bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data
Authors: Li Shuang , Liu Li , Ahmed Zulfiqar , Wang Fuwen , Lei Chuzhao , Sun Fang 
Published: July 2024

Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands.Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors.Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors.Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.
Extracellular matrix substrates differentially influence enteric glial cell homeostasis and immune reactivity
Authors: Schneider Linda , Schneider Reiner , Hamza Ebrahim , Wehner Sven 
Published: July 2024

IntroductionEnteric glial cells are important players in the control of motility, intestinal barrier integrity and inflammation. During inflammation, they switch into a reactive phenotype enabling them to release inflammatory mediators, thereby shaping the inflammatory environment. While a plethora of well-established in vivo models exist, cell culture models necessary to decipher the mechanistic pathways of enteric glial reactivity are less well standardized. In particular, the composition of extracellular matrices (ECM) can massively affect the experimental outcome. Considering the growing number of studies involving primary enteric glial cells, a better understanding of their homeostatic and inflammatory in vitro culture conditions is needed.MethodsWe examined the impact of different ECMs on enteric glial culture purity, network morphology and immune responsiveness. Therefore, we used immunofluorescence and brightfield microscopy, as well as 3’ bulk mRNA sequencing. Additionally, we compared cultured cells with in vivo enteric glial transcriptomes isolated from Sox10iCreERT2Rpl22HA/+ mice.ResultsWe identified Matrigel and laminin as superior over other coatings, including poly-L-ornithine, different lysines, collagens, and fibronectin, gaining the highest enteric glial purity and most extended glial networks expressing connexin-43 hemichannels allowing intercellular communication. Transcriptional analysis revealed strong similarities between enteric glia on Matrigel and laminin with enrichment of gene sets supporting neuronal differentiation, while cells on poly-L-ornithine showed enrichment related to cell proliferation. Comparing cultured and in vivo enteric glial transcriptomes revealed a 50% overlap independent of the used coating substrates. Inflammatory activation of enteric glia by IL-1β treatment showed distinct coating-dependent gene expression signatures, with an enrichment of genes related to myeloid and epithelial cell differentiation on Matrigel and laminin coatings, while poly-L-ornithine induced more gene sets related to lymphocyte differentiation.DiscussionTogether, changes in morphology, differentiation and immune activation of primary enteric glial cells proved a strong effect of the ECM. We identified Matrigel and laminin as pre-eminent substrates for murine enteric glial cultures. These new insights will help to standardize and improve enteric glial culture quality and reproducibility between in vitro studies in the future, allowing a better comparison of their functional role in enteric neuroinflammation.
Unraveling the causal link: fatty acids and inflammatory bowel disease
Authors: Zhou Yi , Zhou Zhenhua 
Published: July 2024

BackgroundPrevious observational studies have revealed the strong relationship between fatty acids (FA) and inflammatory bowel disease (IBD). Nonetheless, due to the inherent limitations of retrospective research, the causality between the two has not been clearly established.MethodsGenetic variants associated with the 17 FA indicators were derived from genome-wide association studies. Summary statistics for the discovery cohort and testing cohort for IBD, including ulcerative colitis (UC) and Crohn’s disease (CD), were available from IIBDGC and FinnGen, respectively. Bidirectional MR analysis and sensitivity analysis with multiple measures were applied to comprehensively investigate the causal link between FA and IBD.ResultsCombining the results of various MR methods, the validation of testing cohort, and the merging of meta-analysis, we demonstrated that genetically predicted Omega-3 FA levels, Ratio of Omega-3 FA to total FA, Docosahexaenoic acid (DHA) levels, and Ratio of DHA to total FA reduced the risk of IBD, UC, and CD. Meanwhile, multivariate MR suggested that the risk effects of Omega-3 FA and DHA for UC and CD were mainly affected by Saturated FA and Monounsaturated fatty acid (MUFA). Furthermore, although there was the causal association between Ratio of MUFA to total FA as well as Ratio of Polyunsaturated fatty acid (PUFA) to MUFA and CD, sensitivity analysis prompted that the findings were not robust. None of the above results had a reverse causal effect.ConclusionThis MR investigation provided evidence of causality between diverse FA and IBD. These findings offered new insights into the treatment and prevention of IBD.
Palliative care and COVID-19: acknowledging past mistakes to forge a better future
Authors: Andrade Camila Rabelo Monteiro de , Luz Fernanda Silva Trindade , Oliveira Neimy Ramos de , Kopittke Luciane , Santa Rosa Luiza Marinho Motta , Gomes Angelica Gomides dos Reis , Bartolazzi Frederico , Francisco Saionara Cristina , Costa Felicio Roberto da , Jorge Alzira de Oliveira , Cimini Christiane Corrêa Rodrigues , Carneiro Marcelo , Ruschel Karen Brasil , Schwarzbold Alexandre Vargas , Ponce Daniela , Ferreira Maria Angélica Pires , Guimarães Júnior Milton Henriques , Silveira Daniel Vitório , Aranha Fernando Graça , Carvalho Rafael Lima Rodrigues de , Godoy Mariana Frizzo de , Viana Lucas Macedo Pereira , Hirakata Vânia Naomi , Bicalho Maria Aparecida Camargos , Marcolino Milena Soriano 
Published: July 2024

ContextCOVID-19 induces complex distress across physical, psychological, and social realms and palliative care (PC) has the potential to mitigate this suffering significantly.ObjectivesTo describe the clinical characteristics and outcomes of COVID-19 patients with an indication of PC, compared to patients who had no indication, in different pandemic waves.MethodsThis retrospective multicenter observational cohort included patients from 40 hospitals, admitted from March 2020 to August 2022. Patients who had an indication of palliative care (PC) described in their medical records were included in the palliative care group (PCG), while those who had no such indication in their medical records were allocated to the non-palliative care group (NPCG).ResultsOut of 21,158 patients, only 6.7% had indication for PC registered in their medical records. The PCG was older, had a higher frequency of comorbidities, exhibited higher frailty, and had a higher prevalence of clinical complications and mortality (81.4% vs. 17.7%, p &lt; 0.001), when compared to the NPCG. Regarding artificial life support, the PCG had a higher frequency of dialysis (20.4% vs. 10.1%, p &lt; 0.001), invasive mechanical ventilation (48.2% vs. 26.0%, p &lt; 0.001) and admission to the intensive care unit (53.6% vs. 35.4%, p &lt; 0.001). These differences were consistent across all three waves.ConclusionA low proportion of patients received PC. Patients in PCG were more fragile, had more clinical complications, and had a higher mortality. On the contrary to our expectations, they received more artificial life support in all three waves. Taken together, these findings suggest that decisions regarding PC indication were made too late, within a context of end-of-life and therapeutic failure.
Assessing fatigue in women over 50 years with rheumatoid arthritis: a comprehensive case-control study using the FACIT-F scale
Authors: Valencia-Muntalà Lidia , Gómez-Vaquero Carmen , Berbel-Arcobé Laura , Benavent Diego , Vidal-Montal Paola , Juanola Xavier , Narváez Javier , Nolla Joan M. 
Published: July 2024

IntroductionData on prevalence of fatigue in rheumatoid arthritis (RA) patients in the era of biological treatments remains scarce, with a lack of case-control studies. This study evaluates the prevalence of fatigue in Spanish women over 50 years with RA using the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) scale, explores its association with RA-related variables, and seeks to identify the primary factors influencing fatigue. Ultimately, our objective is to underscore the clinical significance of fatigue as a comorbidity and to advocate for its systematic evaluation in routine clinical practice.MethodsIn a case-control study at a tertiary university hospital, 191 women over 50 years (mean age: 67.5 ± 8.8 years) meeting ACR 2010 criteria for RA and age-matched controls were assessed using the FACIT-F scale, SF-12 questionnaire, and RA-related clinical measures.ResultsFatigue was significantly more prevalent in the RA group (61%) compared to controls (37%, p &lt; 0.001), with RA patients showing lower mean FACIT-F scores (36.0 ± 10.6 vs. 40.0 ± 0.6, p &lt; 0.001). Correlations were noted between FACIT-F scores and C-reactive protein, DAS28, RAPID3, HAQ, and SF-12 scores. A multivariate analysis was performed and four models generated. The final model, with an R2 of 0.817, indicates that fatigue is significantly influenced by disease activity (RAPID 3) and mental and physical health (SF12) and age, explaining 81.7% of the variance in fatigue.ConclusionFatigue remains significantly prevalent and severe in women over 50 years with RA, strongly linked to disease activity, disability, and diminished quality of life. Systematic fatigue assessment and targeted strategies in clinical settings are essential to address this widespread issue. Future research should explore targeted interventions tailored to this demographic to enhance quality of care.
Hematological malignancy-associated pyoderma gangrenosum: evaluating the magnitude of the association
Authors: Kridin Khalaf , Ankary-Khaner Moria , Kridin Mouhammad , Cohen Arnon D. , Badarny Samih 
Published: July 2024

BackgroundHematologic malignancies (HMs) are well-known underlying comorbidities of pyoderma gangrenosum (PG). However, studies quantifying the likelihood of PG after HMs are yet to be performed.ObjectiveTo investigate the bidirectional association between PG and several HMs, namely acute leukemia, chronic leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, and multiple myeloma.MethodsA population-based retrospective cohort study was conducted to study the risk of HMs in patients with PG (n = 302) as compared to age-, sex-and ethnicity-matched control subjects (n = 1,799). A case–control design was used to estimate the likelihood of PG in individuals with a preexisting history of HMs. Adjusted hazard ratios (HRs) and adjusted odds ratios (ORs) were estimated by Cox regression and logistic regression, respectively.ResultsThe prevalence of preexisting HM was higher in patients with PG than in controls (6.7% vs. 0.9%, respectively). The likelihood of having PG was significantly greater among patients with a history of HM (adjusted OR, 7.88; 95% CI, 3.85–16.15; p &lt; 0.001), particularly during the first year following the diagnosis. This association was significant for acute leukemia, chronic leukemia, non-Hodgkin lymphoma, and multiple myeloma but not for Hodgkin lymphoma. The incidence rate of HM was 3.3 (95% CI, 1.2–7.4) and 1.6 (95% CI, 0.9–2.6)/1,000 person-years among patients with PG and controls, respectively. Relative to controls, patients with PG were not more likely to develop subsequent HM (adjusted HR, 2.22; 95%CI, 0.77–6.45; p = 0.142). Compared to other patients with PG, those with HM-associated PG experienced an increased all-cause mortality rate (adjusted HR, 2.19; 95%CI, 1.09–4.40; p = 0.028).ConclusionHM, particularly acute leukemia and multiple myeloma, are associated with an elevated likelihood of provoking PG.
Potential therapeutic targets for pelvic organ prolapse: insights from key genes related to blood vessel development
Authors: Wu Huaye , Yang Lu , Yuan Jiakun , Zhang Ling , Tao Qin , Yin Litong , Yu Xia , Lin Yonghong 
Published: July 2024

ObjectivePelvic organ prolapse (POP) is a disease in which pelvic floor support structures are dysfunctional due to disruption of the extracellular matrix (ECM). The vascular system is essential for maintaining ECM homeostasis. Therefore, this study explored the potential mechanism of blood vessel development-related genes (BVDRGs) in POP.MethodsPOP-related datasets and BVDRGs were included in this study. Differentially expressed genes (DEGs) between the POP and control groups were first identified in the GSE12852 and GSE208271 datasets, and DE-BVDRGs were identified by determining the intersection of these DEGs and BVDRGs. Subsequently, the feature genes were evaluated by machine learning. Feature genes with consistent expression trends in the GSE12852 and GSE208271 datasets were considered key genes. Afterward, the overall diagnostic efficacy of key genes in POP was evaluated through receiver operating characteristic (ROC) curve analysis. Based on the key genes, enrichment analysis, immune infiltration analysis and regulatory network construction were performed to elucidate the molecular mechanisms underlying the functions of the key genes in POP.ResultsA total of 888 DEGs1 and 643 DEGs2 were identified in the GSE12852 and GSE208271 datasets, and 26 candidate genes and 4 DE-BVDRGs were identified. Furthermore, Hyaluronan synthase 2 (HAS2), Matrix metalloproteinase 19 (MMP19) and Plexin Domain Containing 1 (PLXDC1) were identified as key genes in POP and had promising value for diagnosing POP (AUC &gt; 0.8). Additional research revealed that the key genes were predominantly implicated in immune cell activation, chemotaxis, and cytokine release via the chemokine signaling pathway, the Nod-like receptor signaling pathway, and the Toll-like receptor signaling pathway. Analysis of immune cell infiltration confirmed a decrease in the proportion of plasma cells in POP, and MMP19 expression showed a significant negative correlation with plasma cell numbers. In addition, regulatory network analysis revealed that MALAT1 (a lncRNA) targeted hsa-miR-503-5p, hsa-miR-23a-3p and hsa-miR-129-5p to simultaneously regulate three key genes.ConclusionWe identified three key BVDRGs (HAS2, MMP19 and PLXDC1) related to the ECM in POP, providing markers for diagnostic studies and investigations of the molecular mechanism of POP.
EEG microstates are associated with music training experience
Authors: Jiang Yihe , Zheng Maoping 
Published: July 2024

BackgroundMusic training facilitates the development of individual cognitive functions and influences brain plasticity. A comprehensive understanding of the pathways and processes through which music affects the human brain, as well as the neurobiological mechanisms underlying human brain perception of music, is necessary to fully harness the plasticity that music offers for brain development.AimsTo investigate the resting-state electroencephalogram (EEG) activity of individuals with and without music training experience, and explore the microstate patterns of EEG signals.MethodIn this study, an analysis of electroencephalogram (EEG) microstates from 57 participants yielded temporal parameters(mean duration, time coverage, occurrence, and transition probability)of four classic microstate categories (Categories A, B, C, and D) for two groups: those with music training experience and those without. Statistical analysis was conducted on these parameters between groups.ResultsThe results indicate that compared to individuals without music training experience, participants with music training experience exhibit significantly longer mean durations of microstate A, which is associated with speech processing. Additionally, they show a greater time coverage of microstate B, which is associated with visual processing. Transition probabilities from microstate A to microstate B were greater in participants with music training experience compared to those without. Conversely, transition probabilities from microstate A to microstate C and from microstate C to microstate D were greater in participants without music training experience.ConclusionOur study found differences in characteristic parameters of certain microstates between individuals with and without music training experience. This suggests distinct brain activity patterns during tasks related to speech, vision, and attention regulation among individuals with varying levels of music training experience. These findings support an association between music training experience and specific neural activities. Furthermore, they endorse the hypothesis of music training experience influencing brain activity during resting states. Additionally, they imply a facilitative role of music training in tasks related to speech, vision, and attention regulation, providing initial evidence for further empirical investigation into the cognitive processes influenced by music training.
Betaine for the prevention and treatment of insulin resistance and fatty liver in a high-fat dietary model of insulin resistance in C57BL mice
Authors: Kathirvel Elango , Morgan Kengathevy , Malysheva Olga V. , Caudill Marie A. , Morgan Timothy R. 
Published: July 2024

AimThe aim was to investigate mechanisms by which betaine improves hepatic insulin signaling in a dietary mouse model of insulin resistance and fatty liver.MethodsC57BL 6J mice were fed a standard diet (SF), a standard diet with betaine (SFB), a nutritionally complete high fat (HF) diet, or a high fat diet with betaine (HFB) for 14 weeks. In a separate experiment, mice were fed high fat diet for 18 weeks, half of whom received betaine for the final 4 weeks. Activation of insulin signaling in the liver was assessed by western blot. Insulin signaling was also assessed in insulin resistant primary human hepatocytes treated with betaine.ResultsAs compared with SF, mice receiving HF diet were heavier, had more hepatic steatosis, and abnormal glucose tolerance test (GTT). Betaine content in liver and serum was 50% lower in HF than in SF; betaine supplementation restored serum and liver betaine content. Betaine treatment of HF reduced whole body insulin resistance as measured by GTT. Betaine treatment of HF increased tyrosine phosphorylation of insulin receptor substrate-1 and phosphorylation (activation) of Akt, and increased hepatic glycogen content. In vitro, betaine reversed insulin resistance in primary human hepatocytes by increasing insulin-stimulated tyrosine phosphorylation of IRS1 and of Akt.ConclusionBetaine supplementation reduced whole body insulin resistance and increased activation of insulin signaling pathways in the liver in a mouse model of insulin resistance and fatty liver created by feeding a nutritionally complete high fat diet for 14 weeks. Betaine also reduced liver injury as assessed by ALT and by liver histology. In vitro, betaine reversed insulin resistance by increasing insulin-stimulated tyrosine phosphorylation of IRS1 and activation of downstream proteins in the insulin signaling cascade in insulin resistant primary human hepatocytes.
The negative association between the docosapentaenoic acid intake and the incidence of AMD based on NHANES 2005–2008
Authors: Xu Baiwei , Hu Yi , Di Jie , Liu Zhongwei , Yu Ziyan , Han Lin , Ning Yuan 
Published: July 2024

IntroductionAge-related macular degeneration (AMD) is an ophthalmic disease that causes visual impairment and is one of the leading causes of blindness in the elderly. Fatty acids are essential nutrients required by the body and play a cornerstone role in the life activities of the body. Many studies have reported that fatty acids are involved in the development of AMD. To confirm this association, we conducted the present study.MethodsWe analyzed the association between all fatty acid intake and AMD using National Health and Nutrition Examination Survey (NHANES) data from 2005–2008. Quantile regression was performed to assess the effect of fatty acids on AMD at different intake levels.ResultsAfter adjusting for covariates, only saturated fatty acids showed no significant difference between AMD patients and non-AMD patients (23.64 g vs. 26.03 g, p = 0.052). Total fat (70.88 g vs. 78.86 g, p = 0.024), monounsaturated fatty acids (25.87 g vs. 28.95 g, p = 0.019), polyunsaturated fatty acids (15.10 g vs. 17.07 g, p = 0.017) showed significant differences between the two groups. When AMD was considered as an outcome, the association between AMD and docosaentaenoic acid (DPA) was negative in the multivariate logic model (model 1: OR = &lt;0.001, 95% CI = &lt;0.001 ~ 0.734; model 2: OR = &lt;0.001, 95% CI = &lt;0.001 ~ 0.002; model 3: OR = &lt;0.001, 95% CI = &lt;0.001 ~ 0.002). In the quantile regression, DPA was shown to be negatively associated with the presence of AMD only in the fourth quartile in model 2 and model 3 (model 2: OR = &lt;0.001, 95% CI = &lt;0.001 ~ 0.927; model 3: OR = &lt;0.001, 95% CI = &lt;0.001 ~ 0.775).DiscussionTherefore, based on above results, we concluded that DPA intake could prevent the development of AMD.