bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Production of Pseudopregnant Female Mice Using Non-Estrous Individuals and the Whitten Effect
Authors: Noguchi Yuji , Watanabe Eiji 
Published: February 2025

AbstractPseudopregnant recipient females are essential for transplanting early mouse embryos during individualization. Traditionally, pseudopregnancy is induced through mating stimulation with vasectomized males, targeting females in proestrus or estrus. However, group housing of females in animal facilities often leads to fewer females entering estrus due to the Lee-Boot effect. This study focused on utilizing non-estrous females and the Whitten effect to produce pseudopregnant females. Females exhibiting characteristics of non-estrous states were visually selected and paired monogamously with vasectomized males for three consecutive days. This approach resulted in a high copulation success rate of 72.1% (CLEA Japan, Inc.) and 77.0% (Japan SLC, Inc.) on the expected third day. Subsequent embryo transfer using successfully copulated females resulted in offspring from 93.5% of ICR females from CLEA Japan, Inc. and 89.6% of ICR females from Japan SLC, Inc. Additionally, the suitability for embryo transfer could be determined by observing the condition of the ampulla of the oviduct. While this method requires a three-day preparation period compared to conventional approaches, it offers an effective alternative for creating pseudopregnant females for embryo transfer, potentially reducing animal use and associated costs.
A reservoir model of respiration-induced perceptual alternation in binocular rivalry
Authors: Yonekura Shogo , Narita Atsushi , Kanazawa Hoshinori , Kuniyoshi Yasuo 
Published: February 2025

AbstractPerceptual alternation in human binocular rivalry is more likely to occur during certain respiratory phases. In this paper, we show that the respiration dependence of perceptual alternations can be reproduced by a randomly connected recurrent neural network coupled with respiration relevant information via a neuromodulator of norepinephrine (NA). We considered two models of NA modulations; NA increases or decreases the nonlinearity of the activation function of neurons, and we found that the shape of the likelihood function of perceptual alternation depends only on respiratory phase, regardless of whether NA increases or decreases neural nonlinearity. Our results suggest that periodic neuromodulation facilitates the switching of competing neural states in specific phases and that this effect is independent of the excitatory or inhibitory effect of NA.
Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome
Authors: Pfeifer Eugen , d’Humières Camille , Lamy-Besnier Quentin , Plaza-Onate Florian , Denise Remi , Dion Sara , Condamine Bénédicte , Touchon Marie , Ma Laurence , Burdet Charles , Mentre France , Denamur Erick , Rocha Eduardo ,   the PrediRes study group
Published: February 2025

SummaryThe use of antibiotics disrupts the gut microbiota, potentially leading to long-term health issues and the spread of resistance. To investigate the impact of antibiotics on phage populations, we followed 22 healthy individuals two weeks before and up to six months after a three-day course of 3rd-generation cephalosporins. The populations of phages encoded very rarely antibiotic resistance genes and were mostly temperate including many phage-plasmids. Gut phages remained individual-specific even after microbiome perturbation by antibiotics. Yet, we found a 20% decline in phage diversity and abundance the day after treatment, caused by the burst of a few (mostly virulent) phages. We suggest they contribute to the recovery of gut bacterial diversity, since several targetedParabacteroides distasonis, a bacterium thriving after cephalosporin treatment that only proliferated in the absence of these phages. Our findings point out that phages play a crucial role in the gut microbiota’s response to antibiotics by restoring microbial balance and diversity.Graphical abstract
SHINE: Deterministic Many-to-Many clustering of Molecular Pathways
Authors: Chen Lexin , Leung Jeremy M. G. , Zsigmond Krisztina , Chong Lillian T. , Miranda-Quintana Ramón Alain 
Published: February 2025

AbstractState-of-the-art molecular dynamics (MD) simulation methods can generate diverse ensembles of pathways for complex biological processes. Analyzing these pathways using statistical mechanics tools demands identifying key states that contribute to both the dynamic and equilibrium properties of the system. This task becomes especially challenging when analyzing multiple MD simulations simultaneously, a common scenario in enhanced sampling techniques like the weighted ensemble strategy. Here, we present a new module of the MDANCE package designed to streamline the analysis of pathway ensembles. This module integrates n-ary similarity, cheminformatics-inspired tools, and hierarchical clustering to improve analysis efficiency. We present the theoretical foundation behind this approach, termed Sampling Hierarchical Intrinsic N-ary Ensembles (SHINE), and demonstrate its application to simulations of alanine dipeptide and adenylate kinase.
Direct Optical Detection of Factor Xa Activity in Minimally Processed Whole Blood
Authors: Cartwright Alyssa P. , Wollant Benjamin C. , York Elizabeth S. , Zheng Liwei , Yee Steven , Chau Huong C. , Batsuli Glaivy , Soh H. Tom 
Published: February 2025

AbstractThe ability to measure factor Xa activity directly in whole blood samples offers a path toward point-of-care monitoring and personalized anticoagulant dosage, potentially reducing bleeding risk and other anticoagulant-associated complications. We present a strategy to enable direct optical detection of factor Xa in minimally processed whole blood samples. Our strategy relies on a custom FRET-pair labeled DNA-peptide substrate, allowing FRET ratio to be monitored as an indicator of factor Xa activity. Substrates are tethered to a tapered-fiber sensor to allow evanescent detection of fluorescence directly at the sensor surface, minimizing background media interference and enabling detection directly in blood samples. After characterizing the custom substrate and demonstrating the correlation of fiber-based measurements to an existing chromogenic assay, we demonstrate the detection of endogenous factor Xa activity in >85% whole blood. Finally, we demonstrate the detection of therapeutic concentrations of enoxaparin, a widely used anticoagulant, directly in 90% whole blood in less than an hour and correlate these measurements to activated partial thromboplastin time (aPTT) testing. Together, these results indicate a promising strategy to achieve point-of-care factor Xa detection, enabling personalized anticoagulant treatment and reducing adverse outcomes.
RFdiffusion Exhibits Low Success Rate in De Novo Design of Functional Protein Binders for Biochemical Detection
Authors: Jiang Bruce , Li Xiaoxiao , Guo Amber , Wei Moris , Wu Jonny 
Published: February 2025

AbstractThe design of high-affinity protein binders is critical for biochemical detection, yet traditional methods remain labor-intensive. AI-driven tools like RFdiffusion, a RoseTTAFold-based diffusion model, offer promising alternatives for generating protein structures with tailored binding interfaces. This study evaluates RFdiffusion’s efficacy in designingde novobinders for six targets: Strep-Tag II (a peptide tag) and five eukaryotic proteins (STAT3, FGF4, EGF, PDGF-BB, and CD4). Five binders were designed for each target and experimentally validated. While two Strep-Tag II binders outperformed streptavidin in Western blot assays, none matched the sensitivity of anti-Strep-Tag II antibodies. Binders for the other targets failed due to low expression, nonspecific binding, or undetectable affinity. Despite generating structurally diverse candidates, RFdiffusion’s success rate was limited by low-affinity designs and inconsistent recombinant expression. These results underscore the need for further optimization of AI-driven protein design tools for practical biochemical applications.
Pathology of Influenza A (H5N1) infection in pinnipeds reveals novel tissue tropism and vertical transmission
Authors: Fiorito Carla , Colom Ana , Fernández Antonio , Alonso-Almorox Paula , Andrada Marisa , Lombardo Daniel , Sierra Eva 
Published: February 2025

ABSTRACTIn 2023, an unprecedented outbreak of highly pathogenic avian influenza (HPAI) H5N1 resulted in the death of thousands of pinnipeds along the Argentinean coast, raising concerns about its ecological and epidemiological impact. Here, we present clinical, pathological, and molecular findings associated with HPAI H5N1 infection in pinnipeds from Chubut, Argentina. Necropsies were conducted on three South American Sea Lions (SASLs) (Otaria flavescens) and one Southern Elephant Seal (SES) (Mirounga leonina), followed by histopathological, immunohistochemical and RT-sqPCR analyses. Neurological clinical signs were observed in two SASLs, with one also exhibiting respiratory distress. Neuropathological findings included lymphoneutrophilic meningoencephalomyelitis and choroiditis, neuronal necrosis, gliosis, hemorrhages, and perivascular cuffing. Viral antigen was localized in neurons, glial cells, choroid plexus epithelial cells, ependymal cells, and the neuropil. Systemic manifestations included HPAI-related necrotizing myocarditis in the elephant seal and placental necrosis in a sea lion, with fetal tissues testing positive for HPAIV. Pulmonary lesions were minimal, limited to bronchial glands in one individual. RT-sqPCR confirmed HPAI H5 in all tested animals. Our findings highlight the neurotropism of HPAI H5N1 in pinnipeds, and expand the known systemic effects of the virus, revealing new tissue tropism and vertical transmission.
Multiplexed CRISPRi Reveals a Transcriptional Switch Between KLF Activators and Repressors in the Maturing Neocortex
Authors: Kirk Ryan W , Sun Liwei , Xiao Ruixuan , Clark Erin A , Nelson Sacha 
Published: February 2025

AbstractA critical phase of mammalian brain development takes place after birth. Neurons of the mouse neocortex undergo dramatic changes in their morphology, physiology, and synaptic connections during the first postnatal month, while properties of immature neurons, such as the capacity for robust axon outgrowth, are lost. The genetic and epigenetic programs controlling prenatal development are well studied, but our understanding of the transcriptional mechanisms that regulate postnatal neuronal maturation is comparatively lacking. By integrating chromatin accessibility and gene expression data from two subtypes of neocortical pyramidal neurons in the neonatal and maturing brain, we predicted a role for the Krüppel-Like Factor (KLF) family of Transcription Factors in the developmental regulation of neonatally expressed genes. Using a multiplexed CRISPR Interference (CRISPRi) knockdown strategy, we found that a shift in expression from KLF activators (Klf6, Klf7) to repressors (Klf9, Klf13) during early postnatal development functions as a transcriptional ‘switch’ to first activate, then repress a set of shared targets with cytoskeletal functions includingTubb2bandDpysl3. We demonstrate that this switch is buffered by redundancy between KLF paralogs, which our multiplexed CRISPRi strategy is equipped to overcome and study. Our results indicate that competition between activators and repressors within the KLF family regulates a conserved component of the postnatal maturation program that may underlie the loss of intrinsic axon growth in maturing neurons. This could facilitate the transition from axon growth to synaptic refinement required to stabilize mature circuits.
Repeated application of bifocal transcranial alternating current stimulation (tACS) improves network connectivity and driving performance: a double-blind sham control study
Authors: Fujiyama Hakuei , Bowden Vanessa K. , Tang Alexander D , Tan Jane , Librizzi Elisha , Loft Shayne 
Published: February 2025

AbstractMounting evidence suggests that transcranial alternating current stimulation (tACS) can enhance response inhibition, a cognitive process crucial for sustained effort and decision-making. However, most prior studies have focused on within-session effects, with limited investigation into the effects of repeated applications, which are crucial for clinical applications. We examined the effects of repeated bifocal tACS targeting the right inferior frontal gyrus (rIFG) and pre-supplementary motor area (preSMA), regions implicated in response inhibition, on inhibitory control. We also explored changes to functional connectivity and whether this stimulation improved simulated driving performance. Thirty young adults (18–35 years) were assigned to either a sham or tACS group (20 Hz, 20 minutes), undergoing five stimulation sessions over two weeks. Resting-state electroencephalography (EEG) was used to assess functional connectivity between the preSMA and rIFG during the first and fifth bifocal tACS sessions and at a 7-day follow-up. Response inhibition was measured using a stop-signal task (SST) administered throughout the sessions. Participants completed two simulated driving tasks (braking, general driving) before the first and after the final tACS intervention. Results revealed a significant improvement in functional connectivity in the tACS group across sessions, although no changes were observed in response inhibition and the braking task. Notably, general driving performance improved, with participants demonstrating closer adherence to the speed limit and greater spare attentional capacity. These findings highlight the potential of repeated bifocal tACS to enhance functional connectivity and related cognitive and motor processes, suggesting promising clinical applications for addressing issues related to cortical connectivity.
Sparse deconvolution of cell type medleys in spatial transcriptomics
Authors: Sogunmez Erdogan Nuray , Eroglu Deniz 
Published: February 2025

AbstractMapping cell distributions across spatial locations with whole-genome coverage is essential for understanding cellular responses and signaling pathways. However, current deconvolution models often assume strong overlap between reference and spatial datasets, neglecting biological constraints like sparsity and cell-type variations. As a result, these methods rely on brute-force algorithms that ignore tissue complexity, leading to inaccurate predictions, particularly in heterogeneous or unmatched datasets.We introduce Weight-Induced Sparse Regression (WISpR), a machine learning algorithm that integrates spot-specific hyperparameters and sparsity-driven modeling. Unlike brute-force methods, WISpR accurately predicts cell-type distributions while maintaining biological coherence, even in unmatched datasets. Benchmarking against five leading methods across ten datasets, WISpR consistently outperformed competitors and predicted cellular landscapes in both normal and cancerous tissues.By leveraging sparse cell-type arrangements, WISpR provides biologically informed, high-resolution cellular maps. Its ability to decode tissue organization in both healthy and diseased states marks a major advancement in spatial transcriptomics, setting a new standard for accurate deconvolution.
Correlation ofin vitrobiofilm formation capacity with persistence of antibiotic-resistantEscherichia colion gnotobiotic lamb’s lettuce
Authors: Schlechter Rudolf O. , Marti Elisabet , Remus-Emsermann Mitja N. P. , Drissner David , Gekenidis Maria-Theresia 
Published: February 2025

AbstractBacterial contamination of fresh produce is a growing concern for food safety, as apart from human pathogens, antibiotic-resistant bacteria can persist on fresh leafy produce. A prominent persistence trait in bacteria is biofilm formation, as it provides increased tolerance to stressful conditions. We screened a comprehensive collection of 174 antibiotic-susceptible and -resistantEscherichia colioriginating from fresh leafy produce and its production environment. We tested the ability of these strains to produce biofilms, ranging from none or weak to extreme biofilm-forming bacteria. Next, we tested the ability of selected antibiotic-resistant isolates to colonize gnotobiotic lamb’s lettuce (Valerianella locusta) plants. We hypothesized that a higherin vitrobiofilm formation capacity correlates with increased colonization of gnotobiotic plant leaves. Despite a marked difference in the ability to formin vitrobiofilms for a number ofE. colistrains,in vitrobiofilm formation was not associated with increased survival on gnotobioticV. locustaleaf surfaces. However, all tested strains persisted for at least 21 days, highlighting potential food safety risks through unwanted ingestion of resistant bacteria. Population densities of biofilm-formingE. coliexhibited a complex pattern, with subpopulations more successful in colonizing gnotobioticV. locustaleaves. These findings emphasise the complex behaviour of antibiotic-resistant bacteria on leaf surfaces and their implications to human safety.ImportanceEach raw food contains a collection of microorganisms, including bacteria. This is of special importance for fresh produce such as leafy salads or herbs, as these foods are usually consumed raw or after minimal processing, whereby higher loads of living bacteria are ingested than with a food that is heated before consumption. A common bacterial lifestyle involves living in large groups embedded in secreted protective substances. Such bacterial assemblies, so-called biofilms, confer high persistence and resistance of bacteria to external harsh conditions. In our research we investigated whether strongerin vitrobiofilm formation of antibiotic-resistantEscherichia colicorrelates with a better survival on lamb’s lettuce leaves. Although no clear correlation was observed between biofilm formation capacity and population density on the salad, all tested isolates could survive for at least three weeks with no significant decline over time, highlighting a potential food safety risk independently ofin vitrobiofilm formation.
MAIT cells protect in severe pneumococcal pneumonia by regulating neutrophil/macrophage antimicrobial activities
Authors: Barsac Emilie , Gonzalez Loïc , Ilango Guy , Hankard Antoine , Jouan Youenn , Lemoine Roxane , Minhas Vikrant , Lenain Marion , Benard Matthieu , Fernandez Mégane , Gaudio Albanne , Si-Tahar Mustapha , Guillon Antoine , Mallevaey Thierry , Ganskow Charity Siu Gee , Klahn Philipp , Veening Jan-Willem , Salou Marion , Lantz Olivier , Baranek Thomas , Paget Christophe 
Published: February 2025

SummaryMucosal-Associated Invariant T (MAIT) cells populate the lung tissue where they contribute to defense against respiratory infections. While MAIT cells have been implicated in host resistance to infections caused by Gram-negative bacteria, their contribution in immunity against Gram-positive bacteria-driven pneumonia is still enigmatic. Here, we demonstrate that both mouse and human MAIT cells are activated during severe infection caused byStreptococcus pneumoniae,the major cause of community-acquired bacterial pneumonia. Upon infection, lung MAIT cells undergo a transcriptional reprogramming associated with acquisition of potent antimicrobial properties. MAIT cell-deficient mice are more susceptible to pneumococcal pneumonia, including higher mortality, uncontrolled bacterial growth and dissemination, and impaired neutrophil and interstitial macrophage activity. Moreover, prophylactic stimulation of MAIT cells using cognate antigen protects from pneumococcus-induced lethal pneumonia. These findings demonstrate that MAIT cells are key cellular actors during Gram-positive bacterial infections.
Evaluating the use of Monte Carlo simulation for statistically assessing topological congruence of phylogenetic trees
Authors: DuBose James G. 
Published: February 2025

AbstractMany questions in evolutionary biology involve assessing the topological congruence between phylogenetic trees. However, quantification of tree congruence provides a single measurement that is often difficult to contextualize and use to make inferences. One approach to statistically inform measurements of tree congruence is to generate null congruence distributions using Monte Carlo simulations, which can then be used for hypothesis testing. Although this approach has previously been used in empirical studies, its validity and effectiveness have yet to be tested. Here, I evaluate this method in combination with a variety of commonly used congruence metrics. I first explore how the number of simulations conducted influences the stability of null model generation. I then explore the error and power associated with different congruence metrics and tree sizes. These findings reveal nuances to this approach that are important for researchers to consider when using it to make evolutionary inferences. Finally, I introducemanticore, an R library that provides a simple interface for researchers to utilize this approach.
Dispersive interactions determine Urea and TMAO thermodynamic effects across the protein folding landscape
Authors: Pereira Ander Francisco , Martínez Leandro 
Published: February 2025

ABSTRACTThe molecular mechanisms by which osmolytes promote protein denaturation or protection are under permanent debate, because the characterization of the structure and solvation of denatured states is a major challenge. Here we show that similar qualitative interactions occur between urea and TMAO and the β-sheet SH3 domain and the helical B domain of protein A (BdpA). The strength of non-specific interactions is the determining feature for cosolvent preferential accumulation or exclusion and dictate the free energy differences of native and denatured states. Urea and TMAO hydrogen-bonds with the proteins, on the other side, are disfavored in the denatured states relative to water. Notably, urea destabilizes partially denatured states of BdpA, which are only marginally affected by TMAO, demonstrating that osmolytes can also selectively interfere with denaturation pathways. These analyses are possible by the study of the solvation structures throughout complete folding landscapes using coarse-grained and atomistic simulations, the use of minimum-distance distribution functions, and the Kirkwood-Buff solvation theory. Cosolvent effects on folding free energies match experimental data within 1 kcal mol-1, validating force-fields and analysis methods. These findings provide a novel perspective on osmolyte-protein interplay, with implications for solvent and biomolecular design.