bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction of blood biomarkers of metabolic disorders in Holstein cattle using parametric and nonparametric models
Authors: Mota Lucio F. M. , Giannuzzi Diana , Pegolo Sara , Sturaro Enrico , Gianola Daniel , Negrini Riccardo , Trevisi Erminio , Ajmone Marsan Paolo , Cecchinato Alessio 
Published: April 2024

Abstract
Background
Metabolic disturbances adversely impact productive and reproductive performance of dairy cattle due to changes in endocrine status and immune function, which increase the risk of disease. This may occur in the post-partum phase, but also throughout lactation, with sub-clinical symptoms. Recently, increased attention has been directed towards improved health and resilience in dairy cattle, and genomic selection (GS) could be a helpful tool for selecting animals that are more resilient to metabolic disturbances throughout lactation. Hence, we evaluated the genomic prediction of serum biomarkers levels for metabolic distress in 1353 Holsteins genotyped with the 100K single nucleotide polymorphism (SNP) chip assay. The GS was evaluated using parametric models best linear unbiased prediction (GBLUP), Bayesian B (BayesB), elastic net (ENET), and nonparametric models, gradient boosting machine (GBM) and stacking ensemble (Stack), which combines ENET and GBM approaches.

Results
The results show that the Stack approach outperformed other methods with a relative difference (RD), calculated as an increment in prediction accuracy, of approximately 18.0% compared to GBLUP, 12.6% compared to BayesB, 8.7% compared to ENET, and 4.4% compared to GBM. The highest RD in prediction accuracy between other models with respect to GBLUP was observed for haptoglobin (hapto) from 17.7% for BayesB to 41.2% for Stack; for Zn from 9.8% (BayesB) to 29.3% (Stack); for ceruloplasmin (CuCp) from 9.3% (BayesB) to 27.9% (Stack); for ferric reducing antioxidant power (FRAP) from 8.0% (BayesB) to 40.0% (Stack); and for total protein (PROTt) from 5.7% (BayesB) to 22.9% (Stack). Using a subset of top SNPs (1.5k) selected from the GBM approach improved the accuracy for GBLUP from 1.8 to 76.5%. However, for the other models reductions in prediction accuracy of 4.8% for ENET (average of 10 traits), 5.9% for GBM (average of 21 traits), and 6.6% for Stack (average of 16 traits) were observed.

Conclusions
Our results indicate that the Stack approach was more accurate in predicting metabolic disturbances than GBLUP, BayesB, ENET, and GBM and seemed to be competitive for predicting complex phenotypes with various degrees of mode of inheritance, i.e. additive and non-additive effects. Selecting markers based on GBM improved accuracy of GBLUP.
Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds
Authors: Shi Jinping , Li Zemin , Jia Li , Ma Yue , Huang Yongliang , He Pengjia , Ran Tao , Liu Wangjing , Zhang Wangdong , Cheng Qiang , Zhang Zhao , Lei Zhaomin 
Published: April 2024

Abstract
Background
In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

Result
The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

Conclusions
These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.
scCompressSA: dual-channel self-attention based deep autoencoder model for single-cell clustering by compressing gene–gene interactions
Authors: Zhang Wei , Yu Ruochen , Xu Zeqi , Li Junnan , Gao Wenhao , Jiang Mingfeng , Dai Qi 
Published: April 2024

Abstract
Background
Single-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases. Due to highly-stochastic transcriptomics data, accurate detection of cell types is still challenged, especially for RNA-sequencing data from human beings. In this case, deep neural networks have been increasingly employed to mine cell type specific patterns and have outperformed statistic approaches in cell clustering.

Results
Using cross-correlation to capture gene–gene interactions, this study proposes the scCompressSA method to integrate topological patterns from scRNA-seq data, with support of self-attention (SA) based coefficient compression (CC) block. This SA-based CC block is able to extract and employ static gene–gene interactions from scRNA-seq data. This proposed scCompressSA method has enhanced clustering accuracy in multiple benchmark scRNA-seq datasets by integrating topological and temporal features.

Conclusion
Static gene–gene interactions have been extracted as temporal features to boost clustering performance in single-cell clustering For the scCompressSA method, dual-channel SA based CC block is able to integrate topological features and has exhibited extraordinary detection accuracy compared with previous clustering approaches that only employ temporal patterns.
Screening and classification of rosehip (Rosa canina L.) genotypes based on horticultural characteristics
Authors: Mertoğlu Kerem , Durul Melekber Sulusoglu , Korkmaz Nazan , Polat Mehmet , Bulduk Ibrahim , Esatbeyoglu Tuba 
Published: April 2024

Abstract
Background
During the pandemic, the interest in colorful wild small fruits increased due to their positive effects on health. Also it has become very important to offer species with high nutritional value as fresh or processed products for human consumption due to increasing world population and decreasing arable land. In this context, we characterized the horticultural characteristics of 11 rosehip genotypes grown from seeds.

Results
Citric acid was determined as the main organic acid in all the genotypes investigated. The mean values of the organic acids obtained from all the genotypes were found to be as follows: citric acid (7177 mg L–1), malic acid (3669 mg L–1), tartaric acid (1834 mg L–1), oxalic acid (1258 mg L–1), carboxylic acid (631.9 mg L–1), shikimic acid (157.8 mg L–1), ascorbic acid (155 mg L–1), and acetic acid (20.9 mg L–1). Ellagic acid was the dominant phenolic compound (90.1 mg L–1 – 96.2 mg L–1) in all genotypes. The average values obtained from all genotypes for total phenolics, total flavonoids, and antioxidant activity were 37 261 mg GAE L–1, 526.2 mg quercetin L–1, and 93.6%, respectively. These characteristics had the lowest coefficients of variation, which indicated that all genotypes were similar regarding high biochemical with antioxidant effect. In addition, fruit width, fruit length, and fruit weight varied between 13.0 and 17.3 mm, 20.7 and 25.5 mm, and 1.4 and 2.7 g, respectively.

Conclusions
The genotypes were categorized according to different purposes, such as suitability for wine production, making vinegar, etc. While the pomological characteristics were strongly positively correlated among themselves, they were generally found to be negatively correlated with the phytochemical characteristics. Categorizing genotypes according to different usage purposes can improve the agricultural and industrial application of rosehip and enhance their breeding efficacy.
Effect of intravenous anesthetic drugs on fertilization rate in oocyte retrieval
Authors: Liu Yanfang , Gao Yongtao , Lu Cuie , Chen Junjie , Huang Saisai 
Published: April 2024

Abstract
Background
The purpose of this study was to investigate the effects of intravenous anesthetic drugs on fertilization rate in subjects receiving oocyte retrieval by assisted reproduction technology (ART).

Methods
A retrospective cohort study was designed. The clinical information of subjects who received oocyte retrieval procedure was collected. The subjects were divided into two groups based on the type of anesthesia used: the no-anesthesia group and the intravenous anesthesia group. Propensity score matching (PSM) was performed and multiple linear regression analyses were conducted. Fertilization rate was compared between the two groups before and after PSM.

Results
A total of 765 subjects were divided into two groups: the no-anesthesia group (n = 482) and the intravenous anesthesia group (n = 283). According to propensity scores, 258 pairs of subjects were well matched, and the baseline data between the two groups were not significantly different (P > 0.05). Fertilization rate was 77% in the intravenous anesthesia group, and 76% in the no-anesthesia group, without significant between-group difference (P = 0.685). Before matching, Poisson regression analysis showed no effect of intravenous anesthetic drugs on fertilization rate (RR = 0.859, 95%CI: 0.59 to 1.25, P = 0.422). After matching, no difference was found either (RR = 0.935, 95%CI: 0.67 to 1.29, P = 0.618).

Conclusion
Intravenous anesthetic drugs may exert no effects on fertilization rate in subjects receiving ART.
Procyanidin B2 alleviates oxidized low-density lipoprotein-induced cell injury, inflammation, monocyte chemotaxis, and oxidative stress by inhibiting the nuclear factor kappa-B pathway in human umbilical vein endothelial cells
Authors: Yuan Limei , Fan Lihua , Zhang Zhiqiang , Huang Xing , Liu Qingle , Zhang Zhiguo 
Published: April 2024

Abstract
Background
Oxidized low-density lipoprotein (ox-LDL) can initiate and affect almost all atherosclerotic events including endothelial dysfunction. In this text, the role and underlying molecular basis of procyanidin B2 (PCB2) with potential anti-oxidant and anti-inflammatory activities in ox-LDL-induced HUVEC injury were examined.

Methods
HUVECs were treated with ox-LDL in the presence or absence of PCB2. Cell viability and apoptotic rate were examined by CCK-8 assay and flow cytometry, respectively. The mRNA and protein levels of genes were tested by RT-qPCR and western blot assays, respectively. Potential downstream targets and pathways of apple procyanidin oligomers were examined by bioinformatics analysis for the GSE9647 dataset. The effect of PCB2 on THP-1 cell migration was examined by recruitment assay. The effect of PCB2 on oxidative stress was assessed by reactive oxygen species (ROS) level, malondialdehyde (MDA) content, and mitochondrial membrane potential (MMP).

Results
ox-LDL reduced cell viability, induced cell apoptosis, and facilitated the expression of oxidized low-density lipoprotein receptor 1 (LOX-1), C-C motif chemokine ligand 2 (MCP-1), vascular cell adhesion protein 1 (VCAM-1) in HUVECs. PCB2 alleviated ox-LDL-induced cell injury in HUVECs. Apple procyanidin oligomers triggered the differential expression of 592 genes in HUVECs (|log2fold-change| > 0.58 and adjusted p-value < 0.05). These dysregulated genes might be implicated in apoptosis, endothelial cell proliferation, inflammation, and monocyte chemotaxis. PCB2 inhibited C-X-C motif chemokine ligand 1/8 (CXCL1/8) expression and THP-1 cell recruitment in ox-LDL-stimulated HUVECs. PCB2 inhibited ox-LDL-induced oxidative stress and nuclear factor kappa-B (NF-κB) activation in HUVECs.

Conclusion
PCB2 weakened ox-LDL-induced cell injury, inflammation, monocyte recruitment, and oxidative stress by inhibiting the NF-κB pathway in HUVECs.
Association of inflammatory biomarkers with overall survival in burn patients: a systematic review and meta-analysis
Authors: Nourigheimasi Shima , Yazdani Erfan , Ghaedi Arshin , Khanzadeh Monireh , Lucke-Wold Brandon , Dioso Emma , Bazrgar Aida , Ebadi Mehrnoosh , Khanzadeh Shokoufeh 
Published: April 2024

Abstract
Introduction
The inflammatory response to burn injuries can lead to organ dysfunction that ultimately results in increased mortality and morbidity. This meta-analysis was conducted to determine the efficacy of inflammatory biomarkers, including the neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), procalcitonin (PCT), and C-reactive protein (CRP) as predictive tools of mortality among burn patients.

Material and methods
The biomarker levels of survivors and non-survivors were consolidated according to guidelines for Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Three main databases were searched electronically: PubMed, Web of Science, and Scopus, on December 8, 2022. The Newcastle–Ottawa Quality Assessment Scale (NOS) was used to evaluate and score the methodological quality of the included studies. The standard mean difference (SMD) with a 95% confidence interval (CI) was utilized.

Results
Twenty-four studies were included in our systematic review and meta-analysis, (3636 total burn patients), of whom 2878 survived. We found that deceased burn patients had elevated levels of NLR (SMD = 0.60, 95% CI; 0.19–1.00, P < 0.001), CRP (SMD = 0.80, 95% CI; 0.02–1.58, P = 0.04), and PCT (SMD = 0.85, 95% CI; 0.45–1.24, P < 0.001), compared to survivors. However, we found no association between PLR and mortality among burn patients (SMD = 0.00, 95% CI; -0.14–0.15, P < 0.001). In addition, CRP was significantly higher in non-survivors (SMD = 0.80, 95% CI; 0.02–1.58, P =0.04). Similar results were also found about PCT (SMD = 0.85, 95% CI; 0.45–1.24, P < 0.001). When we analyzed the PCT data, collected in the first 24-48 hours, we found similar results; the PCT level was significantly higher in non-survivors in the immediate postinjury-period (SMD = 0.67, 95% CI; 0.31–1.02, P < 0.001). There was no publication bias among studies on the role of NLR in burn (Egger’s test P = 0.91). The based cut-off values for NLR (13), CRP (71), and PCT (1.77) yielded sensitivities of 69.2%, 100%, and 93.33%, and specificities of 76%, 72.22%, and 72.22% respectively.

Discussion/Conclusions
PCT is a marker of sepsis, therefore its elevated level is presumably associated with a higher incidence and severity of sepsis among non-survivors. In addition, NLR and CRP are promising biomarkers for predicting and guiding prevention against burn deaths in clinical settings.
Exploring factors influencing time from dispatch to unit availability according to the transport decision in the pre-hospital setting: an exploratory study
Authors: Farhat Hassan , Makhlouf Ahmed , Gangaram Padarath , Aifa Kawther El , Khenissi Mohamed Chaker , Howland Ian , Abid Cyrine , Jones Andre , Howard Ian , Castle Nicholas , Al Shaikh Loua , Khadhraoui Moncef , Gargouri Imed , Laughton James , Alinier Guillaume 
Published: April 2024

Abstract
Background
Efficient resource distribution is important. Despite extensive research on response timings within ambulance services, nuances of time from unit dispatch to becoming available still need to be explored. This study aimed to identify the determinants of the duration between ambulance dispatch and readiness to respond to the next case according to the patients’ transport decisions.

Methods
Time from ambulance dispatch to availability (TDA) analysis according to the patients’ transport decision (Transport versus Non-Transport) was conducted using R-Studio™ for a data set of 93,712 emergency calls managed by a Middle Eastern ambulance service from January to May 2023. Log-transformed Hazard Ratios (HR) were examined across diverse parameters. A Cox regression model was utilised to determine the influence of variables on TDA. Kaplan–Meier curves discerned potential variances in the time elapsed for both cohorts based on demographics and clinical indicators. A competing risk analysis assessed the probabilities of distinct outcomes occurring.

Results
The median duration of elapsed TDA was 173 min for the transported patients and 73 min for those not transported. The HR unveiled Significant associations in various demographic variables. The Kaplan–Meier curves revealed variances in TDA across different nationalities and age categories. In the competing risk analysis, the ‘Not Transported’ group demonstrated a higher incidence of prolonged TDA than the ‘Transported’ group at specified time points.

Conclusions
Exploring TDA offers a novel perspective on ambulance services’ efficiency. Though promising, the findings necessitate further exploration across diverse settings, ensuring broader applicability. Future research should consider a comprehensive range of variables to fully harness the utility of this period as a metric for healthcare excellence.
Advancing health equity for Indigenous peoples in Canada: development of a patient complexity assessment framework
Authors: Sehgal Anika , Henderson Rita , Murry Adam , Crowshoe Lynden , Barnabe Cheryl 
Published: April 2024

Abstract
Background
Indigenous patients often present with complex health needs in clinical settings due to factors rooted in a legacy of colonization. Healthcare systems and providers are not equipped to identify the underlying causes nor enact solutions for this complexity. This study aimed to develop an Indigenous-centered patient complexity assessment framework for urban Indigenous patients in Canada.

Methods
A multi-phased approach was used which was initiated with a review of literature surrounding complexity, followed by interviews with Indigenous patients to embed their lived experiences of complexity, and concluded with a modified e-Delphi consensus building process with a panel of 14 healthcare experts within the field of Indigenous health to identify the domains and concepts contributing to health complexity for inclusion in an Indigenous-centered patient complexity assessment framework. This study details the final phase of the research.

Results
A total of 27 concepts spanning 9 domains, including those from biological, social, health literacy, psychological, functioning, healthcare access, adverse life experiences, resilience and culture, and healthcare violence domains were included in the final version of the Indigenous-centered patient complexity assessment framework.

Conclusions
The proposed framework outlines critical components that indicate the presence of health complexity among Indigenous patients. The framework serves as a source of reference for healthcare providers to inform their delivery of care with Indigenous patients. This framework will advance scholarship in patient complexity assessment tools through the addition of domains not commonly seen, as well as extending the application of these tools to potentially mitigate racism experienced by underserved populations such as Indigenous peoples.
Accessibility and availability of maternal and reproductive health care services: ensuring health equity among rural women in Southern India
Authors: Jeganathan Geetha , Srinivasan Sampath Kumar , Ramasamy Senthilkumar , Govindharaj Pitchaimani 
Published: April 2024

Abstract
Introduction
The health of women is of particular concern because they often have greater health needs than men and many women still lack access to quality healthcare services, preventing their ability to attain the best possible level of health. Hence, this study aimed to assess the accessibility and availability of health services among rural women.

Methods
A household survey was conducted by using a multi-stage sample with 407 married women aged 18–45 years, having at least one child and living in Tiruchirappalli District, Tamil Nadu were recruited for this study. A semi-structured questionnaire was used to collect data about the demographic status, and accessibility and availability of health services.

Results
Of the 407 respondents, 70% were aged between 26 and 40 years, 73% were working as farmers and labourers and 77% were living in nuclear families. 71% of them had enjoyed hospital facilities near their residence and 83% of the hospitals were run by the government. In village health nurse service (VHN), 34% of the respondents had received all services from VHN and 86% did not face any kind of gender inequality and almost all of them were satisfied with the service provided by the VHN. Almost all the respondents (98%) were satisfied with the availability of health services and 92% of them benefited from the government scheme related to childbirth.

Conclusion
This study showed that overall, the women were satisfied with the availability of healthcare services and reproductive health services. Moreover, almost all of them benefited from the government scheme related to childbirth.