bluuebunny/crossref_metadata_2025_split huggingface dataset:
The multi-organ landscape of B cells highlights dysregulated memory B cell responses in Crohn's disease
Authors: Chen Dianyu , Xu Song , Li Shuyan , Wang Qiuying , Li Hui , He Danyang , Chen Yan , Xu Heping 
Published: January 2025

Abstract
Crohn's disease (CD) is a prevalent type of inflammatory bowel disease (IBD) with dysregulated antibody responses. However, there is a lack of comprehensive analysis of B cell responses in CD. Here, we collected B cells from the small intestine, colon and blood of CD patients and control subjects. Through the coupled analysis of transcriptome and immunoglobulin (Ig) gene in individual cells, we characterized the cellular composition, transcriptome and Ig clonotype in different B cell subtypes. We observed shared disruptions in plasma cell (PC) responses between different IBD subtypes. We revealed heterogeneity in memory B cells (MBCs) and showed a positive correlation between gut resident-like MBCs and disease severity. Furthermore, our clonotype analysis demonstrated an increased direct differentiation of MBCs into PCs in CD patients. Overall, this study demonstrates significantly altered B cell responses associated with chronic inflammation during CD and highlights the potential role of mucosal MBCs in CD pathogenesis.
Regulating the cobalt phthalocyanine molecules by introducing adjacent cubic molybdenum carbide nanoparticles for accelerated proton transfer towards efficient CO2 reduction reaction
Authors: Lin Yunxiang , Wang Shaocong , Liu Hengjie , Liu Xue , Yang Li , Su Xiaozhi , Shan Lei , Li Xiyu , Song Li 
Published: January 2025

Abstract
Electrochemical CO2 reduction reaction (CO2RR) is an important application that can considerably mitigate environmental and energy crises. However, the slow proton-coupled electron transfer process continues to limit overall catalytic performance. Fine-tuning the reaction microenvironment by accurately constructing the local structure of catalysts provides a novel approach to enhancing reaction kinetics. Here, cubic-phase α-MoC1−x nanoparticles were incorporated into a carbon matrix and coupled with cobalt phthalocyanine molecules (α-MoC1−x–CoPc@C) for the co-reduction of CO2 and H2O, achieving an impressive Faradaic efficiency for CO close to 100%. Through a combination of in-situ spectroscopies, electrochemical measurements, and theoretical simulations, it is demonstrated that α-MoC1−x nanoparticles and CoPc molecules with the optimized local configuration serve as the active centers for H2O activation and CO2 reduction, respectively. The interfacial water molecules were rearranged, forming a dense hydrogen bond network on the catalyst surface. This optimized microenvironment at the electrode–electrolyte interface synergistically enhanced water dissociation, accelerated proton transfer, and improved the overall performance of CO2RR.
Protein phosphatase PP2C2 dephosphorylates transcription factor ZAT5 and modulates tomato fruit ripening
Authors: Li Yafei , Chang Yanan , Wang Yiran , Gan Chaolin , Li Chonghua , Zhang Xuejun , Guo Yang-Dong , Zhang Na 
Published: January 2025

Abstract
Although C2H2 zinc finger transcription factors are important in plant growth, development, and stress resistance, their specific roles in fruit ripening have been less explored. Here, we demonstrate that the C2H2 zinc finger transcription factor 5 (SlZAT5) regulates fruit ripening in tomato (Solanum lycopersicum L.). Overexpression of SlZAT5 delayed ripening, while its knockout accelerated it, confirming its role as a negative regulator. SlZAT5 functions as a transcriptional repressor by directly inhibiting ripening-related genes, including SlACS4, SlPL8, and SlGRAS38, thereby delaying ripening. Furthermore, SlZAT5 interacts with the type 2C protein phosphatase SlPP2C2, which regulates the repressor activity of SlZAT5 by dephosphorylating SlZAT5 at Ser-65. This interaction is crucial in modulating ethylene production, thereby influencing the ripening process. These findings reveal a regulatory function of SlZAT5 in tomato fruit development, offering insights into the SlZAT5-SlPP2C2 module and potential targets for genetic modification to improve fruit quality and extend fruit shelf life.
Internal Structure of Decaying Solitary Waves: Comparison of Analytic and Numerical Results
Authors: Grundy Dane , Hammerton P W 
Published: January 2025

Abstract
The evolution of solitary waves governed by perturbations of the Korteweg-de Vries (KdV) equation is considered, focussing in particular on the Burgers-Korteweg-de Vries (BKdV) equation. Using matched asymptotic expansions the structure of the wave is determined for all timescales. A tail appears behind the main waveform, the structure of which is determined in the form of a convolution integral. Numerical results are presented using a pseudospectral scheme but modified so that linear terms are incorporated into an integrating factor. All details of the asymptotic structure of the waveform are validated by numerical results. Comparisons are made with earlier asymptotic analyses of decaying solitary waves.
A review of reviews of patient-reported measures in psychosis: Need to consider factors affecting equity and the involvement of patients
Authors: Nair Neha , Abou-Farhat Maria , Kaur Navdeep , Jones Nev , Mohan Greeshma , Boruff Jill , Iyer Srividya N 
Published: January 2025

Abstract

Background
Patient-reported measures are increasingly valued in psychosis care and research. For patient-reported measures to reflect patient perspectives, patients must be involved in developing them. Further, their development and evaluation must consider sociodemographic characteristics influencing patient experiences and outcomes and measurement. As reviews reflect the state of the field and guide clinicians/researchers in selecting measures, our aim was to evaluate literature reviews of patient-reported measures on their consideration of factors affecting equity and patient involvement.

Study design
For this review of reviews, we searched three databases (MEDLINE, Embase, PsycINFO) for reviews on patient-reported measures in psychosis. Two reviewers independently screened titles, abstracts, and full-texts, and descriptively synthesized and appraised the quality of included reviews. Using Cochrane’s PROGRESS-plus and a Canadian equity framework, reviews were evaluated on their consideration of sociodemographic characteristics, accessibility and patient involvement.

Study results
Of 10 reviews (six systematic, four non-systematic; 1,111 studies; 313 measures), six limited their search to English. Barring two reviews that reported the age, gender, and countries of samples in included studies, the reviews did not extract/comment on population/socio-demographic characteristics. One commented on one measure’s readability; none commented on samples’ literacy levels. Four reviews considered the availability of translations; only one evaluated cross-cultural validity. Only two considered costs of measures. Only one evaluated patient involvement in developing patient-reported measures. One referenced equity frameworks/standards.

Conclusions
Reviews of patient-reported measures in psychosis demonstrate minimal attention to equity and patient involvement. We offer recommendations to strengthen patient-reported measures research by attending to equity, diversity, and patient-centrism.
The value of 5-HT, leptin, and NE in the classification of premature ejaculation
Authors: Chen Zhimin , Zhang Xiansheng 
Published: January 2025

Abstract

Background
While premature ejaculation (PE) can be divided into lifelong PE (LPE), acquired PE, natural variable PE (NPE), and subjective PE (SPE), there is no objective method to classify PE.

Aim
To determine the value of serum serotonin (5-HT), leptin, and norepinephrine (NE) levels in the classification of PE.

Methods
From July 2023 to July 2024, we recruited 150 participants and divided them into 4 groups: LPE (43 cases), NPE (32 cases), SPE (35 cases), and non-PE (40 cases) groups. All participants' baseline data, premature ejaculation diagnostic tool score, and intravaginal ejaculation latency time were investigated. In addition, all participants' serum 5-HT, leptin, and NE levels were measured.

Outcome
Serum 5-HT, NE, and leptin levels were compared among all groups.

Results
Serum 5-HT levels were lower and NE and leptin levels were higher in the LPE group compared to the SPE, NPE, and non-PE groups (P &lt; .05). However, serum 5-HT, leptin, and NE levels were not significantly different among the non-PE, NPE, and SPE groups (P &lt; .05). In addition, serum 5-HT &lt;95.0 ng/mL, NE &gt;543.0 ng/L, and leptin &gt;19.8 ng/mL may be predictive indicators of LPE.

Clinical Significance
Based on serum 5-HT, NE, and leptin levels, LPE can be distinguished from SPE and NPE, which provides an objective basis for the treatment of PE.

Strengths and Limitations
There is no effective method to classify PE. The main limitation of this study is the limited sample size.

Conclusion
The serum 5-HT, leptin, and NE levels in PE patients may contribute to the classification of PE.
Secondary Trauma Impact Scale: Development and Initial Validation
Authors: Bride Brian E 
Published: January 2025

Abstract
Instruments currently utilized in research on secondary traumatic stress (STS) fail to measure distress and impairment. To fill this gap, this article describes the development and initial validation of a new instrument designed to measure distress and impaired functioning related to work-related secondary trauma exposure. The Secondary Trauma Impact Scale (STIS) is a brief screening measure consisting of six items, each measuring a different domain of distress and impairment. Domains include social, occupational, familial, sexual, psychological, and physical functioning. Secondary analysis was conducted on data collected from 577 master’s-level social workers for a previously reported study. Results strongly support the reliability and factorial, convergent, and discriminant validity of the STIS. The ability to explicitly measure secondary trauma-related distress and impairment with a reliable and valid instrument will allow social workers to obtain more precise estimates of the prevalence of STS, identification of risk and resilience factors, and evaluation of interventions targeting the impact of STS on individuals and organizations.
Traffic Flow Prediction for Highway Based on Multi-Task Spatiotemporal Graph Network
Authors: Gao Jinyong , Luo Sheng , Tian Junshan , Zhou Cheng , An Lianhua 
Published: January 2025

Abstract
Efficient and precise traffic flow prediction holds great importance in effective traffic management. This research presents a novel prediction model that integrates highway spatial changes and flow-related information (speed and vehicle composition). The highway is divided into segments, using key reference points like tunnels, toll stations, and ramps. An adaptive graph convolutional network is employed to capture relationships between these segments. The network automatically adjusts adjacency matrix weights, facilitating the extraction of spatial flow features. Incorporating flow related information, a multi-task module attention fusion network is introduced. The main task is traffic flow prediction, with average travel speed and vehicle composition as auxiliary tasks. This approach enhances feature acquisition and improves prediction accuracy. In experiments using Fuzhou–Jingtan Expressway data, the model significantly enhances prediction accuracy by at least 55%. Ablation experiments validate the effectiveness of the designed modules, improving the model's accuracy from 20% to 45%.
Clostridium novyitype B causes fatal hemorrhagic disease in wild Asian elephants
Authors: Padhi Soumesh Kumar , Pahari Avishek , Behera Bikash Kumar , Dash Manojita , Dash Richa , Sahoo Niranjana , Nath Indramani , Acharya Aditya Prasad , Panda Susen Kumar , Mahapatra Subrata , Nair Manoj V. 
Published: January 2025

AbstractThe population of Asian elephants, an endangered species, is decreasing significantly due to anthropogenic interference in India. Research on Asian elephant disease is largely confined to observations reported from captive populations. The present study explored 11 disease investigation cases whose clinicopathological changes were similar to those of fatal hemorrhagic disease caused byBacillus anthracis. We used molecular diagnostic approaches such as PCR (polymerase chain reaction), quantitative PCR, 16S metagenomics analysis and whole-metagenome sequencing for identification of the etiological agent responsible for these wild elephant mortalities. 16S metagenomics analysis revealed the presence ofClostridium hemolyticumas the dominant bacteria in all the mortality events. In contrast, flagellin gene-specific identification of all the samples and whole metagenomics analysis of blood samples collected from the ear pinna of a freshly deceased elephant revealedClostridium novyitype B as the sole pathogenic agent responsible for the death of elephants. This study provides the first evidence of the involvement ofClostridium novyitype B in the death of wild elephants with similar clinical manifestations to anthrax. The current study also provides ample evidence of the need to explore investigations of emerging diseases of wild elephants to conserve these large mammals.
Hypoxia-related immune subsets induced bySalmonellaTyphi infection link early bacterial gut invasion to human infection outcomes
Authors: Ben-Moshe Noa Bossel , Avivi Shelly Hen , Efrati Liron Levy , Veinman Leia , Hill Jennifer , O’Connor Daniel , Verheul Marije , Stockdale Lisa , McLean Florence , Pollard Andrew , Avraham Roi 
Published: January 2025

AbstractSalmonellaTyphi (S.Typhi), the causative agent of typhoid disease, remains a major public health concern. Owing to the human-restricted nature ofS. Typhi, current studies of typhoid pathogenesis in animal models are limited to a murine non-typhoidal pathogen. Furthermore, human studies are limited to analyses of peripheral immune responses which are blind to tissue-specific immunity and do not allow perturbations. What is now needed is an integrative approach that will provide mechanistic insights intoS. Typhi pathogenesis and immune correlates of infection outcome. Here, we performed an integrated single-cell analysis of immune responses from the humanS.Typhi challenge model and mouse model of typhoid disease, to associate biological mechanism with human infection outcome. Most prominent, we revealed immune subsets with a hypoxia-related signature in circulating immune cells from individuals that develop disease in the human challenge model. This signature was also evident in the mouse model in activated macrophages infiltrating into the Peyer’s patches, but not during infection with a mutant strain impaired for gut invasion. We further identified hypoxia-related signature as a general immune correlate of disease outcome in other infection- and inflammatory-related diseases. Collectively, using integrated analysis of mouse and human infection models, we revealed a hypoxia-related signature that link immune responses during bacterial invasion to increased risk of developing typhoid disease in humans, suggesting a possible causative role during the development of typhoid disease.
Molecular re-adaptation : compensatory evolution following deleterious episodes of GC-biased gene conversion in rodents
Authors: Riffis Marie , Saclier Nathanaëlle , Galtier Nicolas 
Published: January 2025

AbstractGC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favours the accumulation of deleterious AT to GC substitutions in proteins, moving them away from their fitness optimum. In many mammals recombination hotspots have a rapid turnover, leading to episodic gBGC, with the accumulation of deleterious mutations stopping when the recombination hotspot dies. Selection is therefore expected to act to repair the damage caused by gBGC episodes through compensatory evolution. However, this process has never been studied or quantified so far. Here, we analysed the nucleotide substitution pattern in coding sequences of a highly diversified group ofMurinaerodents. Using phylogenetic analyses of about 70,000 coding exons, we identified numerous exon-specific, lineage-specific gBGC episodes, characterised by a clustering of synonymous AT to GC substitutions and by an increasing rate of non-synonymous AT to GC substitutions, many of which are potentially deleterious. Analysing the molecular evolution of the affected exons in downstream lineages, we found evidence for pervasive compensatory evolution after deleterious gBGC episodes. Compensation appears to occur rapidly after the end of the episode, and to be driven by the standing genetic variation rather than new mutations. Our results demonstrate the impact of gBGC on the evolution of amino-acid sequences, and underline the key role of epistasis in protein adaptation. This study contributes to a growing body of literature emphasizing that adaptive mutations, which arise in response to environmental changes, are just one subset of beneficial mutations, alongside mutations resulting from oscillations around the fitness optimum.
Derivation of cardiac reference ranges forMus musculususing the Collaborative Cross and identification of new cardiac models
Authors: Popp Julia L. , Patel Krishna , Cuomo Danila , Lynch Rachel M. , Leung Steve W. , Berridge Brian R. , Rusyn Ivan , Chiu Weihsueh A. , Threadgill David W. 
Published: January 2025

AbstractContemporary approaches for developing interventions and assessing pre-clinical cardiovascular risk frequently utilize animal andin vitromodels. However, these models currently lack normal species-specific reference ranges similar to what exists for humans. The genetically diverse Collaborative Cross (CC) population that models human genetic heterogenetiety was characterized to develop mouse-specific cardiac reference ranges forMus muscuslus, the most commonly used pre-clincial model. Heart function was analyzed in males and females from 58 CC strains and C57BL/6J using high-frequency ultrasound under both conscious and anesthetized conditions, as well as conscious electrocardiography to develop two standard deviation-based reference ranges. The sources and magnitude of measurement variability were identified, and inter-laboratory comparisons determined to quantify phenotypic robustness and heritability. Strain was the largest source of variability, while laboratory where data were collected was also significant but sex was not. Additionally, strains were identified that have characteristics of disease-associated phenotypes in cardiac function and electrophysiology similar to human cases including dilated cardiomyopathy, systolic cardiomyopathy, cancer therapy-related cardiac dysfunction, and long QT. These new models allow a more natural, and therefore more translatable progession to a cardiac disease state, supporting development of strain-specific models for cardiac pathologies, ultimately allowing more accurate diagnoses and informative safety assessments in humans.Article SummaryThe Collaborative Cross (CC) mouse reference population, modeling human genetic diversity, was utilized to derive cardiac reference values forMus musculus. Strain was the primary source of variability, with the laboratory also playing a significant role, while sex had no impact. Despite inter-laboratory reproducibility challenges, the study identified strains resembling disease-associated phenotypes that offer a more natural progression to cardiac disease and provide crucial data for early disease identification and accurate safety assessments in humans.
Spatio-temporal dynamics of ingroup interactions in macaques
Authors: Kononowicz Tadeusz W. , Rolando Felipe , Maigre Lucas , Sirigu Angela , Duhamel Jean-René , Ballesta Sébastien , Wirth Sylvia 
Published: January 2025

SummaryWhen sharing a space with others, many species including humans evolved a compromise regulating occupancy influenced by social determinants. For example, students in a classroom tend to sit close to their friends, keeping the same spots across days, revealing the social structure in the classroom. This place preference suggests that factors such as social hierarchy and affiliation can shape space utilization; contrasting with random walk models of agents moving at random in any given direction. Here, we asked whether spatial occupancy of macaques (Macaca fascicularisandM. mulatta) within a unisex group, reveals a structured space utilization beyond simple spatial affordance within the finite space. To this end, in two groups of four animals, we analyzed the simultaneously recorded positions of each individual while the group roamed in an enclosure. The data was gathered using automated devices that allow measuring accurate concomitant positions and calculate precise inter-individual distance, which is impossible in classical ethology even using GPS devices. Thus, our setup opens new possibilities using modelling approach, to characterize social interaction dynamics in small enclosures. We found that (1) The identity of each animal could be decoded from its individual pattern of spatial occupancy, revealing that each animal sustained a spatial footprint across multiple days. (2) Average distance between monkeys was a proxy of their social hierarchy, confirming that interpersonal distance is correlated to affiliation and dominance hierarchy. (3) Alternating the social context by removing one of the monkeys revealed that only removing the closest social partner influenced occupancy. (4) Finally, the distribution of distance between pairs of monkeys was bimodal and was modeled using random walk approach with an additional parameter reflecting propensity to stay in close proximity, which was again related to dominance hierarchy. These analyses reveal that space utilization is structured as a function of social determinants in macaques and simple modeling approach to further study group organization in neuro-ethological settings.
Quantifying Differences in Neural Population Activity With Shape Metrics
Authors: Barbosa Joao , Nejatbakhsh Amin , Duong Lyndon , Harvey Sarah E. , Brincat Scott L. , Siegel Markus , Miller Earl K. , Williams Alex H. 
Published: January 2025

AbstractQuantifying differences across species and individuals is fundamental to many fields of biology. However, it remains challenging to draw detailed functional comparisons between large populations of interacting neurons. Here, we introduce a general framework for comparing neural population activity in terms ofshape distances. This approach defines similarity in terms of explicit geometric transformations, which can be flexibly specified to obtain different measures of population-level neural similarity. Moreover, differences between systems are defined by a distance that is symmetric and satisfies the triangle inequality, enabling downstream analyses such as clustering and nearest-neighbor regression. We demonstrate this approach on datasets spanning multiple behavioral tasks (navigation, passive viewing of images, and decision making) and species (mice and non-human primates), highlighting its potential to measure functional variability across subjects and brain regions, as well as its ability to relate neural geometry to animal behavior.