bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteomic profiling reveals sexual dimorphism in the retina and RPE of C57BL6 mice
Authors: Jang Geeng-Fu , Crabb John S. , Grenell Allison , Wolk Alyson , Campla Christie , Luo Shiming , Ali Mariya , Hu Bo , Willard Belinda , Anand-Apte Bela 
Published: October 2024

Abstract
Background
Sex as a biological variable is not a common consideration in molecular mechanistic or preclinical studies of retinal diseases. Understanding the sexual dimorphism of adult RPE and retina under physiological conditions is an important first step in improving our understanding of sex-based physio-pathological mechanisms.

Methods
Isobaric tags for relative and absolute quantitation (iTRAQ) were used for quantitative proteomics of male and female mouse retina and RPE (10 mice of each sex for each tissue type). Differentially expressed proteins were subjected to Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA).

Results
Differential expression analysis identified 21 differentially expressed proteins in the retina and 58 differentially expressed proteins in the RPE. Ingenuity pathway analysis identified the top canonical pathways differentially activated in the retina to be calcium transport I, nucleotide excision repair, molecular transport and cell death and survival. In the RPE, the top canonical pathways were calcium signaling, dilated cardiomyopathy signaling, actin cytoskeletal signaling and cellular assembly and organization.

Conclusions
These results provide insights into sex differences in the retina and RPE proteome of mice and begin to shed clues into the sexual dimorphism seen in retinal diseases.
Single-cell analysis of nasal epithelial cell development in domestic pigs
Authors: Wang Wenqian , Liu Ruiling , Zhong Qiu , Cao Yunlei , Qi Jiaxin , Li Yuchen , Yang Qian 
Published: October 2024

AbstractThe nasal mucosa forms a critical barrier against the invasion of respiratory pathogens. Composed of a heterogeneous assortment of cell types, the nasal mucosa relies on the unique characteristics and complex intercellular dynamics of these cells to maintain their structural integrity and functional efficacy. In this study, single-cell RNA sequencing (scRNA-seq) of porcine nasal mucosa was performed, and nineteen distinct nasal cell types, including nine epithelial cell types, five stromal cell types, and five immune cell types, were identified. The distribution patterns of three representative types of epithelial cells (basal cells, goblet cells, and ciliated cells) were subsequently detected by immunofluorescence. We conducted a comparative analysis of these data with published human single-cell data, revealing consistent differentiation trajectories among porcine and human nasal epithelial cells. Specifically, basal cells serve as the initial stage in the differentiation process of nasal epithelial cells, which then epithelial cells. This research not only enhances our understanding of the composition and transcriptional signature of porcine nasal mucosal cells but also offers a theoretical foundation for developing alternative models for human respiratory diseases.
Volume-based selection in Pinus pinaster Aiton breeding: evaluating resistance to Bursaphelenchus xylophilus (Steiner & Buhrer) Nickle and wood properties
Authors: Torres-Sánchez Esteban , Acosta Juan José , Hodge Gary R. , Prada Eva , Menéndez-Gutiérrez María , Díaz Raquel 
Published: October 2024

Abstract
Key message
Genetic parameter estimates at age 12 years for trunk volume in Pinus pinaster displayed low to moderate heritability for growth and stem form, whereas wood properties showed high heritability. No correlation was detected between resistance to the nematode Bursaphelenchus xylophilus and growth, stem form, or wood properties. However, certain families stood out, showing favorable values across all traits, including resistance to the nematode.

Context
The breeding program for Pinus pinaster should advance towards a second-generation breeding population based on volume, stem form, and resistance to Bursaphelenchus xylophilus, with the challenge of incorporating novel traits of importance.

Aims
We focused on assessing the genetic parameters of growth, stem form, wood properties, and resistance to B. xylophilus as well as exploring the relationship between these traits.

Methods
We evaluated 116 half-sib families at three ages (7, 12, and 17 years) in seven progeny trials established in 2005, analyzing growth, stem form, and wood traits. Resistance to B. xylophilus was assessed in 91 of the 116 half-sib families at age 2 by artificial inoculation tests under greenhouse conditions.

Results
Advancing the selection age to 12 years proved to be feasible for volume selection in Galician P. pinaster. All traits, including resistance to B. xylophilus, showed potential for genetic improvement. Remarkably, resistance to B. xylophilus was not correlated to any other trait.

Conclusion
Excluding the most susceptible families to B. xylophilus from the Galician P. pinaster breeding program would not result in a significant decrease in volume, stem form, or wood properties.
New generalized Jacobi–Galerkin operational matrices of derivatives: an algorithm for solving the time-fractional coupled KdV equations
Authors: Ahmed H. M. 
Published: October 2024

AbstractThe present paper investigates a new method for computationally solving the time-fractional coupled Korteweg–de Vries equations (TFCKdVEs) with initial boundary conditions (IBCs). The method utilizes a set of generalized shifted Jacobi polynomials (GSJPs) that adhere to the specified initial and boundary conditions (IBCs). Our approach involves constructing operational matrices (OMs) for both ordinary derivatives (ODs) and fractional derivatives (FDs) of the GSJPs we employ. We subsequently employ the collocation spectral method using these OMs. This method successfully converts the TFCKdVEs into a set of algebraic equations, greatly simplifying the task. In order to assess the efficiency and precision of the proposed numerical technique, we utilized it to solve two distinct numerical instances.
Grazing exclusion promotes soil organic carbon accumulation in Tibetan grasslands with lower temperatures
Authors: Zhang Guangru , Tan Xiangping , He Jinhong , Luo Dengnan , Zeng Xiang , Liang Minqi , Cao Ruochen , Peng Siyuan , Li Pan , Tao Long , Ibrahim Muhammed Mustapha , Hu Zhongmin 
Published: October 2024

Abstract
Background
Grazing exclusion is a practical approach to restore vegetation in degraded grasslands and enhance soil organic carbon (SOC) sequestration. However, the dynamics and drivers of SOC in grasslands after grazing exclusion have not been well documented, especially in ecosystems with cold climates.

Methods
Here, we established 14 paired treatments (grazing exclusion vs. free-grazing) along a 600-km transect in the northeastern zone of the Qinghai-Tibet Plateau. After six years, we analyzed vegetation biomass dynamics and measured the soil physicochemical properties and organic C concentration across three depths (0–10, 10–20, and 20–30 cm).

Results
Grazing exclusion significantly increased above- and belowground biomass (139.85% and 43.30%, respectively), pH (1.38%), total phosphorus (3.29%), nitrate nitrogen (18.03%), and ammonium nitrogen (17.81%), but significantly decreased soil bulk density (2.43%) and clay content (10.49%), particularly in 0–30 cm. Specifically, SOC concentrations positively responded to grazing exclusion (0–10 cm) in 9 of the 14 sites evaluated. The effects of grazing exclusion on SOC concentrations were significantly higher in areas with a mean annual temperature (MAT) below 0 °C compared to those in sites with a high MAT (> 0 °C). The SOC concentrations significantly correlated with the mean annual precipitation (MAP) in both treatments, but these correlations diminished with increasing soil depth. Ridge regression analysis showed that soil chemical properties (e.g., total nitrogen and phosphorus) positively influenced SOC accumulation, while MAT negatively influenced it after grazing exclusion. Path analysis further revealed that MAT indirectly regulated SOC dynamics via soil chemical properties.

Conclusions
Our study highlights that grazing exclusion results in an asynchronous SOC and plant biomass accumulation and may be more beneficial for SOC sequestration in Qinghai-Tibet Plateau grasslands with lower temperatures. Also, humid climates promote SOC concentration in alpine grasslands. These results could help develop management practices and policies that promote sustainable grassland management.
Young people’s civic engagement in Italy: evidence on grade 8 students from the international civic and citizenship education study (ICCS) 2016
Authors: Damiani Valeria , Caponera Elisa , Losito Bruno , Palmerio Laura , Agrusti Gabriella 
Published: October 2024

AbstractCivic engagement represents a key aspect of a democratic society and is itself a multidimensional construct. Research has shown that the promotion of civic engagement is an important component of civic and citizenship education intended in a broad sense, pertaining to formal, non-formal and informal learning situations. Within a national scenario characterised by increasing levels of general institutional disaffection and a lack of electoral and political involvement, the recent reform in the area of civic and citizenship education (Law 92/2019) has led to lively debates on the status of its implementation in Italian schools and recent research at the national level has highlighted the lack of activities to promote students’ engagement. This study further investigates the ICCS 2016 findings on civic engagement of Italian students with two objectives: to identify possible groups of Italian eighth-grade students on the basis of their level of civic engagement and to examine the associations among these groups and some key factors reflecting school contexts and students’ attitudes and behaviours. To reach these goals, the data analyses encompassed a latent profile analysis and a logistic regression model. The latent profile analysis allowed the identification of three groups of Italian students: disengaged, moderately engaged and engaged students. The results of the regression model showed that engaged students were characterised by a higher level of citizenship self-efficacy. These findings confirm those of previous research on the key role of internal self-efficacy in promoting students’ civic engagement.
Integrating Big Data, Artificial Intelligence, and motion analysis for emerging precision medicine applications in Parkinson’s Disease
Authors: Dipietro Laura , Eden Uri , Elkin-Frankston Seth , El-Hagrassy Mirret M. , Camsari Deniz Doruk , Ramos-Estebanez Ciro , Fregni Felipe , Wagner Timothy 
Published: October 2024

AbstractOne of the key challenges in Big Data for clinical research and healthcare is how to integrate new sources of data, whose relation to disease processes are often not well understood, with multiple classical clinical measurements that have been used by clinicians for years to describe disease processes and interpret therapeutic outcomes. Without such integration, even the most promising data from emerging technologies may have limited, if any, clinical utility. This paper presents an approach to address this challenge, illustrated through an example in Parkinson’s Disease (PD) management. We show how data from various sensing sources can be integrated with traditional clinical measurements used in PD; furthermore, we show how leveraging Big Data frameworks, augmented by Artificial Intelligence (AI) algorithms, can distinctively enrich the data resources available to clinicians. We showcase the potential of this approach in a cohort of 50 PD patients who underwent both evaluations with an Integrated Motion Analysis Suite (IMAS) composed of a battery of multimodal, portable, and wearable sensors and traditional Unified Parkinson's Disease Rating Scale (UPDRS)-III evaluations. Through techniques including Principal Component Analysis (PCA), elastic net regression, and clustering analysis we demonstrate how this combined approach can be used to improve clinical motor assessments and to develop personalized treatments. The scalability of our approach enables systematic data generation and analysis on increasingly larger datasets, confirming the integration potential of IMAS, whose use in PD assessments is validated herein, within Big Data paradigms. Compared to existing approaches, our solution offers a more comprehensive, multi-dimensional view of patient data, enabling deeper clinical insights and greater potential for personalized treatment strategies. Additionally, we show how IMAS can be integrated into established clinical practices, facilitating its adoption in routine care and complementing emerging methods, for instance, non-invasive brain stimulation. Future work will aim to augment our data repositories with additional clinical data, such as imaging and biospecimen data, to further broaden and enhance these foundational methodologies, leveraging the full potential of Big Data and AI.
Heatmap analysis of modeled coastal tsunamis using different bathymetry data resolutions
Authors: Felix Raquel , Hubbard Judith , Wilson Kaya , Switzer Adam 
Published: October 2024

AbstractWe examined how variations in the horizontal resolution of bathymetry influence the behavior of modeled tsunamis at shallow depths nearshore. This was done using the Cornell Multi-grid Coupled Tsunami Model (COMCOT) to simulate tsunamis with resampled bathymetric data at resolutions of 5, 10, 20, 30, 40, 50, 100, 200, and 300 meters, derived from 1-m resolution NOAA coastal LiDAR data sets (at water depths of less than or equal to 30 m) and soundings. In total, we utilized 1,080 data sets, comprising 9 resolutions across 30 sets at 4 different sites. In addition, we included the 15-arc second grid ($$\sim$$
∼
455 m) 2021 GEBCO data for comparison. We initiated a 5-m high tsunami wave offshore and propagated it towards the coast, then used the resulting maximum wave heights for each resolution to quantify the differences across varying resolutions. Using the 5 m bathymetry as the reference model, we observed that data sets with 10–50 m resolutions can reproduce tsunamis reasonably well. The maximum heights are overestimated by less than or equal to 5% or underestimated by less than or equal to 10%, and the first wave arrival time is $$\sim$$
∼
10% earlier than expected. Coarser bathymetries show an increasing trend of height underestimation, with the GEBCO model underestimating it by as much as 70%. Coarser bathymetry models have more variable first wave arrival time, with waves arriving up to 20% later or up to 10% earlier than expected. Overall, a reasonably accurate result can be achieved using a bathymetric resolution in the 10 m–50 m range, and is achievable with reasonable computational efficiency (at least 80% faster than simulations using the 5 m model on high-performance computing). This study highlights the importance of shallow bathymetry data quality in the numerical modeling of tsunami propagation.
DLK1 and DLK2, two non-canonical ligands of NOTCH receptors, differentially modulate the osteogenic differentiation of mesenchymal C3H10T1/2 cells
Authors: Rodríguez-Cano María-Milagros , González-Gómez María-Julia , Monsalve Eva-María , Díaz-Guerra María-José M. , Kassem Moustapha , Laborda Jorge , Nueda María-Luisa , Baladrón Victoriano 
Published: October 2024

Abstract
Background
C3H10T1/2 is a mesenchymal cell line capable of differentiating into osteoblasts, adipocytes and chondrocytes. The differentiation of these cells into osteoblasts is modulated by various transcription factors, such as RUNX2. Additionally, several interconnected signaling pathways, including the NOTCH pathway, play a crucial role in modulating their differentiation into mature bone cells. We have investigated the roles of DLK1 and DLK2, two non-canonical inhibitory ligands of NOTCH receptors, in the osteogenic differentiation of C3H10T1/2 cells.

Results
Our results corroborate existing evidence that DLK1 acts as an inhibitor of osteogenesis. In contrast, we demonstrate for the first time that DLK2 enhances this differentiation process. Additionally, our data suggest that NOTCH2, 3 and 4 receptors may promote osteogenesis, as indicated by their increased expression during this process, whereas NOTCH1 expression, which decreases during cell differentiation, might inhibit osteogenesis. Moreover, treatment with DAPT, a NOTCH signaling inhibitor, impeded osteogenic differentiation. We have confirmed the increase in ERK1/2 MAPK and p38 MAPK phosphorylation in C3H10T1/2 cells induced to differentiate to osteoblasts. Our new findings reveal increased ERK1/2 MAPK phosphorylation in differentiated C3H10T1/2 cells with a decrease in DLK1 expression or an overexpression of DLK2, which is coincident with the behavior of those transfectants where we have detected an increase in osteogenic differentiation. Additionally, p38 MAPK phosphorylation increases in differentiated C3H10T1/2 cells with reduced DLK1 levels.

Conclusions
Our results suggest that DLK1 may inhibit osteogenesis, while DLK2 may promote it, by modulating NOTCH signaling and the phosphorylation of ERK1/2 and p38 MAPK pathways. Given the established inhibitory effect of DLK proteins on NOTCH signaling, these new insights could pave the way for developing future therapeutic strategies aimed at treating bone diseases.
Comment on: Fetal femur length and risk of diabetes in adolescence: a prospective cohort study
Authors: Fatima Zainab , Kakar Arifa Inayatullah , Idrees Usama , Oduoye Malik Olatunde , Nwadinigwe Uzodinma 
Published: October 2024

AbstractWe read the article "Fetal Femur Length and Risk of Diabetes in Adolescence: A Prospective Cohort Study" by Sayeed et al. with great interest. The authors present compelling evidence linking mid-trimester impaired femur growth with elevated prediabetic biomarkers in Bangladeshi adolescents. However, we believe the study would benefit from considering additional factors. Maternal gestational diabetes, a well-known risk factor for type 2 diabetes mellitus (T2DM) in offspring, and family history of diabetes, which reflects genetic predisposition, should be included. Socioeconomic factors, which influence health outcomes, also warrant attention. Including these variables would provide a more comprehensive understanding of the relationship between fetal femur length and T2DM risk in adolescents.
An anthropomorphic phantom for atrial transseptal puncture simulation training
Authors: Zeidan Aya Mutaz , Xu Zhouyang , Leung Lisa , Byrne Calum , Sabu Sachin , Zhou Yijia , Rinaldi Christopher Aldo , Whitaker John , Williams Steven E. , Behar Jonathan , Arujuna Aruna , Housden R. James , Rhode Kawal 
Published: October 2024

Abstract
Background
Transseptal puncture (TSP) is a critical prerequisite for left-sided cardiac interventions, such as atrial fibrillation (AF) ablation and left atrial appendage closure. Despite its routine nature, TSP can be technically demanding and carries a risk of complications. This study presents a novel, patient-specific, anthropomorphic phantom for TSP simulation training that can be used with X-ray fluoroscopy and ultrasound imaging.

Methods
The TSP phantom was developed using additive manufacturing techniques and features a replaceable fossa ovalis (FO) component to allow for multiple punctures without replacing the entire model. Four cardiologists and one cardiology trainee performed TSP on the simulator, and their performance was assessed using four metrics: global isotropy index, distance from the centroid, time taken to perform TSP, and a set of 5-point Likert scale questions to evaluate the clinicians’ perception of the phantom’s realism and utility.

Results
The results demonstrate the simulator’s potential as a training tool for interventional cardiology, providing a realistic and controllable environment for clinicians to refine their TSP skills. Experienced cardiologists tended to cluster their puncture points closer to regions of the FO associated with higher global isotropy index scores, indicating a relationship between experience and optimal puncture localization. The questionnaire analysis revealed that participants generally agreed on the phantom’s realistic anatomical representation and ability to accurately visualize the TSP site under fluoroscopic guidance.

Conclusions
The TSP simulator can be incorporated into training programs, offering trainees the opportunity to improve tool handling, spatial coordination, and manual dexterity prior to performing the procedure on patients. Further studies with larger sample sizes and longitudinal assessments are needed to establish the simulator’s impact on TSP performance and patient outcomes.
Seven-year overview of antimicrobial resistance in diarrheagenic Escherichia coli from sporadic human diarrhea cases in 20 Chinese provinces
Authors: Han Haihong , Li Weiwei , Liu Jikai , Zhang Xiaoai , Huo Xiang , Sun Yong , Chen Jiancai , Fan Ruyue , Zhang Jing , Chen Yong , Yang Hongxia , Chen Shuai , Li Yanfen , Tan Dongmei , Ma Xuemin , Fan Penghui , Yan Shaofei , Guo Yunchang 
Published: October 2024

AbstractDiarrheagenicEscherichia coliis one of the most prevalent foodborne pathogens and poses significant clinical challenges due to increasing rates of antibiotic resistance. In this study, 9,068 diarrheagenicE. coliisolates from sporadic diarrhea cases across 20 provinces of China from 2016 to 2022 were systematically analyzed to determine the prevalence and distribution of resistance. A total of 14 antibiotics were included in the antimicrobial resistance surveillance. Antimicrobial susceptibility testing indicated that the majority of the isolates (89.3%) were resistant to at least one antimicrobial agent, with a significant proportion (60.3%) demonstrating multidrug resistance. Isolates showed high levels of resistance to ampicillin (68.2%) and high sensitivity to imipenem (97.0%). Over the 7 years, an increasing trend in resistance to cefoxitin and chloramphenicol among the isolates was found. EnteroaggregativeE. coliwas identified as the predominant pathotype. Furthermore, antimicrobial resistance rates were higher among the isolates from infants under 1 year of age compared to other populations and resistance levels differed among pathotypes. In summary, our findings revealed the detailed resistance characteristics of diarrheagenicE. colistrains isolated from human sporadic diarrhea cases in China, offering valuable insights that can inform clinical antibiotic treatment strategies and priorities.