bluuebunny/crossref_metadata_2025_split huggingface dataset:
A combination of phenotypic responses and genetic adaptations enablesStaphylococcus aureusto withstand inhibitory molecules secreted byPseudomonas aeruginosa
Authors: Schwyter Lukas , Niggli Selina , Zajac Natalia , Poveda Lucy , Wolski Witold Eryk , Panse Christian , Schlapbach Ralph , Kümmerli Rolf , Grossmann Jonas 
Published: February 2025

AbstractStaphylococcus aureusandPseudomonas aeruginosafrequently co-occur in infections, and there is evidence that their interactions can negatively affect disease outcomes.P. aeruginosais known to be dominant, often compromisingS. aureusthrough the secretion of inhibitory compounds. We previously demonstrated thatS. aureuscan become resistant to growth-inhibitory compounds during experimental evolution. While resistance arose rapidly, the underlying mechanisms were not obvious as only a few genetic mutations were associated with resistance, while ample phenotypic changes occurred. We thus hypothesize that resistance may result from a combination of phenotypic responses and genetic adaptation. Here, we tested this hypothesis using proteomics. We first focused on an evolved strain that acquired a single mutation intcyA(encoding a transmembrane transporter unit) upon exposure toP. aeruginosasupernatant. We show that this mutation leads to a complete abolishment of transporter synthesis, which confers moderate protection against PQS and selenocystine, two toxic compounds produced byP. aeruginosa. However, this genetic effect was minor compared to the fundamental phenotypic changes observed at the proteome level when both ancestral and evolvedS. aureusstrains were exposed toP. aeruginosasupernatant. Major changes involved the downregulation of virulence factors, metabolic pathways, membrane transporters, and the upregulation of ROS scavengers and an efflux pump. Our results suggest that the observed multi-variate phenotypic response is a powerful adaptive strategy, offering instant protection against competitors in fluctuating environments and reducing the need for hard-wired genetic adaptations.ImportanceDifferent bacterial pathogens can co-occur in infections, where they interact with one another and influence disease severity. Previous research showed that pathogens can evolve and adapt to co-infecting species. Here, we show that evolution through genetic mutations and selection are not necessarily required to change pathogen behavior. Instead, we found that the human pathogenStaphylococcus aureusis able to plastically respond to the presence ofPseudomonas aeruginosa, a competing pathogen. Through proteomics and metabolomics, we demonstrate thatS. aureusundergoes substantial proteomic alterations in response toP. aeruginosaby down-regulating virulence factor expression, changing metabolism, and mounting protective measures against toxic compounds. Our work highlights that pathogens possess sophisticated mechanisms to respond to competitors to secure growth and survival in polymicrobial infections. We predict such plastic responses to have significant impacts on infection outcomes.
Deciphering Cell-Type and Temporal-Specific Matrisome Expression Signatures in Human Cortical Development and Neurodevelopmental Disorders via scRNA-Seq Meta-Analysis
Authors: Gim Do Hyeon , Assir Muhammad Z.K. , Fowler Paul A. , Morgan Michael D. , Berg Daniel A. , Kang Eunchai 
Published: February 2025

AbstractHuman cortical development is a complex process involving the proliferation, differentiation, and migration of progenitor cells, all coordinated within a dynamic extracellular matrix (ECM). ECM plays a crucial role in guiding these processes, yet its specific contributions and the implications of its dysregulation in neurodevelopmental disorders (NDDs) remain underexplored. In this study, we conducted a meta-analysis of single-cell RNA sequencing (scRNA-seq) data from 37 donors, gestational weeks (GWs) 8 to 26 across six independent studies to elucidate cell type-specific matrisome gene expression signatures and their dynamics in the developing human cortex. Our analysis identified distinct matrisome gene signatures across various cell types, with significant temporal changes during cortical development. Notably, a substantial proportion of matrisome genes are associated with NDDs, exhibiting cell type, temporal and disease specificity. These findings highlight the critical role of cell type-specific matrisome regulation in cortical development and its potential involvement in NDD pathogenesis. This study provides a comprehensive map of cell type-specific matrisome signatures in the developing human cortex and highlights the importance of ECM in both normal development and the pathogenesis of NDDs.
Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA
Authors: Mascarenhas Shyan , Hodgins Harold P. , Doxey Andrew C. 
Published: February 2025

AbstractBackgroundAncient DNA collected from archaeological specimens not only provides a window into ancient human genetic diversity but also contains a rich mixture of associated microbial DNA including potential pathogens. In recent work, we identifiedC. tetaniand tetanus neurotoxin (TeNT) genes in ancient DNA datasets collected from human archaeological specimens. However, the reasons underlying the occurrence of these toxin genes and the extent to which other toxin genes are present in ancient DNA is unclear.MethodsHere, we performed a large-scale analysis of 6,435 ancient DNA (aDNA) sequencing datasets including human and non-human sources, searching for 49 clostridial neurotoxin types and subtypes, as well as 3 additional unrelated toxins.ResultsOur search identified a total of 105 ancient DNA datasets (1.6%) containing significant matches to one or more neurotoxin genes. Consistent with our earlier work, TeNT genes were most common, found in 50 ancient DNA datasets. In addition, we identified sequences encoding diverse botulinum neurotoxins including BoNT/C (40 samples), BoNT/D (6 samples), BoNT/B (4 samples), BoNT/E (1 sample), and theEnterococcus-associated BoNT/En (10 samples). TeNT genes were detected in a broad range of ancient samples including human and animal (horse, wild bear, chimpanzee) remains, whereas the largest diversity of toxins was detected in aDNA from Egyptian mummies. Phylogenetic and sequence analysis of the identified matches revealed close identity to modern forms of these toxins. Damage analysis revealed several toxin genes with hallmarks of ancient DNA associated damage, indicative of an ancient origin.ConclusionsOur work reveals that clostridial neurotoxin genes occur frequently in aDNA samples, including human and animal-associated toxin variants. We conclude that the frequent association of these genes with aDNA likely reflects a strong ecological association of pathogenic clostridia with decaying human and animal remains and possible post-mortem colonization of these samples.
mTOR regulates Wnt signaling to promote tension-mediated lens vesicle closure
Authors: Wang Qian , Wu Hao , Mao Yingyu , Chow Alyssa , Bouaziz Michael , Wu Yihua , Zhang Xin 
Published: February 2025

AbstractLens vesicle closure is a pivotal event in ocular morphogenesis, and its disruption underlies Peters anomaly, a leading congenital cause of corneal opacity. Here, we elucidate a mechanistic hierarchy in which mTOR-Wnt signaling orchestrates cytoskeletal tension to drive this process. Conditional ablation of mTOR in the lens ectoderm induces aberrant corneal-lenticular stalk formation and transdifferentiation of the ciliary margin into neural retina. mTOR inhibition suppresses Wnt3 expression, and Wnt3 displayed a similar lens stalk phenotype, positioning mTOR as an upstream regulator of Wnt ligand production. Complete ablation of lens-derived Wnt ligands via deletion of the Wnt transporter Wls exacerbates developmental defects, triggering anterior lens herniation and ciliary margin development failure. Disruption of β-catenin-mediated Wnt signaling or dual deletion of Wnt co-receptors Lrp5/6 in lens ectoderm similarly prevents vesicle closure, recapitulating lens herniation. Strikingly, Rac1 deletion rescues corneal-lenticular stalk phenotypes in mTOR, Wls, and β-catenin mutants, directly linking Wnt effectors to cytoskeletal remodeling. Our findings establish an mTOR-Wnt-Rac1 signaling axis as the core regulator of cytoskeletal tension required for lens vesicle closure.
Single-nucleus multiomics of murine gonadal cells reveals transcriptional regulatory network underlying supporting lineage differentiation
Authors: Chen Yu-Ying , Rodriguez Karina , Alexander Adriana K. , Xu Xin , Papas Brian , Estermann Martin A. , Yao Humphrey Hung-Chang 
Published: February 2025

AbstractSex determination of mammalian gonads hinges upon sex-specific differentiation of gonadal supporting cells: Sertoli cells in the testis and granulosa cells in the ovary. To gain insights into how supporting cells acquire their identities, we performed joint single-nucleus transcriptomics and chromatin accessibility assays on murine gonadal cells across sex determination. By contrasting sex-specific gene expression and corresponding chromatin accessibility among progenitor and differentiated cells, we discovered that sex-specific chromatin regions in supporting cells are established shortly after sex determination, accompanied by the acquisition of active histone marks. The presence of potential transcription factor binding motifs in the open chromatin regions revealed regulatory networks underlying ovary-enriched factors LEF1 and MSX1, which promote granulosa fate by inducing granulosa-specific genes such asFoxl2andFst. Our results not only identify the gene regulatory framework underlying supporting cell sex differentiation, but also provide invaluable resources for the field.TeaserSex-specific changes in chromatin and gene expression underly the divergent developmental fates of the bipotential gonadal primordium.
Cell Type-Agnostic Transcriptomic Signatures Enable Uniform Comparisons of Neurodevelopment
Authors: Venkatesan Sridevi , Werner Jonathan M. , Li Yun , Gillis Jesse 
Published: February 2025

SummarySingle-cell transcriptomics has revolutionized our understanding of neurodevelopmental cell identities, yet, predicting a cell type’s developmental state from its transcriptome remains a challenge. We perform a meta-analysis of developing human brain datasets comprising over 2.8 million cells, identifying both tissue-level and cell-autonomous predictors of developmental age. While tissue composition predicts age within individual studies, it fails to generalize, whereas specific cell type proportions reliably track developmental time across datasets. Training regularized regression models to infer cell-autonomous maturation, we find that a cell type-agnostic model achieves the highest accuracy (error = 2.6 weeks), robustly capturing developmental dynamics across diverse cell types and datasets. This model generalizes to human neural organoids, accurately predicting normal developmental trajectories (R = 0.91) and disease-induced shiftsin vitro. Furthermore, it extends to the developing mouse brain, revealing an accelerated developmental tempo relative to humans. Our work provides a unified framework for comparing neurodevelopment across contexts, model systems, and species.
A network of coiled-coil and actin-like proteins controls the cellular organization of magnetosome organelles in deep-branching magnetotactic bacteria
Authors: Russell Virginia V. , Iavarone Anthony T. , Ozyamak Ertan , Grant Carly , Komeili Arash 
Published: February 2025

AbstractMagnetotactic Bacteria (MTB) are a diverse group of microorganisms that use magnetosomes, organelles composed of magnetite or greigite, to navigate along geomagnetic fields. While MTB span several phyla and exhibit diverse phenotypes, magnetosome formation has been mechanistically studied in only two species ofAlphaproteobacteria. Here, we useDesulfovibrio magneticusRS-1 to uncover the mechanisms behind tooth-shaped magnetosome assembly in deep-branching MTB. Our findings reveal that RS-1 magnetic particles initially form randomly within the cell before localizing to the positive cell curvature. Genetic and proteomic analyses indicate that early biomineralization involves membrane-associated proteins found in all MTB, while later stages depend on coiled-coil (Mad20, 23, 25, and 26) and actin-like (MamK and Mad28) proteins, most of which are unique to deep-branching MTB. These findings suggest that while biomineralization originates from a common ancestor, magnetosome chain formation has diverged evolutionarily among different MTB lineages.
Fractional and Geometric Neural Dynamics: Investigating Intelligence-Related Differences in EEG Symmetry and Connectivity
Authors: Tozzi Arturo , Jaušovec Ksenija 
Published: February 2025

ABSTRACTUnderstanding intelligence-related variations in electroencephalographic (EEG) activity requires advanced mathematical approaches capable of capturing geometric transformations and long-range dependencies in neural dynamics. These approaches may provide methodological advantages over conventional spectral and connectivity-based techniques by offering deeper insights into the structural and functional organization of neural networks. In this study, we integrate Clifford algebra, Noether’s theorem and fractional calculus to analyze EEG signals from high- and low-IQ individuals, looking for key intelligence-related differences in cortical organization. Clifford algebra enables the representation of EEG signals as multivectors, preserving both magnitude and directional relationships across cortical regions. Noether’s theorem provides a quantitative measure of symmetry properties linked to spectral features, identifying conserved functional patterns across distinct brain regions. Mittag-Leffler functions, derived from fractional calculus, characterize long-range dependencies in neural oscillations, allowing for the detection of memory effects and scale-invariant properties often overlooked by traditional methods. We found significant differences between high- and low-IQ individuals in geometric trajectories, hemispheric connectivity, spectral properties and fractional-order dynamics. High-IQ individuals exhibited increased spectral asymmetry, enhanced spectral differentiation, distinct geometric trajectories and greater fractional connectivity, particularly in frontal and central regions. In contrast, low-IQ individuals displayed more uniform hemispheric connectivity and heightened fractional activity in occipital areas. Mittag-Leffler fractional exponents further indicated that high-IQ individuals possessed more varied neural synchronization patterns. Overall, our multi-faceted approach suggests that intelligence-related neural dynamics are characterized by an asymmetric, functionally specialized and fractionally complex cortical organization. This results in significant differences in network topology, efficiency, modularity and long-range dependencies.
Impurities in a trapped one-dimensional Bose gas of arbitrary interaction strength: Localization-delocalization transition and absence of self-localization
Authors: Breu Dennis , Vidal Marcos Eric , Will Martin , Fleischhauer Michael 
Published: February 2025

We discuss impurities in a one-dimensional Bose gas with arbitrary boson-boson and boson-impurity interactions. To fully account for quantum effects, we employ numerical simulations based on the density-matrix renormalization group (DMRG) and—in the regime of strong boson-boson interactions—the mapping to weakly interacting fermions. A mean-field description of the Bose polaron based on coupled Gross–Pitaevskii Schrödinger equations predicts the existence of a self-localized polaron. We here show that such a solution does not exist and is an artifact of the underlying decoupling approximation. To this end we consider a mobile impurity in a box potential. Our work demonstrates that correlations between the impurity position and the bosons are important even in the limit where mean-field approaches are expected to work well. Furthermore, we derive analytical approximations for the energy of a single polaron formed by a heavy impurity for arbitrary interaction strengths and large but finite boson-boson couplings which accurately reproduce DMRG results. This demonstrates that the polaron problem of a heavy impurity in a one-dimensional Bose gas can be accurately approximated by a proper mean-field description plus a linearized treatment of quantum fluctuations for arbitrary boson-boson and impurity-boson couplings. Finally, we determine the polaron-polaron interaction potential V(r) in the Born-Oppenheimer approximation for small and intermediate distances r, which in the Tonks gas limit is oscillatory due to Friedel oscillations in the Bose gas.

Published by the American Physical Society
2025
Kinetic data-driven approach to turbulence subgrid modeling
Authors: Ortali G. , Gabbana A. , Demo N. , Rozza G. , Toschi F. 
Published: February 2025

Numerical simulations of turbulent flows are well known to pose extreme computational challenges because of the huge number of dynamical degrees of freedom required to correctly describe the complex multiscale statistical correlations of the velocity. On the other hand, kinetic mesoscale approaches based on the Boltzmann equation, have the potential to describe a broad range of flows, stretching well beyond the special case of gases close to equilibrium, which results in the ordinary Navier-Stokes dynamics. Here, we demonstrate that, by properly tuning, a kinetic approach can statistically reproduce the quantitative dynamics of the larger scales in turbulence, thereby providing an alternative, computationally efficient and physically rooted approach toward subgrid scale (SGS) modeling in turbulence. More specifically, we show that by leveraging data from fully resolved direct numerical simulation (DNS), we can learn a collision operator for the discretized Boltzmann equation solver (the lattice Boltzmann method), which effectively implies a turbulence subgrid closure model. The mesoscopic nature of our formulation makes the learning problem fully local in both space and time, leading to reduced computational costs and enhanced generalization capabilities. We show that the model offers superior performance compared to traditional methods, such as the Smagorinsky model, being less dissipative and, therefore, able to more closely capture the intermittency of higher-order velocity correlations. This foundational study lays the basis for extending the proposed framework to different turbulent flow settings and—most importantly—to develop new classes of hybrid data-driven kinetic-based models capable of faithfully capturing the complex macroscopic dynamics of diverse physical systems such as emulsions, non-Newtonian fluid, and multiphase systems.

Published by the American Physical Society
2025
Natural Resources and Geopolitical Risk Impact on Energy Security Risk: The Role of Renewable Energy Consumption and Foreign Direct Investment
Authors: Chen Zhongyao , He Min , Ali Muhammad 
Published: February 2025

ABSTRACTNatural resources and geopolitical risks significantly impact energy security risks. The availability and accessibility of natural resources play a significant role in determining a nation's energy vulnerability. Renewable energy consumption, particularly foreign direct investment in renewable energy projects, can help mitigate these risks by diversifying energy supplies and reducing the reliance on fossil fuels. This study examines the impact of natural resources and geopolitical risk in 38 countries at risk of geopolitical conflict between 1990 and 2021 using CO2 emissions, renewable energy consumption, and foreign direct investment as controlling variables. The long‐run analysis is based on slope heterogeneity, Westerlund cointegration, Arellano–Bond dynamic panel‐data estimation, and Robust, correlated panels corrected standard errors (PCSEs). The results indicate that the energy security index is positively associated with natural resources, geopolitical risk, CO2 emissions, and renewable energy consumption. Foreign direct investment is negatively associated with the energy security index in selected geopolitical risk countries. Improving energy security requires addressing multiple policy implications. Natural resource availability, geopolitical risk mitigation, CO2 emissions reduction, and increased renewable energy consumption are key factors. However, the negative association between FDI and energy security in selected geopolitical risk countries emphasizes the importance of careful evaluation of foreign investments to ensure their compatibility with energy security objectives. By implementing appropriate policies, countries can enhance their energy security, promote sustainable development, and mitigate risks posed by geopolitical uncertainties.
Turtle Ant Resemblance in a New World Stink Bug, Preliminary Evidence for Mimicry
Authors: Serna‐Muñoz Sebastian , Novais Samuel 
Published: February 2025

ABSTRACTIn mimicry, a species signals a fitness cost or benefit to a receiver by resemblance to another model species. While ants are among the most frequent models, few cases of ant mimicry are known in stink bugs (Pentatomidae). Here, using a geometric morphometric analysis, we propose that Rio nymphs might mimic Cephalotes ants.
The Adoption Problem in the Philosophy of Logic
Authors: Fairbank Viviane , Hlobil Ulf 
Published: February 2025

ABSTRACTIn the philosophy of logic, the Adoption Problem is a challenge to the claim that reasoners can, in certain ways, rationally change which logic they use. The (alleged) problem is that if someone does not already infer in accordance with some fundamental logical principles (such as Universal Instantiation or Modus Ponens), then they cannot rationally begin to do so: the “adoption” of these principles is either unnecessary or impossible. In the literature, three issues have emerged as especially contentious: (1) How should we understand the argument for the Adoption Problem? What exactly is the argument's conclusion, and how is it established, if at all? (2) How could someone who thinks that the rational adoption of logic is possible respond to the Adoption Problem? (3) What are the consequences of the Adoption Problem for related issues in the philosophy of logic? In this paper, we address each question in turn. We suggest that the Adoption Problem is best understood in the form of an inconsistent quartet of theses regarding logical inference. We classify positions on logical adoption in terms of which of these theses is abandoned, and we show that such a taxonomy of positions is useful for delineating the scope and consequences of the Adoption Problem.
Analysis of Pull-in Parameters of a micro electro mechanical Beam with van der Waals force using Modified couple stress theory
Authors: Saw Gyana Ranjan , Singh Suraj , Chakraborty Goutam 
Published: February 2025

Abstract
This study investigates the pull-in parameters of a microcantilever beam influenced by electrostatic and van der Waals forces in MEMS devices. The classical continuum theory(CCMT) is inadequate because of the presence of nonpolar molecules, voids, and dielectric materials at the micro or nanoscale. Modified couple stress theory(MCST) is a nonclassical continuum technique used in microbeams for evolution of the length scale parameter(lm). Non-linearity due to large scale deflection and van der Waals force is highly significant at the micro scale. The Galerkin method is used to solve the governing equation of microbeam model. The comparison of eigenfrequencies is conducted by numerical, finite element based method while varying the mass of microplate. The pull-in phenomena occurs when the actuating force is exceeds the mechanical force. The static pull-in parameters are determined using on CCMT, and Meshless local petrov galerkin(MLPG) methods and verified through COMSOL software. The pull-in voltage(Vpi), displacement(wpi), van der Waals parameter(Cpi) are in close match with numerical and analytical methods. The variation lm is influenced by damping constant, stiffness of microbeam under dynamic pull-in conditions.