/EBPα isoform expression is conserved in killifish. Disruption of the uORF selectively eliminates the truncated isoform, leading to unrestrained activity of the full-length C/EBPα isoforms. This genetic modification significantly extended both the median and maximal lifespan and improved the healthspan of maleN. furzeri. These results highlight a conserved mechanism ofCEBPAgene regulation across species and its potential role in modulating the lifespan and aging phenotypes.
A cocktail of B vitamins with nicotinamide riboside, folate and cobalamin preserves cardiac function and mitochondrial oxidative capacities in a mouse model of heart failure
Authors: Boitard Solène E. , Delouche Morgane , Karoui Ahmed , Gressette Mélanie , Momken Iman , Bouchard Bertrand , Mercier-Nomé Françoise , Imbard Apolline , Lemaire Christophe , Garnier Anne , Ruiz Matthieu , Mericskay Mathias , Piquereau Jérôme 
Published: February 2025

AbstractDespite a substantial therapeutic arsenal to treat patients affected by heart failure (HF), no treatment specifically targets alterations of cardiac energy metabolism and mitochondrial functions. Yet, these alterations are now well-known and their involvement in HF pathophysiology has been demonstrated for years. Based on the results of previous studies demonstrating the cardiac preventive effects of B vitamins when introduced before inducing cardiac pressure overload in mice, we investigated the efficacy of a diet supplemented with a B vitamin cocktail (B3, B9 and B12 (3VitB)) to restore energy metabolism and improve cardiac function in an animal model of established HF. Heart Failure was induced by transverse aortic constriction (TAC) in male and female C57Bl6N mice and 3VitB treatment was introduced four weeks later in animals meeting criteria of heart failure with restricted ejection fraction. A 20-week survival study showed a significant longer life expectancy in TAC males treated with Vit3B in comparison with TAC males fed with normal diet, and this was associated with a reduction in the over time TAC-induced alterations of ejection fraction, stroke volume, and systolic and diastolic left ventricular diameter. Although, these effects on survival and cardiac function were less clear in females due to their higher resistance to TAC, the Vit3B cocktail was beneficial in females as 8 weeks of treatment improved physical capacities and led to milder cardiomyocyte stress-induced hypertrophy in similar ways to those observed in males. In both sexes, 3VitB treated TAC mice exhibited higher mitochondrial oxidative capacities than TAC mice fed with normal diet. This was at least partly supported by the maintenance of the mitochondrial biogenesis process activation, demonstrated by the higher expression of genes such asTfamand NRF1 protein level in 3VitB treated TAC groups. Interestingly, our results revealed sex-specificities not only in response to cardiac pressure overload but also in response to 3VitB treatment that acted through different mechanisms that involved AMPK in males and SIRT1 in females. Overall, this study demonstrated the efficacy of 3VitB to preserved cardiac function and energy metabolism in an established HF model, especially in males that are more sensitive to cardiac pressure overload. This confers credit to vitamin supplementations and to metabolic therapy as new strategies in the treatment of HF.
ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and a multi-database search strategy
Authors: Lyu Mengge , Chen Yi , Hu Pingping , Zhang Guangmei , Ma Kunpeng , Zhang Xuedong , Liu Pu , Zhang Sai , Li Xiangqing , Sun Rui , Guo Tiannan 
Published: February 2025

AbstractCo-fractionation mass spectrometry (CF-MS) enables large-scale profiling of endogenous protein-protein interactions. Protein complexes identified by CF-MS using different databases are typically integrated. However, this integration uses varying cutoffs, leading to inconsistencies in protein complex identification. Here, we present ProteoAutoNet, a robotic experimental platform integrating multi-database search strategy into machine learning models, for high-throughput CF-MS analysis. This workflow increases the throughput of sample processing from protein complex to peptide by about two times. We then applied this workflow to map protein interaction networks in thyroid cancer cell lines, identifying significantly upregulated proteasome and prefoldin complexes in lung metastatic follicular thyroid carcinoma cell line FTC238 compared to normal thyroid cell line Nthy-ori 3-1. Notably, we identified a novel protein interaction network comprising PFAS, TGM2, and HK1 that was significantly upregulated in the papillary thyroid carcinoma cell line TPC-1. ProteoAutoNet provides an improved approach for investigating protein-protein interactions and uncovering novel networks, driving advancements in high-throughput proteomics research.
Multiple Effects of Artificial Lighting at Night on Male Glow-worms’ Mate Searching Behaviour
Authors: Moubarak Estelle M. , Fernandes A. Sofia David , Stewart Alan J. A. , Niven Jeremy E. 
Published: February 2025

AbstractArtificial lighting at night (ALAN) has been identified as a driver of insect decline, disrupting their ecology, behaviour and physiology. Recent studies have begun to identify the mechanisms by which ALAN affects nocturnal insects but focus primarily on moths. In glow-worms (Lampyris noctiluca), population survival relies on males detecting and reaching the glow emitted by bioluminescent females at night. Despite evidence suggesting many deleterious effects of ALAN on their mating success, little is known about the behavioural mechanisms underlying those effects. Using a translational approach, we assessed males’ ability to detect and approach females, both in nocturnal conditions and under ALAN showing that males land near a female before walking towards it. Thus, males navigate through dense vegetation to find a mate. Males walking on a trackball were highly reliable in adjusting their course to rapid left to right shifts of a green LEDs mimicking females’ glow, reorienting in less than 1 second. Under ALAN, males’ reliability to detect the dummy female was significantly hindered, along with their speed, stamina and orientation. This indicates ALAN has multiple simultaneous impacts on the ability of males to reach females, impairing their mating with potentially severe consequences on glow-worm’s population survival.
MoDorado: Enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers
Authors: Rübsam Franziskus N. M. , Liu-Wei Wang , Sun Yu , Patel Bhargesh Indravadan , van der Toorn Wiep , Piechotta Michael , Dieterich Christoph , von Kleist Max , Ehrenhofer-Murray Ann E. 
Published: February 2025

ABSTRACTRapid and accurate identification of tRNA modifications is crucial for understanding their role in protein translation and disease. However, their detection on tRNAs is challenging due to their high modification density. Recently, modification calling models for nanopore direct RNA sequencing became available for pseudouridine (Ψ), m6A, inosine and m5C, as part of the Dorado basecaller. Applying the Ψ model to tRNAs, we have mapped both known and novel Ψ sites inSchizosaccharomyces pombeand assigned the responsible pseudouridine synthetases. Furthermore, we have developed MoDorado, an algorithm to detect modifications beyond those used in model training (“off-label use”) by measuring prediction differences of pre-trained machine learning models. By leveraging the Ψ/m6A/inosine/m5C models, MoDorado detected seven additional modifications (ncm5U, mcm5U, mcm5s2U, m7G, queuosine, m1A, and i6A), thus generating a tRNA modification map ofS. pombe. This work demonstrates the potential of pre-trained models in determining the intricate landscape of tRNA modifications.
Mycelium Biocomposites from Agricultural and Paper waste: Sustainable alternative to plastic foam based secondary packaging
Authors: Biby Sandra Rose , Surendran Vivek , Kundanati Lakshminath 
Published: February 2025

AbstractPlastic foams, which were once lauded as a breakthrough invention in packaging and insulation industries, have gradually evolved into a global problem and are more concerning in developing nations because of ineffective waste management systems. The convenience and pervasiveness of these come at a high cost with adverse effects on human health and our planet’s ecosystems as they are not biodegradable. It is pivotal that an alternative and sustainable solution is found to address this problem. Mycelium-based biocomposites, made up of root-like networks called hyphae are sought out as a potential substitute for plastic-based foams as they are biodegradable. They employ a waste-to-value strategy by using agricultural wastes as a growing media for the mycelium. The study primarily focuses on the comparative analysis of mycelium-based biocomposites with existing foam materials such as Expanded PolyStyrene (EPS) and evaluates their efficacy as a biodegradable packaging material. Thus, we plan to identify the efficacious strain of mycelium fromPleurotus ostreatusorGanoderma lucidumand also explore various substrate materials such as cocopith, cardboard, paper, and sawdust. Our preliminary compression results show that the biocomposites can be engineered to have Young’s modulus ranging from 1-3 MPa for both strains. These results show that mycelium-based biocomposites can be a promising alternative to EPS /Styrofoam and move towards a sustainable solution that can reduce the dependence on non-biodegradable foam-based materials in developing nations like India.
From literature to biodiversity data: mining arthropod organismal and ecological traits with machine learning
Authors: Cornelius Joseph , Detering Harald , Lithgow-Serrano Oscar , Agosti Donat , Rinaldi Fabio , Waterhouse Robert M. 
Published: February 2025

AbstractThe fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organisms and their ecologies. However, access to and extraction of relevant data from this extensive resource remain challenging. Advances in text and data mining (TDM) and Natural Language Processing (NLP) techniques offer new opportunities for liberating such information from the literature. Testing and using such approaches to annotate articles in machine actionable formats is therefore necessary to enable the exploitation of existing knowledge in new biology, ecology, and evolution research. Here we explore the potential of these methods to annotate and extract organismal and ecological trait data for the most diverse animal group on Earth, the arthropods. The article processing workflow uses manually curated trait dictionaries with trained NLP models to perform labelling of entities and relationships of thousands of articles. A subset of manually annotated documents facilitated the formal evaluation of the performance of the workflow in terms of entity recognition and normalisation, and relationship extraction, highlighting several important technical challenges. The results are made available to the scientific community through an interactive web tool and queryable resource, the ArTraDB Arthropod Trait Database. These methodological explorations provide a framework that could be extended beyond the arthropods, where TDM and NLP approaches applied to the taxonomy and biodiversity literature will greatly facilitate data synthesis studies and literature reviews, the identification of knowledge gaps and biases, as well as the data-informed investigation of ecological and evolutionary trends and patterns.
TISSLET Tissues-based Learning Estimation for Transcriptomics
Authors: Miloudi Ahmed , Al-Qahtani Aisha , Hashir Thamanna , Chikri Mohamed , Bensmail Halima 
Published: February 2025

In the context of multi-omics data analytics for various diseases, transcriptome-wide association studies leveraging genetically predicted gene expression hold promise for identifying novel regions linked to complex traits. However, existing methods for multi-tissue gene expression prediction often fail to account for tissue-tissue expression interactions, limiting their accuracy and effectiveness.This research addresses the challenge of predicting gene expression across multiple tissues by incorporating tissue-tissue expression correlations based on a nonlinear multivariate model. Our findings demonstrate that this model excels in estimating tissue-tissue interactions and accurately predicting missing data. These results have significant implications for multi-omics data analytics and transcriptome-wide association studies, suggesting a novel approach for identifying regions associated with complex traits.
Mother-child autonomic nervous system interaction as an indication of parental stress: 24-hour cross recurrence plot analysis
Authors: Li Jiarui , Matsunaga Michiko , Myowa Masako , Nagai Yukie 
Published: February 2025

AbstractMothers and children interact through behaviors and mutual physiological signals. Recent research has suggested that physiological interactions are sensitive biomarkers for parenting challenges such as childcare stress. Most studies have focused on short-term, activity-based interactions. However, few studies have examined longer timescale data, such as interactions containing circadian rhythms, which are closely associated with stress. This study aimed to explore the link between childcare stress and mother-child autonomic nervous system activities in daily interactions using 24-hour at-home data. Cross-recurrence plots were used to quantify interactive patterns to reflect the rich nonlinear dynamics of autonomic nervous system signals and the complex interplay between mothers and children. The relationships between quantified low-dimensional cross-recurrence plot representations and parenting stress were evaluated through multiple regression analysis. The day-to-night mother-child autonomic nervous system patterns, quantified through cross-recurrence plots, significantly predict maternal parenting stress, surpassing the predictions achieved by separately analyzing individual autonomic nervous system activity using recurrence plots.
Tracing the function expansion for a primordial protein fold in the era of fold-based function prediction: beta-trefoil
Authors: Goswami Moushmi , Srinivasan Subhashini 
Published: February 2025

ABSTRACTThe incredibly narrow protein fold bottleneck, which separates the billions of unique proteins on one side to deliver diverse biological functions on the other, arises from folds tolerating mutations during evolution. One such fold, called beta-trefoil, is present in functionally diverse proteins including cytokines involved in the immune system. The unrecognizable sequence-level diversity even among paralogs of interleukin-1, one of the cytokines within the same chromosomal locus, suggests the resilience of this fold to mutational on-slaught. Furthermore, beta-trefoil containing-proteins are known to exist along with other domains allowing them to bind to diverse macromolecular types in achieving the observed functional diversity. In this study, we use the beta-trefoil, a fold prevalent across kingdoms, to assess the reach and limitations of function prediction using fold-fold comparison. We found thirty-two distinct functions for proteins containing at least one trefoil domain by mining both the PDB and AlphaFold databases. Among the novel domain architecture including trefoil domain, we find domains such as chitinase, lipase, beta-glucosidase, protein kinase, peptidoglycan-binding + peptidase matrixin, glycosyl hydrolases family 3 + PA14 + fibronectin type- III, alpha galactosidase A, PhoD-like phosphatase, insecticidal crystal toxin, trypsin, alginate lyase and two unknown domains. The limitations of structure-structure comparison tools may arise from converging evolution in folds. This was addressed by creating phylogenetic tree from structure-based multiple sequence alignment of trefoil domains from diverse kingdoms and functions. The clades by kingdoms as opposed to functions may support the hypothesis that beta-trefoil evolved independently, perhaps creating a twilight zone in function prediction using fold-fold comparison.