bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between the atherogenic index of plasma and abdominal aortic calcification: results from the National Health and Nutrition Examination Survey 2013–2014
Authors: Su Xiaozhou , Zhao Chunli , Li Donghua , Zhang Xianwei 
Published: February 2025

BackgroundCoronary artery calcification and cardiovascular disease are associated with elevated levels of atherogenic plasma index (AIP). However, the relationship with abdominal aortic calcification (AAC) remains unclear. This study aimed to explore the association between AIP and AAC using the National Health and Nutrition Examination Survey (NHANES) database.MethodsA cross-sectional analysis was conducted on 2,811 individuals aged 40 years or older from the 2013–2014 NHANES dataset. Participants with missing AAC-24 scores, AIP data, or covariate information were excluded. AAC was quantified using the Kauppila score (AAC-24), with a score &gt; 0 indicating the presence of AAC, and severe AAC (SAAC) being defined as an AAC-24 score ≥ 6. Multivariable regression models and restricted cubic spline analyses were employed to assess the associations between AIP and AAC. Sensitivity analysis was used to validate the robustness of the findings.ResultsThe study population had a mean age of 57.7 years, with 48.22% being male. A significant positive association was found between AIP and both the AAC score and the risk of AAC and SAAC, particularly in females. For the overall population, each unit increase in AIP was associated with an overall increase in AAC-24 score of 0.90 (95% CI: 0.22, 1.58; p = 0.009), and for women, the AAC risk and SAAC risk would be 4.01-fold higher (95% CI: 1.65, 9.74; p = 0.002) and 9.37-fold higher (95% CI: 2.37, 37.03; p = 0.001). No significant associations were found in males. Further analysis revealed a significant interaction between AIP and gender regarding both AAC scores and the risk of SAAC.ConclusionsThis study demonstrates a positive relationship between AIP and increased AAC scores, as well as a higher risk of AAC and SAAC in U.S. women. However, these findings require further investigation to confirm the observed gender-specific differences.
Alteration of chromatin states perturb the transcription regulation of gene during hydronephrosis
Authors: Wang Xiao-Hui , Zhang Shu-Feng , Wu Hai-Ying , Gao Jian , Wang Lin , Yin Yao , Wang Xuhui 
Published: February 2025

BackgroundGene expression is abnormal in disease compared to normal tissue same as the regulatory elements. Regulatory element binding with transcription factors managed transcription of gene, which usually require chromatin accessible.MethodsTo reveal potential epigenetic mechanism during hydronephrosis, we first used RNA-seq to finger out the disfunction genes during hydronephrosis, then combined with ATAC-seq, and BS-seq to reveal the related disfunction regulatory elements.ResultsFinally, we find that 860 differentially genes and 2429 dynamic chromatin open regions between normal and hydronephrosis tissue. Though, most of disfunction genes and regulatory elements significantly enriched in chronic kidney disease GO term, only small part of regulatory element target genes overlapped with truly disfunction genes. And we also find out an important gene OTUD6B, which overexpression in disease tissue is manipulated by distal regulatory element through chromatin loop, and confirm the importance of epigenetic mechanism in disease.ConclusionIn summary, we found many hub genes and potential therapeutic target during hydronephrosis, and also confirmed that epigenetic play important role in gene expression and relevant in disease progress.
Hypomethylation of GCNT2 isoform A correlates with transcriptional expression and is associated with poor survival in acute myeloid leukemia
Authors: Wu De-hong , Qiu Hong-chun , Xu Jing , Lin Jiang , Qian Jun 
Published: February 2025

BackgroundThe function of GCNT2 has been documented to act as an oncogenic driver or tumor suppressor in different types of tumor, but the role of GCNT2 and the epigenetic regulation mechanism in AML, however, has not yet been clarified. This study aimed to assay the expression and methylation profile of GCNT2 in AML, and further elucidate the clinical significance.MethodsMultiple datasets from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas projects (TCGA) were used to explore the expression and methylation profile of GCNT2 in normal hematopoiesis and AML. A pan-cancer analysis was performed to define the survival implications of GCNT2 across multiple cancers including AML. The relationships between GCNT2 expression/methylation and clinicopathologic features were investigated using a TCGA-AML dataset. Correlation analysis was performed to explore the relationship between transcriptional expression and DNA methylation. Differentially expressed genes (DEGs) on the KEGG pathway and GO terms were visualized using DAVID. Gene Set Enrichment Analysis (GESA) was carried out to assess the underlying mechanism. The relationship between methylation and immune cell infiltration was also examined.ResultsGCNT2 expression was highest in hematopoietic stem cells (HSC) but gradually decreased during the hematopoiesis differentiation, the monocytes, however, remained a high level of GCNT2 as an exception. In AML, GCNT2 was down-regulated as compared to normal hematopoiesis but was much higher in contrast to normal peripheral blood samples. Data from a pan-cancer analysis revealed that high-expressed GCNT2 contributed to a worse OS for AML. DNA methylation of GCNT2 showed a distinctive co-methylation pattern in AML and significantly negatively correlated with transcriptional expression. Methylation in the transcriptional start site of isoform A plays a critical role in the epigenetic regulation of GCNT2 expression. The silence of GCNT2 in AML was attributed to DNA methylation. Hypomethylation of isoform A significantly predicted poor survival in AML, linking to several cytogenetic and molecular abnormalities, such as t (8:21), inv (16), t (15;17), and genes mutations of DNMT3A, CEBPA, RUNX1, and WT1. Enrichment analysis disclosed that hypomethylation of isoform A was involved in the immune system, and it was further revealed that hypomethylation of isoform A was tightly associated with immune cell infiltration and could be served as a promising indicator for immunotherapy.ConclusionsOur comprehensive research demonstrated that GCNT2 acted as an oncogene in AML, and was epigenetically regulated by DNA methylation in isoform A. Hypomethylation of isoform A could be served as a promising indicator to identify the high-risk AML patients who might be responsive to immunotherapy.
The protective role of muscone in the development of COPD
Authors: Feng Tiantian , Guo Xiaolong , Chen Wei , Zhang Yanying , Dai Runjing , Zhang Yinfang , Liu Yongqi , Liu Yiya , Song Peng , Fan Jingchun 
Published: February 2025

BackgroundMuscone, a key component of musk, exhibits anti-inflammatory properties. However, its therapeutic potential in inflammatory lung diseases, such as chronic obstructive pulmonary disease (COPD), remains largely unexplored. This study aimed to investigate whether Muscone could exert a protective effect in a mouse model of COPD in vivo.MethodsA COPD animal model was established by exposing mice to cigarette smoke (CS) and administering lipopolysaccharide (LPS) intranasally. After 4 weeks, mice were treated daily with dexamethasone (DEX) or different doses of Muscone for 3 weeks. Mouse body weight, lung function, and histopathology were determined. Serum levels of cytokines (IL-38, IL-1β, IL-17, TGF-β, IFN-γ) were measured using ELISA and qRT-PCR. Lung expression of CXCR3, IFN-γ, IL-17A, and RORγt was assessed by immunofluorescence.ResultsThe body weight of COPD mice was significantly lower than that of Muscone-treated COPD mice, consistent with decreased lung function, accompanied by reduced circulating and lung IL-38 levels. After Muscone administration, lung function was significantly improved, accompanied by upregulation of circulating and lung anti-inflammatory cytokines, including IL-38, in a dose-dependent manner, while the expression of pro-inflammatory cytokines was significantly reduced. Additionally, Muscone significantly inhibited the protein expression of CXCR3, IFN-γ, IL-17A, and RORγt in lung tissues of COPD mice.ConclusionThis study demonstrates that Muscone improves lung function in mice with COPD, potentially through a mechanism that may involve the modulation of cytokine expression, including the potential upregulation of anti-inflammatory cytokines such as IL-38. The precise underlying mechanisms of Muscone’s therapeutic effects in COPD remain to be fully elucidated. Further research is needed to investigate the correlation between COPD lung pathophysiology and the specific effects of Muscone treatment, including a more detailed analysis of the balance between pro- and anti-inflammatory mediators in COPD animal models, particularly utilizing IL-38 GKO mice to further investigate the role of IL-38 in mediating the therapeutic effects of Muscone.
Impact of different 3D regions of interest on quantifying dynamic lumbar vertebral microstructure in ovariectomized rats—a micro-CT study
Authors: Xu Huihui , Liu Hong , Liu Meijie , Li Yan , Pan Jinghua , Wang Shaojun , Wang Guowei , Liu Xin , Liu Ying , Hou Xiaoqin , Zhao Hongyan 
Published: February 2025

IntroductionThe selection of regions of interest (ROIs) is crucial for accurate microcomputed tomography (micro-CT) analysis. Distinct ROI selection methods exist for lumbar vertebras in osteoporotic animal model research. However, whether different ROIs directly affect the results of quantitative micro-CT-based microarchitectural data is still unknown. This study aimed to compare the diagnostic accuracy of two commonly used ROIs of lumbar vertebras in ovariectomized (OVX) rats at different time points.MethodsRats were randomly divided into the baseline group, the sham/OVX-operated groups, with 12- or 24-weeks sham (Sham 12w or Sham 24w)/12- or 24-weeks (OVX 12w or OVX 24w)-operated group (n = 6 in every group). The fifth lumbar vertebras were collected and scanned using micro-CT. Quantitative analyses of bone microarchitecture parameters were conducted separately for the central ROI (ROI 1) and overall ROI (ROI 2).ResultsThe results indicated that the Tb.N of baseline group rats for ROI 1 was significantly lower than that for ROI 2. The Tb.Th of rats of the Sham 12w and Sham 24w groups was significantly increased compared to that of the baseline group rats using the ROI 2 analysis. The bone mineral density (BMD) and bone volume fraction (BV/TV) were significantly lower by the ROI 1 than by the ROI 2 in all groups. The BMD and BV/TV also showed a significant reduction at 24 weeks postoperatively compared with those at 12 weeks postoperatively. Bland–Altman analysis showed good consistency between the two different ROI selection methods.ConclusionThis study found that capturing peripheral trabeculas (overall ROI) does not explain the increased Tb.Th in healthy mice and decreased Tb.N in OVX mice; both findings indicate that this is evident in both ROI. Moreover, this study suggested the potential value of the central ROI (effective and quicker) for evaluating osteoporosis of the lumbar vertebras in OVX rats and provides a basis for analyzing the morphological changes of lumbar trabecular.
Healthcare professionals and scientists’ collaboration with biobanks: a pilot study on the assessment of knowledge and attitudes toward biospecimen donation
Authors: Mikhailova Anastasiia A. , Bogomiagkova Elena S. , Nasykhova Yulia A. , Illarionov Roman A. , Danilova Maria M. , Tonyan Ziravard N. , Chernykh Vyacheslav B. , Kovalenko Ludmila V. , Bespalova Olesya N. , Glotov Andrey S. 
Published: February 2025

BackgroundDifficulties in the biobank progress are often associated with insufficient public awareness, but it is also worth paying attention to healthcare and science professionals who play an important role in the development of this area. This article presents results of the research on awareness toward biobanking and motivation to collaborate among employees of 3 medical and scientific organizations in Russia.MethodsThe anonymous survey was carried out via an online platform. The research included 176 healthcare and science professionals. To assess the differences between the groups the Pearson Chi-square test and the contingency coefficient were used. To find correlations between nominal and interval variables the Eta criterion was applied.ResultsIt was found that 88.1% of respondents were aware of biobanking in general, however, 15.0% were not aware of a biobank in their organization or had difficulty in answering this question. The experience of cooperation with biobanks was not particularly extensive – more than half of the respondents (60.3%) indicated that they had never contacted biobanks. 11.9% of participants became donors themselves. 35.0% - suggested to their friends and patients to become donors, while 86.2% were willing to do this in the future. The study showed that the respondents who already had experience working with biobanks, as well as those who themselves act as a donor, rated the importance of their activities higher.ConclusionIt is important to increase not only awareness but also motivation to cooperate with biobanks and be willing to take on different roles.
Bibliometric analysis of preoperative radiotherapy for locally advanced rectal cancer: evolution and future
Authors: Weng Zhen-Hong , Hu Hao-Kai , Zhou Zi-Shan , Huang Li-Sheng , Chen Bin-Bin , Lin Jia-Rui 
Published: February 2025

BackgroundPreoperative radiotherapy of rectal cancer has been a hot topic of research in recent years with the introduction of total neoadjuvant therapies and immunotherapeutic agents. We utilized bibliometrics and visualization analysis to examine studies in this field, aiming to identify current hotspots and research trends.MethodWe searched the Web of Science database for all publications related to preoperative radiotherapy of rectal cancer in the past 10 years. Using bibliometric analysis software, such as VOSviewer, CiteSpace and R-studio, we extracted and analyzed the data, summarizing the publication output of countries, institutions, authors, and journals in this field, and analyzing their relationships. We also summarized the keywords, burst words, and most cited articles, and analyzed the relationships among them.ResultsWe found 794 publications in the field, sourced from 217 journals or books, involving 5,805 authors from various organizations and countries. Through bibliometric analysis, we observed a growing trend in the number of publications in preoperative radiotherapy of rectal cancer over the past 10 years. China, United States and Italy were the top countries in terms of publication output. Sun Yat-sen University, Fujian University, and Fudan University were the top three medical centers in terms of publication output, while Leiden University from Netherlands led globally in terms of citation impact. Professor Zhen Zhang, Sanjun Cai, and Ji Zhu were the top three authors with the highest publication output. The most highly cited journals in this field includes “The Lancet Oncology,” “J Clinical Oncology,” and “Annals of Oncology.” Journals such as “Radiotherapy and Oncology,” “Frontiers in Oncology,” and “BMC Cancer” have the highest number of articles published. Based on the analysis of keywords and burst words, we found that “preoperative chemoradiation” and “oral capecitabine” were the research hotspots before 2016, while the focus shifted to “short-course radiotherapy” and “long-term outcomes” after 2017. Currently, the most frequently cited publications mainly summarize multicenter clinical studies and total neoadjuvant treatment models and immunotherapy.ConclusionResearch on preoperative radiotherapy of rectal cancer is increasing year by year, and attracting attention from high-cited journals such as “The Lancet Oncology,” “JCO,” and “Annals of Oncology.” Based on current data, the total neoadjuvant treatment models and radiation combined with immunotherapy are the research trends.
Genome-wide CRISPR/Cas9 screening identifies key profibrotic regulators of TGF-β1-induced epithelial-mesenchymal transformation and pulmonary fibrosis
Authors: Tan Chunjiang , Wang Juan , Ye Xiangrong , Kasimu Kaidirina , Li Ye , Luo Feng , Yi Hui , Luo Yifeng 
Published: February 2025

BackgroundThe idiopathic pulmonary fibrosis (IPF) is a progressive and lethal interstitial lung disease with high morbidity and mortality. IPF is characterized by excessive extracellular matrix accumulation (ECM) and epithelial-mesenchymal transformation (EMT). To date, few anti-fibrotic therapeutics are available to reverse the progression of pulmonary fibrosis, and it is important to explore new profibrotic molecular regulators mediating EMT and pulmonary fibrosis.MethodsBased on our model of TGF-β1-induced EMT in BEAS-2B cells, we performed the genome-wide CRISPR/Cas9 knockout (GeCKO) screening technique, pathway and functional enrichment analysis, loss-of-function experiment, as well as other experimental techniques to comprehensively investigate profibrotic regulators contributing to EMT and the pathogenesis of pulmonary fibrosis.ResultsUtilizing the GeCKO library screening, we identified 76 top molecular regulators. Ten candidate genes were subsequently confirmed by integrating the high-throughput data with findings from pathway and functional enrichment analysis. Among the candidate genes, knockout of COL20A1 and COL27A1 led to decreased mRNA expression of ECM components (Fibronectin and Collagen-I), as well as an increased rate of cell apoptosis. The mRNA expression of Collagen-I, together with the cell viability and migration, were inhibited when knocking out the WNT11. In addition, a decrease in the protein deposition of ECM components was observed by suppressing the expression of COL20A1, COL27A1, and WNT11.ConclusionOur study demonstrates that the COL20A1, COL27A1, and WNT11 serve as key profibrotic regulators of EMT. Gaining understanding and insights into these key profibrotic regulators of EMT paves the way for the discovery of new therapeutic targets against the onset and progression of IPF.
Electroencephalographic differences between waking and sleeping periods in patients with prolonged disorders of consciousness at different levels of consciousness
Authors: Li Keke , Li Man , Liu Wanqing , Wu Yanzhi , Li Fang , Xie Jingwei , Zhou Shaolong , Wang Sen , Guo Yongkun , Pan Jiahui , Wang Xinjun 
Published: February 2025

ObjectiveThis study aimed to explore differences in sleep electroencephalogram (EEG) patterns in individuals with prolonged disorders of consciousness, utilizing polysomnography (PSG) to assist in distinguishing between the vegetative state (VS)/unresponsive wakefulness syndrome (UWS) and the minimally conscious state (MCS), thereby reducing misdiagnosis rates and enhancing the quality of medical treatment.MethodsA total of 40 patients with prolonged disorders of consciousness (pDOC; 27 patients in the VS/UWS and 13 in the MCS) underwent polysomnography. We analyzed differential EEG indices between VS/UWS and MCS groups and performed correlation analyses between these indices and the Coma Recovery Scale-Revised (CRS-R) scores. The diagnostic accuracy of the differential indices was evaluated using receiver operating characteristic (ROC) curves.Results1. The fractal dimension (Higuchi’s fractal dimension (HFD)) of patients in the MCS tended to be higher than that of patients in the VS/UWS across all phases, with a significant difference only in the waking phase (p &lt; 0.05). The HFD in the waking phase was positively correlated with the CRS-R score and exhibited the highest diagnostic accuracy at 88.3%. The Teager–Kaiser energy operator (TKEO) also showed higher levels in patients in the MCS compared to those in the VS/UWS, significantly so in the NREM2 phase (p &lt; 0.05), with a positive correlation with the CRS-R score and diagnostic accuracy of 75.2%. The δ-band power spectral density [PSD(δ)] in the patients in the MCS was lower than that in those in the VS/UWS, significantly so in the waking phase (p &lt; 0.05), and it was negatively correlated with the CRS-R score, with diagnostic accuracy of 71.5%.ConclusionPolysomnography for the VS/UWS and MCS revealed significant differences, aiding in distinguishing between the two patient categories and reducing misdiagnosis rates. Notably, the HFD and PSD(δ) showed significantly better performance during wakefulness compared to sleep, while the TKEO was more prominent in the NREM2 stage. Notably, the HFD exhibited a robust correlation with the CRS-R scores, the highest diagnostic accuracy, and immense promise in the clinical diagnosis of prolonged disorders of consciousness.
Association between preoperative inflammatory status via CALLY index and postoperative pneumonia occurrence in resectable esophageal squamous cell carcinoma patients: a retrospective cohort study
Authors: Fan Mengtao , Zhu Yihan , Qian Long , Hu Chuanxian , Ding Hui 
Published: February 2025

BackgroundPostoperative pneumonia significantly affects recovery and prognosis in patients with esophageal squamous cell carcinoma. The CALLY index, derived from preoperative hematological parameters, may serve as a predictive marker for such complications.ObjectivesTo assess the association between preoperative inflammatory status via the CALLY index and the occurrence of postoperative pneumonia in patients with resectable ESCC.MethodsA retrospective cohort study was conducted from January 2020 to December 2022 at The Affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University. A total of 215 patients who met inclusion criteria were analyzed. Clinical data, including CALLY indices calculated preoperatively, were collected. Propensity score matching was applied to minimize confounding biases. The predictive value of the CALLY index was assessed using receiver operating characteristic analysis, and logistic regression was used to identify factors associated with postoperative pneumonia.ResultsROC curve analysis demonstrated the CALLY index had an area under the curve of 0.764 for predicting postoperative pneumonia, with a cutoff value of 1.97 achieving 67.69% sensitivity and 84.67% specificity. In multivariate analysis, a lower CALLY index was significantly associated with increased pneumonia risk, independent of other factors (adjusted OR = 0.66, p &lt; 0.001). High CALLY index scores correlated with a decreased likelihood of postoperative pneumonia, reinforcing its utility as a non-invasive prognostic marker.ConclusionsThe CALLY index is a robust, independent predictor of postoperative pneumonia in patients with resectable ESCC. Preoperative assessment of this index could enhance risk stratification and guide proactive management strategies to improve postoperative outcomes.