bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proprioceptive synaptic dysfunction is a key feature in mice and humans with spinal muscular atrophy
Authors: Simon Christian M , Delestrée Nicolas , Montes Jacqueline , Sowoidnich Leonie , Gerstner Florian , Carranza Erick , Buettner Jannik M , Pagiazitis John G , Prat-Ortega Genis , Ensel Scott , Donadio Serena , Dreilich Vanessa , Carlini Maria J , Garcia Jose L , Kratimenos Panagiotis , Chung Wendy K , Sumner Charlotte J , Weimer Louis H , Pirondini Elvira , Capogrosso Marco , Pellizzoni Livio , De Vivo Darryl C , Mentis George Z 
Published: February 2025

Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by a varying degree of severity that correlates with the reduction of SMN protein levels. Motor neuron degeneration and skeletal muscle atrophy are hallmarks of SMA, but it is unknown whether other mechanisms contribute to the spectrum of clinical phenotypes.
Here, through a combination of physiological and morphological studies in mouse models and SMA patients, we identify dysfunction and loss of proprioceptive sensory synapses as key signatures of SMA pathology. We demonstrate that Type 3 SMA patients exhibit impaired proprioception, and their proprioceptive synapses are dysfunctional as measured by the neurophysiological test of the Hoffmann reflex (H-reflex). We further show moderate loss of spinal motor neurons along with reduced excitatory afferent synapses and altered potassium channel expression in motor neurons from Type 1 SMA patients. These are conserved pathogenic events found in both severely affected patients and mouse models. Lastly, we report that improved motor function and fatigability in ambulatory Type 3 SMA patients and mouse models treated with SMN-inducing drugs correlate with increased function of sensory-motor circuits that can be accurately captured by the H-reflex assay.
Thus, sensory synaptic dysfunction is a clinically relevant event in SMA, and the H-reflex is a suitable assay to monitor disease progression and treatment efficacy of motor circuit pathology.
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database
Authors: Wiegers Thomas C , Davis Allan Peter , Wiegers Jolene , Sciaky Daniela , Barkalow Fern , Wyatt Brent , Strong Melissa , McMorran Roy , Abrar Sakib , Mattingly Carolyn J 
Published: February 2025

Abstract
The Comparative Toxicogenomics Database (CTD) is a manually curated knowledge- and discovery-base that seeks to advance understanding about the relationship between environmental exposures and human health. CTD’s manual curation process extracts from the biomedical literature molecular relationships between chemicals/drugs, genes/proteins, phenotypes, diseases, anatomical terms, and species. These relationships are organized in a highly systematic way in order to make them not only informative but also scientifically computational, enabling inferential hypotheses to be formed to address gaps in understanding. Integral to CTD’s functionality is the use of structured, hierarchical ontologies and controlled vocabularies to describe these molecular relationships. Normalizing text (i.e. translating raw text from the literature into these controlled vocabularies) can be a time-consuming process for biocurators. To facilitate the normalization process and improve the efficiency with which our scientists curate the literature, CTD evaluated and integrated into the curation process PubTator 3.0, a state-of-the-art, AI-powered resource which extracts and normalizes from the literature many of the key biomedical concepts CTD curates. Here, we describe CTD’s long-standing history with Natural Language Processing (NLP), how this history helped form our objectives for NLP integration, the evaluation of PubTator against our objectives, and the integration of PubTator into CTD’s curation workflow.
Database URL: https://ctdbase.org
The Power of The Pill: Evidence from Oral Contraceptive Sales
Authors: Ragan Kelly Suzanne 
Published: February 2025

Abstract
The introduction of oral contraception (’the pill’) was a watershed in fertility control. Yet, the pill’s impact on childbearing has been hard to establish due to limited data. I exploit rich data on pill sales across markets and time to characterize how Swedish teens’ access to pharmacies shaped pill sales and fertility after the pill’s introduction. Pill sales are highly sensitive to pharmacy access, and teen fertility responds strongly to pill sales. The unique data establish an important link in the causal chain from pill access to women’s fertility. Estimated fertility responses to the pill could explain the halving of teen births after the pill’s introduction, a finding which is robust to accounting for trends in female education, abortion provision, and other factors.
Effect of previous cardiac surgery on the outcomes of acute type A aortic dissection repair: a nationwide cohort study
Authors: Lin Chun-Yu , Chen Wei-Min , Chang Shu-Hao , Yu Sheng-Yueh , See Lai-Chu 
Published: February 2025

Abstract

OBJECTIVES
The effect of previous cardiac surgery (PCS) on the outcomes of acute type A aortic dissection (ATAAD) repair remains controversial. This study compared the primary outcome (in-hospital mortality) and secondary outcomes (postoperative complications and post-discharge mortality/aortic reoperation rates up to 5 years) of patients who underwent ATAAD repair with and without PCS through a nationwide cohort analysis.

METHODS
We used Taiwan’s National Health Insurance Research Database to enroll patients who underwent ATAAD repair with and without PCS (94 and 4532, respectively) between 2004–07-01 and 2017–03-31. A 1:4 propensity score matching (PSM) was used to create well-balanced PCS (n = 74) and non-PCS (n = 296) groups. Results before and after PSM were aligned to determine the role of PCS in primary and secondary outcomes.

RESULTS
Before PSM, the PCS group was older and had more comorbidities, including diabetes mellitus, heart failure, atrial fibrillation, and malignancy, but less stroke history than the non-PCS group. More patients in the PCS group received coronary artery bypass grafting during the repair than in the non-PCS group. The PCS group had a higher in-hospital mortality than the non-PCS group. After PSM, the in-hospital mortality was similar between the two groups (27.0% versus 26.7%; P = 0.953). For patients who survived to discharge, the all-cause mortality up to 5 years for PCS and non-PCS groups were 29.7% and 18.4% (P = 0.015) before and 29.6% and 23.1% (P = 0.313) after PSM, respectively. The two groups had similar aortic reoperation rates up to 5 years before (13.5% versus 11.7%; P = 0.727) and after PSM (13.8% versus 11.6%; P = 0.776).

CONCLUSIONS
Patients with PCS who underwent ATAAD repair showed higher in-hospital and long-term mortality rates than those without PCS when not controlled for confounding factors. However, the disparity disappeared after PSM, indicating that worse outcomes might be due to its old age and different perioperative characteristics.
The difficulties of disarmament during the French Wars of Religion: the role of Antoine, comte de Crussol
Authors: Nicoll David 
Published: February 2025

Abstract
Reconciliation following conflict is difficult, and the peace edicts that ended the civil wars in sixteenth-century France took time to be enforced. Disarmament following civil war was a lengthy process. This article provides an original insight into the drawn-out disarmament processes following the First War of Religion (1562–63), through the figure of Antoine, comte de Crussol (later duc d’Uzès). The article outlines Crussol’s important role in disarmament across the regions of Languedoc, Dauphiné and Comtat-Venaissin. It argues that Crussol played a critical yet paradoxical part in disarmament, illustrating the ways in which he both delayed and enforced the peace, while emphasizing his loyalty to the crown throughout. This study also demonstrates the crown’s critical role in bringing peace, the capacity of the provincial nobles for peacemaking and the difficult position nobles who had fought against the crown found themselves in at the end of the war.
Predicting Fitness-Related Traits Using Gene Expression and Machine Learning
Authors: Henry Georgia A , Stinchcombe John R 
Published: February 2025

Abstract
Evolution by natural selection occurs at its most basic through the change in frequencies of alleles; connecting those genomic targets to phenotypic selection is an important goal for evolutionary biology in the genomics era. The relative abundance of gene products expressed in a tissue can be considered a phenotype intermediate to the genes and genomic regulatory elements themselves and more traditionally measured macroscopic phenotypic traits such as flowering time, size, or growth. The high dimensionality, low sample size nature of transcriptomic sequence data is a double-edged sword, however, as it provides abundant information but makes traditional statistics difficult. Machine learning (ML) has many features which handle high-dimensional data well and is thus useful in genetic sequence applications. Here, we examined the association of fitness components with gene expression data in Ipomoea hederacea (Ivyleaf morning glory) grown under field conditions. We combine the results of two different ML approaches and find evidence that expression of photosynthesis-related genes is likely under selection. We also find that genes related to stress and light responses were overall important in predicting fitness. With this study, we demonstrate the utility of ML models for smaller samples and their potential application for understanding natural selection.
Randomized experimental test of a reduced-exposure message for an e-cigarette: comprehension and related misperceptions
Authors: McCaffrey Stacey , Shiffman Saul , Sembower Mark A , Black Ryan A 
Published: February 2025

Abstract
Completely switching from cigarette smoking to electronic nicotine delivery systems (ENDS) reduces exposure to toxic substances. Yet, many smokers believe that ENDS are at least as harmful as smoking, making them less likely to switch from cigarettes to ENDS. Effectively communicating reduced-exposure information is critical, but such messages must be properly understood. This online study evaluated comprehension of a factual message, indicating that smokers who switch completely away from smoking to JUUL-brand ENDS can reduce their exposure to harmful chemicals in cigarette smoke. Participants were 12 557 adults 18+ years (smokers, dual users and former and never users of tobacco) randomized to see the reduced-exposure message or to a Control condition. After exposure to the message, the majority of smokers (89%) understood the need to switch completely from cigarettes to JUUL to achieve reduced exposure. Most smokers and nonusers (&gt;75%) did not misperceive JUUL as completely eliminating exposure to harmful chemicals, and &gt;85% understood that using JUUL has risk. Exposure to the message improved understanding of the intended audience for JUUL. Individuals with limited health literacy showed modestly lower comprehension, regardless of condition. Ensuring adequate comprehension of messages about reduced exposure from ENDS is important to ensuring that such messaging can benefit public health.
Erythrocyte Methotrexate–Polyglutamate Concentrations in Pediatric Inflammatory Bowel Disease
Authors: Vermeer Eva , Struys Eduard A , Lin Marry , van Limbergen Johan E , de Boer Nanne K H , Bulatović-Ćalasan Maja , de Meij Tim G J , de Jonge Robert 
Published: February 2025

Abstract

Background and Aims
Therapeutic drug monitoring (TDM) of methotrexate (MTX) is challenging due to its pharmacokinetics and short plasma half-life. Intracellular MTX–polyglutamates (PG1–5), which accumulate over time, have not been assessed in pediatric inflammatory bowel disease (IBD). This study aimed to evaluate erythrocyte MTX-PG as a potential TDM tool in pediatric IBD.

Methods
In this cross-sectional study, MTX-PG concentrations were measured in erythrocytes of children with IBD on stable low-dose MTX for at least 12 weeks using stable-isotope dilution liquid chromatography–tandem mass spectrometry. The influence of administration route, MTX dosage, and anthropometrics on MTX-PG concentrations was examined.

Results
Seventy-eight patients were included, showing MTX-PG3 as the predominant subspecies (median 27.0 nmol/L) with a median MTX-PGtotal of 74.8 nmol/L. A higher MTX dose correlated significantly with elevated levels of MTX-PG3, MTX-PG4, MTX-PG5, and MTX-PGtotal (P &lt; .01). Adjusted for body surface area, MTX dose remained significantly associated with higher MTX-PG concentrations (P &lt; .01). However, comparison by administration route was limited due to a few patients on subcutaneous MTX (n = 4).

Conclusions
We observed high interindividual variability in the reached erythrocyte MTX-PG concentrations. Body surface adjusted or unadjusted MTX dosage showed a positive linear correlation with erythrocyte MTX-PG concentrations in children with IBD. This is a prerequisite for TDM and provides a strong basis for further research into the relation between TDM of MTX, efficacy, and toxicity.
Research on the generation of localized overheating samples and fault prediction models of transformers and based on brain-inspired spiking neural networks
Authors: Zhang Guoliang , Zhang Peng , Zhou Fei , Du Zexu , Chen Jiangqi , Zhang Zhisong , Kong Qingyu 
Published: February 2025

Abstract
The prediction of transformer failures holds significant importance for maintaining the stability of power systems. This paper investigates the application of a brain-inspired spiking neural network model for fault prediction of transformers. The research is grounded in dissolved gas analysis, employing fuzzy reasoning spiking neural P systems to process fuzzy diagnostic knowledge. It constructs a set of sample data associated with localized overheating and utilizes linguistic variables, membership functions, and an inference rule base to conduct fault analysis. The results indicate that this approach significantly enhances the fault identification and predictive capabilities of transformers.
Xylo-oligosaccharides enhance intestinal and thymic immunity by modulating pyroptosis, gut microbiota and Th17/Treg immune response in LPS-challenged piglets
Authors: Sun Weixiao , Liu Guangmang , Shen Fei , Wu De , Lin Yan , Zhang Ruinan , Che Lianqiang , Feng Bin , Zhuo Yong , Xu Shengyu , Hua Lun , Fang Zhengfeng , Jiang Xuemei , Li Jan , Wang Jing 
Published: February 2025

Abstract
Xylo-oligosaccharides (XOS) have been shown to improve the immune system of weaned piglets, but the molecular mechanism of their action remains unclear. Therefore, this study aimed to investigate the impact of XOS on intestinal and thymic immune function in weaned piglets challenged with lipopolysaccharide (LPS) and elucidate the underlying mechanism. In a 2 × 2 factorial arrangement, consisting of diet treatment (basal diet vs 0.02% XOS diet) and immunological challenge [saline vs LPS], 24 piglets were randomly divided into four groups (n = 6): CON group, basal diet + saline; LPS group, basal diet + LPS; XOS group, 0.02% XOS diet + saline; XOS_LPS group, 0.02% XOS diet + LPS. Piglets were fed either the basal or XOS diet for 21 days, followed by intraperitoneal injections of normal saline or LPS on the 22nd day. Ileum, thymus and colon samples were collected 4 hours after the intraperitoneal saline or LPS injection. The piglets fed XOS diet had higher average daily feed intake and average daily weight gain (P &lt; 0.05). The XOS diet increased ileal villus height and decreased crypt depth. XOS also enhanced ileal and thymic antioxidant enzyme activities, anti-inflammatory cytokine expression, and decreased malondialdehyde levels and mRNA abundance of proinflammatory cytokines in piglets (P &lt; 0.05). The XOS diet also downregulated ileal and thymic NOD-like receptor family pyrin domain containing 3 and gasdermin-D gene and protein expression associated with pyroptosis (P &lt; 0.05). Moreover, The XOS diet increased the mRNA abundance of forkhead box P3, signal transducer and activator of transcription 5, and transforming growth factor beta 1 while decreasing signal transducer and activator of transcription 3 and retinoid-related orphan receptor-gammat mRNA abundance (P &lt; 0.05). The XOS diet enhanced forkhead box P3 protein expression and reduced retinoid-related orphan receptor-gammat protein expression following the LPS challenge (P &lt; 0.05). At the same time, The XOS diet affected the gut microbiota and increased levels of short-chain fatty acids (P &lt; 0.05). In conclusion, XOS may modulate ileal and thymic immune function in weaned piglets following a 4-hour LPS challenge by affecting gut microbiota, pyroptosis and Th17/Treg immune responses.
Perceptions of and Opportunities for AMTA Journals: A Mixed Methods Study
Authors: Beer Laura E , Muralidharan Ananya , Montgomery Jaley A , Quiller Leah , Else Barbara A , LaGasse Blythe 
Published: February 2025

Abstract
The Journal of Music Therapy and Music Therapy Perspectives are journals sponsored by the American Music Therapy Association (AMTA). In recent years, the journal leadership teams have been focused on issues of inclusion, access, equity, and social justice, as they relate to the journals. This focus aligned with AMTA’s reorganization process that began in the early 2020s, where principles of social justice were centered as part of the association’s statements related to organizational change. The purpose of this mixed methods study was to gather data related to readers’ use and perceptions of the journals, including perceptions regarding the integration of diversity and social justice. Board-certified music therapists (N = 409) met inclusion criteria and completed an online survey; these data were used to inform focus group questions. We then conducted five focus groups (N = 16 participants) to gather more personal and in-depth responses. Survey data indicated varying opinions related to the use of the journals and inclusion of social justice principles, whereas the focus groups were more unified in their assessment that more work is needed in this area. Participants in the focus groups brought forward issues related to inclusion and access. The readership indicated that the journals currently incorporate some aspects of these principles; however, many readers would like to see more intentional integration of these principles across the journals. Focus group members also provided a variety of action steps for consideration as the journals move forward.
From Fisher to CARA: the evolution of randomization and randomization-based inference
Authors: Rosenberger William Fisher 
Published: February 2025

Abstract
R. A. Fisher was a devoted Darwinian, and, like Darwin, created science out of nothing. The list is long, but one thinks of likelihood-based estimation, analysis of variance, principles of experimental design, and randomization as standing the tests of time. Such accomplishments ‘from scratch’ (or nearly so) can amaze the fine statisticians who made meaningful incremental contributions to work begun by others, the few ‘greats’ among us who invented something important, and the unusually perceptive introductory statistics student, alike. Fisher thought of randomization in the context of agricultural experiments, but it has impacted most profoundly the science of medicine. Bradford Hill brought randomization to clinical trials. The concept of randomization-based inference, now resurrected in causal inference, was largely forgotten as design and analysis became segregated, perhaps due to analysis software packages. This talk will attempt to give the historical context of randomization and randomization-based inference from Fisher to the present day, including newer concepts such as response-adaptive, covariate-adaptive, and covariate-adjusted response-adaptive randomization. It will be challenging to condense a year of material into one hour, but a devoted Fisherian should be able to be efficient and sufficient.
Signatures of black hole seeding in the local Universe: Predictions from the BRAHMA cosmological simulations
Authors: Bhowmick Aklant K , Blecha Laura , Torrey Paul , Somerville Rachel S , Kelley Luke Zoltan , Weinberger Rainer , Vogelsberger Mark , Hernquist Lars , Natarajan Priyamvada , Kho Jonathan , Matteo Tiziana Di 
Published: February 2025

Abstract
The origin of the “seeds” of supermassive black holes (BHs) continues to be a puzzle, as it is currently unclear if the imprints of early seed formation could survive to today. We examine the signatures of seeding in the local Universe using five [18 Mpc]3 BRAHMA simulation boxes run to z = 0. They initialize 1.5 × 105 M⊙ BHs using different seeding models. The first four boxes initialize BHs as heavy seeds using criteria that depend on dense & metal-poor gas, Lyman-Werner radiation, gas spin, and environmental richness. The fifth box initializes BHs as descendants of lower mass seeds (∼103 M⊙) using a new stochastic seed model built in our previous work. In our simulations, we find that the abundances and properties of ∼105 − 106 M⊙ local BHs hosted in M* ≲ 109 M⊙ dwarf galaxies, are sensitive to the assumed seeding criteria. This is for two reasons: 1) there is a substantial population of local ∼105 M⊙ BHs that are ungrown relics of early seeds from z ∼ 5 − 10; 2) BH growth up to ∼106 M⊙ is dominated by mergers in our simulations all the way down to z ∼ 0. As the contribution from gas accretion increases, the signatures of seeding start to weaken in more massive ≳ 106 M⊙ BHs, and they are erased for ≳ 107 M⊙ BHs. The different seed models explored here predict abundances of local ∼106 M⊙ BHs ranging from ∼0.01 − 0.05 Mpc−3 with occupation fractions of $\sim 20-100~{{\%}}$ for M* ∼ 109 M⊙ galaxies. These results highlight the potential for placing constraints on seeding models using local ∼105 − 106 M⊙ BHs hosted in dwarf galaxies. Since merger dynamics and accretion physics impact the persistence of seeding signatures, and both high and low mass seed models can produce similar local BH populations, disentangling their roles will require combining high and low redshift constraints.
2D watershed void clustering for probing the cosmic large-scale structure
Authors: Song Yingxiao , Gong Yan , Xiong Qi , Chan Kwan Chuen , Chen Xuelei , Guo Qi , Liu Yun , Pei Wenxiang 
Published: February 2025

Abstract
Cosmic void has been proven to be an effective cosmological probe of the large-scale structure (LSS). However, since voids are usually identified in spectroscopic galaxy surveys, they are generally limited to low number density and redshift. We propose to utilize the clustering of two-dimensional (2D) voids identified using Voronoi tessellation and watershed algorithm without any shape assumption to explore the LSS. We generate mock galaxy and void catalogs for the next-generation Stage IV photometric surveys in z = 0.8 − 2.0 from simulations, develop the 2D void identification method, and construct the theoretical model to fit the 2D watershed void and galaxy angular power spectra. We find that our method can accurately extract the cosmological information, and the constraint accuracies of some cosmological parameters from the 2D watershed void clustering are even comparable to the galaxy angular clustering case, which can be further improved by as large as ∼30% in the void and galaxy joint constraints. This indicates that the 2D void clustering is a good complement to galaxy angular clustering measurements, especially for the forthcoming Stage IV surveys that detect high-redshift universe.