bluuebunny/crossref_metadata_2025_split huggingface dataset:
Psychosis-linked Symptoms and Structural Brain Patterns in Cognitive Subgroups among Familial High-Risk Children in the ABCD Study
Authors: Türközer Halide Bilge , Karcher Nicole R. , Clauss Jacqueline , Nordentoft Merete , Lewandowski Kathryn E. , Roffman Joshua L. , Öngür Dost 
Published: February 2025

ABSTRACTObjectiveChildren at familial high risk for psychosis (FHR) are at substantially increased risk for psychotic disorders and other serious mental illnesses. Identifying risk subgroups within FHR youth may enhance prediction models to identify children at greatest risk for potential intervention. This study investigated psychosis-linked symptoms and structural brain patterns in neurocognitive subgroups among FHR children in the Adolescent Brain Cognitive Development (ABCD) Study using baseline, 2-year, and 4-year follow-up data.MethodsAmong children with first- and second-degree family history of psychosis, neurocognitive subgroups were defined using NIH Toolbox Cognitive Battery baseline age-corrected total scores: children with low (FHR-LC, 0-33%, n=234), moderate (FHR-MC, 33-66%, n=261), and high (FHR-HC, 66-100%, n=277) cognitive performance. Psychiatric symptoms were assessed using Prodromal Questionnaire-Brief Child Version (PQ-BC) and Childhood Behavior Checklist (CBCL). Regional vulnerability indices (SSD-RVIs), which quantify the similarity of participants’ structural brain patterns to the patterns found in adults with schizophrenia spectrum disorders, were calculated using cortical thickness measures following rigorous quality control.ResultsAt baseline, FHR-LC had significantly higher PQ-BC and CBCL scores, and trend-level higher SSD-RVIs compared to FHR-HC. Longitudinally, PQ-BC and CBCL scores decreased with age across all FHR participants, while SSD-RVIs remained stable. No longitudinal cognitive subgroup-by-age interactions were observed, indicating that subgroup differences persisted over time.ConclusionChildren at FHR who have concurrent poor cognitive performance exhibit elevated and stable clinical and imaging psychosis risk markers. This suggests that they may represent a risk subgroup with elevated vulnerability, presenting an opportunity for early identification and intervention.
Prognostic implications of splenomegaly in BCMA-directed CAR T-Cell therapy for relapsed myeloma
Authors: Wiemers Thomas , Ferle Maximilian , Ader Jonas , Sotikova Veronika , Fandrei David , Grieb Nora , Fischer Luise , Born Patrick , Weidner Heike , Wang Song Yau , Jentzsch Madlen , Franke Georg-Nikolaus , Herling Carmen , Metzeler Klaus , Herling Marco , Heyn Simone , Denecke Timm , Reiche Kristin , Platzbecker Uwe , Vucinic Vladan , Meyer Hans-Jonas , Neumuth Thomas , Merz Maximilian 
Published: February 2025

AbstractB-cell maturation antigen (BCMA)-directed chimeric antigen receptor (CAR) T-cell therapy has shown promise for patients with relapsed or refractory multiple myeloma (RRMM), yet its use is often complicated by adverse events such as cytokine release syndrome and hematologic toxicities. This study evaluates the prognostic significance of spleen size, measured via computed tomography (CT), in predicting clinical outcomes for RRMM patients undergoing CAR T-cell therapy. We retrospectively analyzed data from patients treated with Idecabtagene vicleucel or Ciltacabtagen autoleucel (N=73) and show that enlarged spleen size is associated with severe and prolonged thrombocytopenia, higher metabolic tumor volumes, and elevated soluble BCMA (sBCMA) levels. Our findings indicate that splenomegaly (>340 cm³) is an independent prognostic marker for both progression-free and overall survival, outperforming markers such as sBCMA levels, EASIX, and CAR- Hematotox scores. These results suggest that spleen size could enhance risk stratification in CAR T-cell therapy for RRMM patients, offering a readily accessible tool for guiding monitoring strategies and healthcare resource management.
Peripheral Venous Pressure Accurately Evaluates Congestion in Constrictive pericarditis
Authors: Xia Xue , Zhou Jianzhong 
Published: February 2025

AbstractBackgroundThe primary clinical characteristic of initial constrictive pericarditis(CP) is a cardiac decreased diastolic function, which results in venous congestion, limitation of venous return, and elevated central venous pressure(CVP).Objective was to evaluate the relationship between peripheral venous pressure (PVP) and CVP with the aim to assess the diagnostic value of PVP in CP.MethodsSubjects underwent invasive haemodynamic and low invasive peripheral venous pressure assessment and also underwent physical examination, biochemical indices to assess venous congestion and echocardiography to assess cardiac structure and function. Patients were divided into 2 groups by CVP > 22 cmH2O(Modal 1 defined as CVP > 22 cmH2O; Modal 2 defined as CVP≦22cmH2O).ResultsOf the 36 patients, PVP and CVP had a significant positive association (Pearson’s = 0.831; P < 0.0001), with CVP = 0.962 + 0.907PVP as the regression equation.PVP was negatively correlated with FIB-4 (Pearson’s = −0.425; P=0.01), while it was not statistically significantly correlated with Pro-BNP, albumin, serum Na, hematocrit, hemoglobin, total bilirubin, direct bilirubin, or ARPI. Modal 1 and 2 groups were separated based on CVP > 22 cmH2O. By comparing the area under the curve (AUC) of the participants’ working mass, it was definitively established that 24 cmH2O was the ideal PVP threshold for the diagnosis of CP.ConclusionsIn Constrictive Pericarditis, PVP is a reliable, minimally invasive, and accurate technique for calculating CVP, which is remarkably positively correlated with CVP. Measurement of PVP is therefore important in the assessment of congestion and helps in the early diagnosis of Constrictive Pericarditis when PVP is greater than 24 cmH2O.
Two cowpea Rubisco activase isoforms for crop thermotolerance
Authors: Gjindali Armida , Page Rhiannon , Ashton Catherine J. , Robertson Ingrid , Page Mike T. , Bloemers Duncan , Gould Peter D. , Worrall Dawn , Orr Douglas J. , Carmo-Silva Elizabete 
Published: February 2025

SummaryA vital crop for sub-Saharan Africa, cowpea productivity is threatened by climate change, including increased heatwave intensity, duration, and frequency. Rubisco activase (Rca) is a key molecular chaperone that maintains Rubisco activity and due to its thermal sensitivity is a key target for improving crop climate resilience.We identified and characterised four Rca isoforms inVigna unguiculata(L.) Walp. cv. IT97K-499-35in vitro: Rca1β, Rca8α, Rca10α and Rca10β. Cowpea leaf and plant growth traits were also investigated during a 5-day +10 °C heatwave that included assessment of Rubisco and Rca activity in leaf extracts, and relative changes in the abundance of the four Rca isoforms.Cowpea Rca10α and Rca10β had higher thermal maxima, broader thermal optima and higher rates of ATP hydrolysis and Rubisco reactivationin vitro. In the absence of water deficit, the heatwave caused only mild effects, including increases in leaf temperature and expression ofRca10, small decreases in Rubisco activity and activation state, and unaltered temperature response of Rubisco activation by Rca.The superior Rca10α and Rca10β isoforms offer the prospect of enhancing the thermotolerance of cowpea and other crops in anticipation of more extreme future heatwaves.
Multiple fertility restorer loci for cytoplasmic male sterility caused byorf137in tomato
Authors: Iki Yurie , Harada Issei , Ezura Kentaro , Mashita Seira , Kuwabara Kosuke , Takei Hitomi , Toyoda Atsushi , Shirasawa Kenta , Ariizumi Tohru 
Published: February 2025

AbstractCytoplasmic male sterility (CMS) in plants is caused by incompatibility between nuclear and cytoplasmic genetic information. Fertility can be restored through the action of fertility restoration (RF) genes, which are usually present in the nucleus. CMS lines of tomato (Solanum lycopersicum) have been developed from asymmetric cell fusions, in these lines, cultivated tomato served as a nuclear donor and its wild relative,S. acaule, as a cytoplasm donor. AlthoughRFgenes are present in wild relatives of tomato, no genetic or genomic information on the RF genes is yet available. This study reports anRFgenetic locus,RF1, on chromosome 1 ofS. pimpinellifoliumLA1670 andS. lycopersicumvar.cerasiformeLA1673 that was revealed by bulked segregant analysis and sequencing. An additionalRFlocus,RF2, was identified on chromosome 2 of LA1670. A transgenic approach identified two other candidate genes that also restored fertility. The genomic sequence ofS. cheesmaniaeLA0166 was assembled using high-fidelity, long-read sequencing technology. Sequence comparisons identified further candidateRFgenes on chromosome 1 ofS. cheesmaniaeLA0166. These results suggested that multiple gene loci control the fertility restoration trait in wild relatives of tomato.
Polarizing SNPs without outgroup
Authors: Liang Jinyang , Dutheil Julien Y. 
Published: February 2025

AbstractAsserting which allele is ancestral or derived, known as polarization, is a prerequisite of many population and quantitative genetic methods. In particular, it allows inference of the unfolded site-frequency spectrum (uSFS). The most widely used approaches are based on outgroup data. However, for studies on species for which closely related outgroups are difficult to obtain, information on many sites of interest may be missed due to alignment problems. Here, we present PolarBEAR (Polarization By Estimation of the Ancestral recombination graph), a method that uses the local genealogies from the ancestral recombination graph (ARG) to infer ancestral states. We show that PolarBEAR can reach high accuracy in polarization and uSFS estimation using simulations under several scenarios. This accuracy, however, heavily depends on the ARG used as input. It is maximal when the true ARGs is used, but can be very low depending on the ARG reconstruction method employed. We also applied our method to human population data and compared it with the outgroup-based method est-sfs. Although our method could not infer the ancestral state with high confidence at certain positions, it obtained results for positions that est-sfs could not polarize due to missing outgroup data. The polarization results of the two methods were highly consistent at positions inferred by both methods. The two methods inferred similar uSFS, with PolarBEAR estimating slightly fewer high-frequency derived alleles. Furthermore, we demonstrate that PolarBEAR is robust to the mutation model used, while est-sfs exhibits a bias in the presence of heterogeneous base composition. PolarBEAR can complement outgroup-based methods, or replace them when no appropriate outgroup sequence is available.
Listeria monocytogenescell-to-cell spread bypasses nutrient limitation for replicating intracellular bacteria
Authors: Radhakrishnan Prathima , Theriot Julie A. 
Published: February 2025

ABSTRACTListeria monocytogenesis an intracellular bacterial pathogen that obtains nutrients from the mammalian host cell to fuel its replication in cytosol. Sparse infection of epithelial monolayers byL. monocytogenesresults in the formation of distinct infectious foci, where each focus originates from the initial infection of a single host cell followed by multiple rounds of active bacterial cell-to-cell spread into neighboring host cells in the monolayer. We used time-lapse microscopy to measure changes in bacterial growth rate in individual foci over time and found that intracellular bacteria initially replicate exponentially, but then bacterial growth rate slows later in infection, particularly in the center of the infectious focus. We found that the intracellular replication rate ofL. monocytogenesis measurably decreased by limiting host cell glucose availability, by decreasing the rate of intracellular bacterial oligopeptide import, and, most interestingly, by alterations in host cell junctional proteins that limit bacterial spread into neighboring cells without directly affecting bacterial growth or metabolism. By measuring the carrying capacity of individual host cells, we found that the nutritional density of cytoplasm is comparable to rich medium. Taken together, our results indicate that the rate of intracellularL. monocytogenesreplication is governed by a balance of the rate of nutrient depletion by the bacteria, the rate of nutrient replenishment by the metabolically active host cells, and the rate of bacterial cell-to-cell spread which enables the bacteria to seek out “greener pastures” before nutrient availability in a single host cell becomes limiting.SIGNIFICANCEListeria monocytogenesis a foodborne pathogen that is capable of facultative intracellular growth in a wide variety of mammalian cell types. It uses actin-based motility to spread directly from the cytoplasm of one infected host cell into another. After initially infecting cells in the small intestine,L. monocytogenescan circulate inside of infected macrophages, and subsequently spread to cells of distal organs, where it can cause spontaneous abortions in pregnant women and meningitis in immunocompromised individuals. In addition to facilitating body-wide dissemination, the actin-based cell-to-cell spread ofL. monocytogenescontributes to the ability of the pathogen to evade the cell-mediated arm of the immune system. In this work, we find that cell-to-cell spread also benefits the bacteria in a third way, by enabling the bacteria to overcome the nutrient limitation they would face if they remained confined to a single host cell, such that they never enter stationary phase.
Generative latent diffusion language modeling yields anti-infective synthetic peptides
Authors: Torres Marcelo D. T. , Chen Tianlai , Wan Fangping , Chatterjee Pranam , de la Fuente-Nunez Cesar 
Published: February 2025

AbstractGenerative artificial intelligence (AI) offers a powerful avenue for peptide design, yet this process remains challenging due to the vast sequence space, complex structure–activity relationships, and the need to balance antimicrobial potency with low toxicity. Traditional approaches often rely on trial-and-error screening and fail to efficiently navigate the immense diversity of potential sequences. Here, we introduce AMP-Diffusion, a novel latent diffusion model fine-tuned on antimicrobial peptide (AMP) sequences using embeddings from protein language models. By systematically exploring sequence space, AMP-Diffusion enables the rapid discovery of promising antibiotic candidates. We generated 50,000 candidate sequences, which were subsequently filtered and ranked using our APEX predictor model. From these, 46 top candidates were synthesized and experimentally validated. The resulting AMP-Diffusion peptides demonstrated broad-spectrum antibacterial activity, targeting clinically relevant pathogens—including multidrug-resistant strains—while exhibiting low cytotoxicity in human cell assays. Mechanistic studies revealed bacterial killing via membrane permeabilization and depolarization, and the peptides showed favorable physicochemical profiles. In preclinical mouse models of infection, lead peptides effectively reduced bacterial burdens, displaying efficacy comparable to polymyxin B and levofloxacin, with no detectable adverse effects. This study highlights the potential of AMP-Diffusion as a robust generative platform for designing novel antibiotics and bioactive peptides, offering a promising strategy to address the escalating challenge of antimicrobial resistance.
Pica in childhood: concurrent and sequential psychiatric comorbidity
Authors: Rubino Laura , Bulik Cynthia , Chawner Samuel JRA , Micali Nadia 
Published: February 2025

AbstractObjective:Pica is the persistent eating of non-nutritive, nonfood substances and is associated with serious medical consequences. There has been a lack of research into the psychiatric comorbidities of pica, despite being important for informing clinical care. The current study examines psychiatric comorbidities of pica in childhood and the longitudinal relationship between childhood pica and adolescent eating disorders.Methods:We analyzed data from the Avon Longitudinal Study of Parents and Children study. Pica and psychopathology, assessed with the Development and Well-Being Assessment and the Strengths and Difficulties Questionnaire, were assessed at about 7- and 10-years of age, reported eating disorders (ED) at 14-, 16-, and 18-years of age. We conducted linear and logistic regression models, adjusting for covariates, to identify concurrent psychiatric comorbidities, as well as risk for later EDs.Results. Pica was associated with increased odds of any psychiatric disorder and behavioral disorders in early childhood [OR = 7.30,p< .001 and OR = 5.65,p< .001, respectively] and mid-childhood [OR = 5.75,p< .001 and OR = 10.66,p< .001, respectively], and greater concurrent hyperactivity, conduct problems, peer problems, prosocial and emotional difficulties (p<.01 across analyses). We did not find evidence pica presence increased odds for concurrent emotional disorders nor for later ED risk.Discussion: The association between pica and psychiatric and behavioral disorders, indicates a likely shared aetiology. Our findings provide insight into the psychiatric characteristics of children with pica and highlight they may require complex behavioral support beyond their eating difficulties. [250]Public Significance (for IJED)This study investigated the relationship between pica (the eating of non-food substances) and mental health conditions in childhood. We found that in childhood, pica was associated with increased odds of having behavioral disorders (e.g., ADHD and conduct disorder) and mental disorder (e.g., anxiety or ADHD) but not emotional disorders (e.g., OCD and depression). Our findings suggest children with pica may require complex behavioral support beyond their eating difficulties.
The yeast phosphofructokinase β-subunit has ATP-dependent RNA unwinding activity and modulates cell cycle progression
Authors: Albihlal Waleed S. , Matia-González Ana M. , Schmidt Tobias , Mayer Wieland , Bushell Martin , Niessing Dierk , Barberis Matteo , Schmidt Alexander , Heinisch Jürgen J. , Gerber André P. 
Published: February 2025

AbstractPhosphofructokinase (PFK) is a rate-limiting glycolytic enzyme that also possesses an unexplored RNA binding activity. Here, we show that the α- and β-subunits of yeast PFK, encoded byPFK1andPFK2, respectively, bind hundreds of mRNAs in cells, including one’s coding for proteins involved in regulation of mitotic cell cycle. Pkf2p directly binds in a Mg-ATP-dependent manner to short GA-, UC-, AU- and U-rich motifs overrepresented in its mRNA targets. Strikingly, Pfk2p displays directional 5’ - 3’ double-stranded RNA unwinding activity not seen with Pfk1p. Furthermore, Pfk2p dynamically associates with ribosomes and promotes translation of cell cycle genes. Consequently,pfk2Δ,but notpfk1Δ,mutant cells show severely delayed G1/S phase transition which is independent of the enzyme’s glycolytic activity. Our results uncovered a hidden function for the Pfk2 subunit as a translational activator of mitotic cell cycle gene transcripts possibly through energy-dependent RNA unwinding activity.
Multilingual Computational Models Reveal Shared Brain Responses to 21 Languages
Authors: de Varda Andrea Gregor , Malik-Moraleda Saima , Tuckute Greta , Fedorenko Evelina 
Published: February 2025

AbstractAt the heart of language neuroscience lies a fundamental question: How does the human brain process the rich variety of languages? Recent developments in Natural Language Processing, particularly in multilingual neural network language models, offer a promising avenue to answer this question by providing a theory-agnostic way of representing linguistic content across languages. Our study leverages these advances to ask how the brains of native speakers of 21 languages respond to linguistic stimuli, and to what extent linguistic representations are similar across languages. We combined existing (12 languages across 4 language families; n=24 participants) and newly collected fMRI data (9 languages across 4 language families; n=27 participants) to evaluate a series of encoding models predicting brain activity in the language network based on representations from diverse multilingual language models (20 models across 8 model classes). We found evidence of cross-lingual robustness in the alignment between language representations in artificial and biological neural networks. Critically, we showed that the encoding models can be transferred zero-shot across languages, so that a model trained to predict brain activity in a set of languages can account for brain responses in a held-out language, even across language families. These results imply a shared component in the processing of different languages, plausibly related to a shared meaning space.
SVCFit: Inferring structural variant cellular fraction in tumors
Authors: Liu Yunzhou , Lai Jiaying , Wood Laura D. , Karchin Rachel 
Published: February 2025

AbstractMany tumors evolve through cellular mutation and selection, where subpopulations of cells (subclones) with shared ancestry compete for dominance. Introduction of next generation sequencing enables subclone identification using small somatic. However, there are several advantages to marking subclones with structural variants: they have greater functional impact, play a crucial role in late-stage tumors, and provide a more complete view of genomic instability driving tumor evolution. Here, we present SVCFit, a scalable method to estimate the cellular prevalence of somatic deletions, duplications and inversions. We demonstrate that cellular prevalence estimation can be improved by incorporating distinct read patterns for each structural variant type. Additionally, this improvement is achieved without prior knowledge of tumor purity, which is often inaccurate. Using a combination of simulated data and patient-derived metastatic samples with known mixture proportions, we show that our algorithm achieves significantly greater accuracy than state-of-the-art in estimating the structural variants cellular prevalence (p<0.05). The speed of SVCFit estimation from cost-effective bulk whole-genome sequencing (WGS) makes it well-suited for analyzing large cohorts of sequenced tumor samples, enhancing the accessibility of SV-based clonal reconstruction.
Dietary macronutrients modulate the proteome of brown adipose tissue in males and their female offspring
Authors: Macartney Erin L , Senior Alistair M , Crean Angela J , Small Lewin , Pulpitel Tamara J , Nobrega Marcelo A , Barrès Romain , Simpson Stephen J 
Published: February 2025

AbstractBrown adipose tissue (BAT) dissipates energy as heat, not only under cold exposure but also in the dissipation of excess ingested energy. Therefore, enhancing BAT activity is a potential avenue to combat weight gain. Dietary macronutrient composition influences BAT size and has recently been shown to influence BAT size of daughters through the patriline of C57BL/6J mice. However, the effects of macronutrient composition and any paternal effects on BAT function have yet to be characterised. Using the Geometric Framework for Nutrition, we investigated the effects of macronutrient composition on the BAT proteome in male mice and intergenerational effects in their offspring. In fathers, >50% of the proteome was affected by macronutrient composition, with distinct clusters of proteins that responded in similar ways. We identified two clusters with inverse patterns that correlated with BAT mass. Notably, UCP1 was reduced on low fat diets that promoted increased BAT mass, while there were increased levels of proteins involved in protein turnover on those same diets. The same diets also led to a reduction in proteins involved in purine biosynthesis (often UCP1 inhibitors). We did not find any effects of paternal diet on the BAT proteome in sons, but paternal protein intake negatively affected basigin expression in daughters - a protein that regulates UCP1 transcription. Our results highlight that dietary macronutrient composition in males remodels the protein expression landscape of BAT, and pre-conceptionally reprograms BAT expression profiles of female offspring.