bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sanitation-related empowerment resources are associated with women’s well-being, anxiety, and depression: findings from Bangladesh, India, Senegal, and Uganda
Authors: Mink Thea , Patrick Madeleine , Conrad Amelia , Ahmed Tanvir , Arun Srishty , Ramanarayanan Vinod , Chakraborti Niladri , Reddy Y. Malini , Nagarajan Abhilaasha , Bhan Tanushree , Sinharoy Sheela S. , Caruso Bethany A. 
Published: January 2025

AbstractNascent public health research has identified linkages between sanitation experiences and mental health. The present study examined associations between sanitation-related empowerment resources (Bodily Integrity, Safety and Security, Privacy, and Time) and mental health outcomes (well-being, depression, and anxiety).We conducted a secondary analysis of cross-sectional data collected in 2021-2022 from household surveys of women in Bangladesh, India, Senegal, and Uganda (n = 2,122). The primary exposures were sanitation-related empowerment resources measured using the Agency, Resources, and Institutional Structures for Sanitation-related Empowerment (ARISE) Scales. Three outcomes were assessed: subjective well-being (World Health Organization Well-being Index, WHO-5), anxiety (General Anxiety Disorder measure, GAD-2), and depression (Patient Health Questionnaire, PHQ-2). Linear regressions of the WHO-5, PHQ-2, and GAD-2 scores on the four sanitation-related empowerment resources were conducted.Overall mean scores for well-being were moderate, and overall mean scores for anxiety and depression indicated normal prevalence (well-being mean = 17.2, SD = 5.8, depression mean = 1.1, SD = 1.4; anxiety mean = 1.0, SD = 1.4). In the adjusted well-being model, there was a positive association between Privacy and well-being (β = 2.0, p<.001). In the adjusted depression model, there were negative associations between Bodily Integrity and depression (β = -0.3, p=.002) and between Privacy and depression (β = -0.4, p<.001). In the adjusted anxiety model, there were negative associations between all four resources and anxiety (Bodily Integrity β = -0.7, p<.001; Safety and Security β = -0.3, p=.025; Privacy β = - 0.3, p=.037; Time β = -0.2, p=.009).Our findings provide evidence of associations between women’s sanitation-related resources of Bodily Integrity, Safety and Security, Privacy, and Time and mental health. Sanitation initiatives should aim to enhance and evaluate women’s experiences of these resources given their potential to benefit women’s mental health and well-being.
Molecular characterisation of commonCulicoidesBiting Midges (Diptera: Ceratopogonidae) in Ireland
Authors: Isiye Elsie , Olmeda Angela Valcarcel , Curran Thomas , O’Neill David , de Waal Theo , Barry Gerald , O’Hanlon Aidan , O’Shaughnessy James , McCarthy Nicole Keohane , Vellinga Akke , Jenkinson Audrey , Johnson Alan , Barrett Damien , Costello Sarah , Zintl Annetta , O’Meara Denise 
Published: January 2025

AbstractBackgroundBiting midges in the genusCulicoides(Diptera: Ceratopogonidae) act as vectors for several arboviruses, including Bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity ofCulicoidesspecies. This study represents the first attempt to characteriseCulicoidesin this region using molecular techniques.MethodsAdultCulicoidessamples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. Additionally, using both markers, we inferred the population genetic structure and potential colonisation pathways ofCulicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland.ResultsDNA barcoding facilitated identification of 177 specimens. Eight commonCulicoidesspecies were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of Bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenusAvaritia(C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenusCulicoides s. str.(C. pulicarisandC. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement ofCulicoidessp. which could not be identified to species level through DNA barcoding. Haplotype network analysis ofC. obsoletusshowed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector.ConclusionDNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifyingCulicoides, especially species within theobsoletuscomplex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure ofCulicoidesspp. could be used to model the potential introduction routes of midge-borne pathogens into the country.
Coordination of distinct sources of excitatory inputs enhances motion selectivity in the mouse visual thalamus
Authors: Fei Yue , Luh Michelle , Ontiri Ashley , Ghauri Dawood , Hu Wenxin , Liang Liang 
Published: January 2025

SUMMARYMultiple sources innervate the visual thalamus to influence image-forming vision prior to the cortex, yet it remains unclear how non-retinal and retinal input coordinate to shape thalamic visual selectivity. Using dual-color two-photon calcium imaging in the thalamus of awake mice, we observed similar coarse-scale retinotopic organization between axons of superior colliculus neurons and retinal ganglion cells, both providing strong converging excitatory input to thalamic neurons. At a fine scale of ∼10 µm, collicular boutons often shared visual feature preferences with nearby retinal boutons. Inhibiting collicular input significantly suppressed visual responses in thalamic neurons and specifically reduced motion selectivity in neurons preferring nasal-to-temporal motion. The reduction in motion selectivity could be the result of silencing sharply tuned direction-selective colliculogeniculate input. These findings suggest that the thalamus is not merely a relay but selectively integrates inputs from multiple regions to build stimulus selectivity and shape the information transmitted to the cortex.HIGHLIGHTSChronic dual-color calcium imaging reveals diverse visual tuning of collicular axonal boutons.Nearby collicular and retinal boutons often share feature preferences at ∼10 µm scaleSilencing of collicular input suppresses visual responses in the majority of thalamic neurons.Silencing of collicular input reduces motion selectivity in thalamic neurons.
Network-based framework for studying etiology and phenotype diversity in primary ciliopathies
Authors: Aarts E.M. , Laman Trip D.S. , Neatu R. , Martin C.G. , Riley B. , Kraus A. , Green A. , Al-Hamed M.H. , Armstrong R.E. , Sayer J.A. , Bachmann-Gagescu R. , Beltrao P 
Published: January 2025

AbstractRecent advances in sequencing technologies have increasingly enabled the identification of genetic causes for human monogenic diseases. However, systematic understanding remains limited due to the rarity, genetic heterogeneity, and complex genotype-phenotype relationships of these diseases. Primary ciliopathies are a diverse group of rare disorders caused by variants in genes associated with the cilium, a cellular organelle involved in signaling during development and cell homeostasis. These genetic variants result in a wide spectrum of clinical phenotypes involving the brain, eye, kidney and skeleton. It remains unclear to what extent this phenotypic diversity can be attributed to the disease-causing genes and their specific roles in ciliary function. Here, we systematically compared human primary ciliopathies with each other and with mouse phenotypes by propagating known disease genes through a network of protein interactions. Network propagation improved the clustering of primary ciliopathies with shared clinical phenotypes and facilitated the identification of mouse phenotypes closely related to primary ciliopathies due to shared groups of proteins in the interaction network. By leveraging this phenotype-specific approach, we prioritized candidate genes for ciliopathies and identified likely pathogenic variants inCEP43, a novel candidate gene for human primary ciliopathies in three previously unsolved cases. This study demonstrates that network propagation enhances the genetic and phenotypic understanding of primary ciliopathies, aiding in the prioritization of candidate genes and identification of relevant mouse models for these rare disorders, and providing a framework for unraveling shared underlying mechanisms for other rare genetic diseases.
Learning-induced plasticity decreases cortical engram cell dendritic excitability during memory recall
Authors: Rosier Marius , Stuyt George , Godenzini Luca , Ryan Tomás J. , Palmer Lucy M. 
Published: January 2025

SummaryThe ability to associate stimuli to create a memory is one of the most fundamental functions of the brain. Research from the past decade has revealed that memory is encoded in sparse neuronal networks active during learning called engram cells. Although the cortex is recognized as playing an important role in memory, the biophysical properties of cortical engram cells are largely unknown. To address this, we tagged engram cells in the auditory cortex during tone fear conditioning and compared their dendritic and somatic properties with neighbouring non-engram cells. Using two-photon calcium imaging, we show that tuft dendrites of engram cells had dampened, but synchronous, activity during recall.Ex vivopatch-clamp recordings illustrated that engram cells were preferentially connected with neighbouring engram cells and had decreased excitability due to a transient increase in Ih current. Together, these findings reveal Ih-driven intrinsic plasticity which leads to specific information processing in engram cells.
NF-κB is a Central Regulator of Hypoxia-Induced Gene Expression
Authors: Shakir Dilem , Batie Michael , Kwok Chun-Sui , Kenneth Niall S. , Rocha Sonia 
Published: January 2025

AbstractHypoxia is both a physiological and pathological signal in cells. Changes in gene expression play a critical role in the cellular response to hypoxia, enabling cells to adapt to reduced oxygen availability by regulating metabolism, angiogenesis, and survival pathways. These changes are primarily mediated by the HIF family of transcription factors, however other transcription factors such as NF-κB, are also activated in the hypoxic response. Although NF-κB is known to be activated under hypoxic conditions the extent of NF-κB contributions to the hypoxic response remains poorly understood. In this study we analyse hypoxia-induced NF-κB dependent gene expression, to define the NF-κB-dependent hypoxic signature. Our analysis reveals that a significant proportion of hypoxia-induced gene expression changes are NF-κB dependent, with majority of the hypoxia downregulated genes requiring NF-κB for their repression. We show that, while the NF-κB-mediated hypoxic response may vary between cell types, there are a core subset of hypoxia inducible genes that require NF-κB across multiple cell backgrounds. We demonstrate that NF-κB is critical for reactive oxygen species (ROS) generation and regulation of genes involved in oxidative phosphorylation under hypoxic conditions. This work highlights that NF-κB has a central role in hypoxia response, regulating a broader set of genes than previously thought, providing new understanding into the gene expression regulation by hypoxia and NF-κB.
Molecular dynamics guided engineering ofAequorea victoriaGreen Fluorescent Protein chromophore interactions generates a brighter variant with improved photobleaching resistance
Authors: Ahmed Rochelle D. , Jamieson W. David , Vitsupakon Danoo , Zitti Athena , Pawson Kai A. , Castell Oliver K. , Watson Peter D. , Jones D. Dafydd 
Published: January 2025

AbstractFluorescent proteins (FPs) are a crucial tool for cell imaging, but with developments in fluorescence microscopy and researcher requirements there is still a need to develop brighter versions that remain fluorescent for longer. Using short time-scale molecular dynamics-based modelling to predict changes in local chromophore interaction networks and solvation, we constructed anAequorea victoriaGFP (avGFP) variant called YuzuFP that is 1.5 times brighter than the starting superfolding variant (sfGFP) with a near 3-fold increased resistance to photobleachingin situ. YuzuFP contained a single mutation that replaces the chromophore interacting residue H148 with a serine. Longer time scale molecular dynamics revealed the likely mechanism of action is S148 makes more persistent polar interactions with the chromophore phenol group and increases the residency time of an important water molecule. As demonstrated by live cell imaging, YuzuFP not only offers a timely upgrade as a useful green-yellow avGFP for cell imaging applications over longer timescales, but it also provides a basic scaffold for future avGFP engineering efforts.
Protein and genomic language models chart a vast landscape of antiphage defenses
Authors: Mordret Ernest , Hervé Alexandre , Vaysset Hugo , Clabby Tyler , Tesson Florian , Shomar Helena , Lavenir Rachel , Cury Jean , Bernheim Aude 
Published: January 2025

AbstractThe bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted. In this study, we developed language models to predict novel antiphage proteins in two ways: first via fine-tuning ESM2, a protein language model capable of detecting distant homology to known defense proteins, second via a genomic language model with ALBERT architecture which predicts defensive function based on genomic context. We demonstrate that applying these approaches to Actinomycetota - a phylum largely unexplored for antiphage defenses, can accurately predict previously unknown functional defense mechanisms, leading to the discovery and experimental validation of six defense systems with novel antiphage proteins. Analysis of over 30,000 bacterial genomes predicted more than 45,000 uncharacterized protein families potentially involved in antiphage defense, underscoring the vast, untapped diversity of these systems.
Activity dependent Clustering of Neuronal L-Type Calcium Channels by CaMKII
Authors: Yang Qian , Hu Lan , Lawson-Qureshi Dorian , Colbran Roger J. 
Published: January 2025

AbstractNeuronal excitation-transcription (E-T) coupling pathways can be initiated by local increases of Ca2+concentrations within a nanodomain close to the L-type voltage-gated Ca2+channel (LTCC). However, molecular mechanisms controlling LTCC organization within the plasma membrane that help creation these localized signaling domains remain poorly characterized. Here, we report that neuronal depolarization increases CaV1.3 LTCC clustering in cultured hippocampal neurons. Our previous work showed that binding of the activated catalytic domain of Ca2+/calmodulin-dependent protein kinase II (CaMKII) to an RKR motif in the N-terminal cytoplasmic domain of CaV1.3 is required for LTCC-mediated E-T coupling. We tested whether multimeric CaMKIIα holoenzymes can bind simultaneously to co-expressed CaV1.3 α1 subunits with two different epitope tags. Co-immunoprecipitation assays from HEK293T cell lysates revealed that CaMKIIα assembles multimeric CaV1.3 LTCC complexes in a Ca2+/calmodulin-dependent manner. CaMKII-dependent assembly of multi-CaV1.3 complexes is further facilitated by co-expression of the CaMKII-binding LTCC β2a subunit, relative to the β3 subunit, which cannot bind directly to CaMKII. Moreover, clustering of surface localized CaV1.3 α1 subunits in intact HEK293 cells was increased by pharmacological LTCC activation, but only in the presence of co-expressed wild-type CaMKIIα. Moreover, depolarization-induced clustering of surface-expressed CaV1.3 LTCCs in cultured hippocampal neurons was disrupted by suppressing the expression of CaMKIIα and CaMKIIβ using shRNAs. The CaMKII-binding RKR motif is conserved in the N-terminal domain of CaV1.2 α1 subunits and we found that activated CaMKIIα promoted the assembly of CaV1.2 homomeric complexes, as well as CaV1.3-CaV1.2 heteromeric complexesin vitro. Furthermore, neuronal depolarization enhanced the clustering of surface-expressed CaV1.2 LTCCs, and enhanced the colocalization of endogenous CaV1.2 LTCCs with surface-expressed CaV1.3, by CaMKII-dependent mechanisms. This work indicates that CaMKII activation-dependent LTCC clustering in the plasma membrane following neuronal depolarization may be essential for the initiation of a specific long-range signal to activate gene expression.
Host-Specific Adaptations and Global Transmission Potential of a Mexican ToBRFV Isolate: Insights from Genomic Analysis
Authors: Erika Janet Zamora-Macorra , Leobardo Ochoa-Martínez Daniel , Claudia Yaritza Chavarín-Camacho , Hammond Rosemarie W , Katia Aviña-Padilla 
Published: January 2025

AbstractThe tomato brown rugose fruit virus (ToBRFV) poses a severe global threat to tomato and pepper production due to its high transmissibility and genetic adaptability. This study provides an in-depth characterization of a Mexican ToBRFV isolate, integrating genomic variability analysis, host-specific investigations, and seed transmission studies to better understand the virus’s adaptability and dissemination pathways. Phylogenetic analysis places this Mexican isolate in close genetic proximity to strains from Israel and China, suggesting cross-regional transmission potentially facilitated by agricultural trade. Genomic comparison with 100 ToBRFV isolates revealed a notable balance between genomic stability and host-specific adaptations, particularly within the 126-kDa replicase domain proteins critical for viral replication. Specific single nucleotide variants (SNVs) were identified in these regions, exhibiting host-dependent patterns;Solanum lycopersicum(tomato) isolates maintained consistent profiles, whereas isolates fromCapsicum annuum(pepper) andCitrullus lanatus(watermelon) displayed unique substitutions. These variations suggest distinct selection pressures across hosts, potentially optimizing viral replication and survival in specific plant environments. Experimental bioassays confirmed that the Mexican isolate could infect additional species, includingPhysalis ixocarpa, andSolanum melongena, thereby expanding the known host range of ToBRFV. Seed transmission studies conducted onN. rusticarevealed a 30% reduction in germination rates for infected seeds compared to healthy controls, highlighting the virus’s impact on seed viability and underscoring the necessity of stringent biosecurity protocols. This comprehensive analysis enhances our understanding of the Mexican ToBRFV isolate genetic diversity, host specificity, and transmission dynamics.
MicroRNA signatures of VO2peak in older adult participants of the Study of Muscle, Mobility and Aging
Authors: Karere Genesio M. , Hsu Fang-Chi , Hepple Russell T. , Coen Paul M. , Cummings Steve , Newman Anne , Glynn Nancy W. , Sparks Lauren , Lane Nancy E. , Xu Jianzhao , Wagner Nathan , Li Ge , Chan Jeanne , Cox Laura A. , Kritchevsky Stephen 
Published: January 2025

AbstractBackgroundPeak oxygen consumption during exercise (VO2peak), is a direct measure of cardiorespiratory fitness (CF), a key indicator of physical function and overall health. However, the molecular changes that underpin VO2peak variation are not clear. Our objective is to understand the miRNA signatures that relate to VO2peak variation, which could provide insights to novel mechanisms that contribute to low VO2peak.MethodsWe used small RNA sequencing to analyze serum samples from 72 participants (70-79 yrs old, 53% female) of the Study of Muscle, Mobility and Aging (SOMMA). We analyzed samples from individuals with low or high VO2peak (N=18/group) as well as samples from 36 randomly selected participants spanning the entire spectrum of VO2peak. We used LIMMA analysis package for regression analysis and to identify differentially expressed miRNAs. We used receiver operating characteristic curve analysis to evaluate the Area Under the Curve (AUC) and sensitivity and specificity rates.ResultsWe identified 1,055 miRNAs expressed in all serum samples. Expression of 65 miRNAs differed between participants with low and high VO2peak (p < 0.05). After p-value adjustment, expression of 5 miRNAs (miR-1301-3p, -431-5p, -501-5p, -519a-3p, and -18a-3p) remained significantly different (FDR = 0.05). The five miRNAs had AUC ranging from 0.77 to 0.84. The optimal sensitivity and specificity ranged from 70 to 80% and 80 to 90%, respectively. After adjustment for age and sex covariates, 46 miRNAs significantly correlated with VO2peak (p < 0.05) and miR-519a-3p remained significant based on adjusted of p-values.ConclusionsWe identified a miRNA signature of VO2peak in older individuals that might provide insights to novel mechanisms that drive low VO2peak. Future studies will validate the findings in a larger, longitudinal study cohort.
Refining the nuclear mass surface with the mass of
Sn103
Authors: Nies L. , Atanasov D. , Athanasakis-Kaklamanakis M. , Au M. , Bernerd C. , Blaum K. , Chrysalidis K. , Fischer P. , Heinke R. , Klink C. , Lange D. , Lunney D. , Manea V. , Marsh B. A. , Müller M. , Mougeot M. , Naimi S. , Schweiger Ch. , Schweikhard L. , Wienholtz F. 
Published: January 2025

Mass measurements with the ISOLTRAP mass spectrometer at CERN-ISOLDE improve mass uncertainties of neutron-deficient tin isotopes towards doubly magic Sn100. The mass uncertainty of Sn103 was reduced by a factor of 4, and the new value for the mass excess of −67104(18)keV is compared with nuclear and density functional theory calculations. Based on these results and local trends in the mass surface, the masses of Sn101,103, as determined through their QEC values, were found to be inconsistent with the new results. From our measurement for Sn103, we extrapolate the mass excess of Sn101 to −60005(300)keV, which is significantly more bound than previously suggested. By correcting the mass values for Sn101,103, we also adjust the values of Sb104, Te105,107, I108, Xe109,111, and Cs112 near the proton drip line which are connected through their α and proton Q values. The results show an overall smoothening of the mass surface, suggesting the absence of deformation energy above the N=50 shell closure.

Published by the American Physical Society
2025