bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying HIF1A and HGF as two hub genes in aortic dissection and function analysis by integrating RNA sequencing and single-cell RNA sequencing data
Authors: Li Hai-Bing , Liu Chang , Mao Xiang-Di , Yuan Shu-Zheng , Li Li , Cong Xin 
Published: October 2024

ObjectiveAortic dissection (AD) is a severe aortic disease with high mortality, and its pathogenesis remains elusive. To explore the regulatory mechanisms of AD, we integrated public RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) datasets to screen the hub genes of AD and further analyzed their functions, which may provide references to the diagnosis and treatment of AD.MethodsFour AD-related datasets were obtained from the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis and differential expression analysis were applied to identify overlapping genes in dataset GSE153434. Protein–protein interaction (PPI) network was constructed based on overlapping genes. Five methods (closeness, degree, EPC, MCC, and MNN) were used to pick hub genes. The receiver operating characteristic curve was used to evaluate the diagnostic efficiency of the hub genes in extra datasets GSE98770 and GSE52093. scRNA-seq dataset GSE213740 was used to explore the expression and function of the hub genes at the single-cell level. Quantitative real-time polymerase chain reaction was used to verify the expression of hub genes in beta-aminopropionitrile (BAPN)-induced mouse thoracic aortic aneurysm and dissection (TAAD) model.ResultsA total of 71 overlapping genes were screened by intersecting the significant genes in the pink module and the differentially expressed genes. A PPI network with 45 nodes and 74 edges was generated, and five top hub genes (HIF1A, HGF, HMOX1, ITGA5, and ITGB3) were identified. All the hub genes had area under the curve values above 0.55. scRNA-seq data analysis showed that HIF1A was significantly upregulated in macrophages and HGF was significantly upregulated in vascular smooth muscle cells (SMCs) of the ascending aortas in AD patients. HIF1A may transcriptionally regulate multiple downstream target genes involving inflammation (TLR2, ALOX5AP, and MIF), glycolysis (ENO1, LDHA, and GAPDH), tissue remodeling (PLAU), and angiogenesis (SERPIN and VEGFA). HGF may participate in the signaling among SMCs, fibroblasts, and endothelial cells through binding to different receptors (MET, EGFR, IGF1R, and KDR). The mRNA expression of Hif1a, Hgf, and their target genes, including Alox5ap, Serpine1, Tlr2, Plau, Egfr, and Igf1r, was significantly upregulated in aortic tissues of BAPN-treated mice.ConclusionBy integrating RNA-seq and scRNA-seq data, we identified HIF1A and HGF as two hub genes with good diagnostic efficiency for AD. HIF1A in macrophages may promote AD formation by promoting inflammation, glycolysis, tissue remodeling, and angiogenesis, and HGF may mediate signaling among SMCs, fibroblasts, and endothelial cells in the development of AD.
COVID-19 online learning challenges: Kazakhstan secondary schools case study
Authors: Nurgaliyeva Saniya , Bolatov Aidos , Abildina Saltanat , Zeinolla Saule , Kurbonova Bakhtikhon , Kyyakbayeva Ulbossyn 
Published: October 2024

BackgroundThe COVID-19 pandemic necessitated a rapid transition to online learning (OL) globally, posing significant challenges for educational systems. This study investigates the experiences of secondary school students in Kazakhstan, highlighting the adaptation processes, educational outcomes, and challenges faced during this shift.MethodsData were collected through an online survey administered to 3,670 secondary school students across Kazakhstan, selected through convenience sampling. The survey comprised 21 questions using a combination of Likert-type scales and multiple-choice questions to capture students’ demographic details, satisfaction levels, perceived difficulties, and academic performance changes during OL. Data validation was ensured by cross-referencing responses, descriptive statistics, T-tests, ANOVA, correlation analysis, and regression were employed to analyze the data and identify factors influencing students’ attitudes toward OL and the associated challenges.ResultsThe results revealed that satisfaction with OL was positively correlated with satisfaction with education in general and negatively correlated with the level of difficulty in OL (p &lt; 0.001). Rural students, while more satisfied with learning overall (p &lt; 0.001), were less satisfied with OL compared to their urban peers, and also reported greater challenges (p &lt; 0.05). A significant portion of respondents (44.2%) disagreed that OL was an effective learning method, and 43.7% expressed a need for face-to-face interaction with teachers, especially female and rural students (p &lt; 0.001). Most students (40.8%) reported worse learning outcomes with OL, particularly urban students (p &lt; 0.001), and 32.0% noted a decrease in motivation. Regression analysis identified older students and those who experienced greater difficulty with OL as less likely to prefer it, while those who showed improvement in academic performance and motivation were more favorable toward OL. These findings highlight the complexity of educational preferences and the disparities between urban and rural students during the pandemic.ConclusionWhile the findings may be applicable to other countries with similar educational systems, cultural, economic, and technological differences should be considered when generalizing the results. The insights gained from this study will be valuable for policymakers, educators, and academic institutions to improve the resilience and effectiveness of educational practices in the face of such challenges.
Glycemic indicators and mental health symptoms: results from the greater Beirut area cardiovascular cohort
Authors: Chamseddine Zahraa Mohammad , Nasrallah Mona P. , Tamim Hani , Nasreddine Lara , Elbejjani Martine 
Published: October 2024

IntroductionDepression and anxiety present high and complex comorbidity with diabetes. One proposed explanation is that glycemic dysregulations and diabetes-related processes can influence mental health risk. We examined the associations of concurrent and prior glycemic indicators (Hemoglobin A1c (HbA1c) and fasting blood glucose (FBG) levels) with depression and anxiety symptoms in a community-based sample of middle-aged Lebanese adults.MethodsData come from the Greater Beirut Area Cardiovascular Cohort (GBACC), with baseline and 5-year assessments of sociodemographic, lifestyle, and biological factors (n=198). Depression (Patient Health Questionnaire-9) and anxiety (General Anxiety Disorder-7) symptoms were assessed at follow-up. We investigated associations between glycemic indicators and continuous mental health scores using first linear and then piecewise regression models.ResultsAdjusted piecewise regression models showed different associations with mental outcomes across glycemic indicators in the diabetic/clinical compared to the non-diabetic range: Among participants with &lt;126 mg/dl baseline FBG, higher FBG levels in this range were significantly associated with lower depressive (beta=-0.12, 95%CI= [-0.207, -0.032]) and anxiety symptoms (beta=-0.099, 95%CI= [-0.186, -0.012]). In contrast, among participants with baseline FBG levels ≥126 mg/dl, higher FBG levels were significantly associated with higher anxiety symptoms (beta=0.055; 95%CI= 0.008, 0.102). Higher baseline FBG levels in the ≥126 mg/dl range showed a not statistically significant trend for higher depressive symptoms. Although not significant, baseline HbA1c levels showed similar patterns with negative associations with mental health symptoms in the &lt;6.5% range.DiscussionResults show that FBG levels were associated with poorer mental health symptoms only in the clinical/diabetic range, and not in the normal range. Associations were observed with baseline glycemic indicators, highlighting potentially early and prolonged associations with mental health. Findings highlight the importance of clinical changes in glycemic indicators for mental health and motivate further research into the transition toward adverse associations between diabetes and mental health.
Contribution of cervical incompetence to occurrence of second trimester abortion in patients with polycystic ovary syndrome during the frozen embryo transfer cycle
Authors: Cheng Tingting , Shi Hao , Bu Zhiqin , Yu Yiping , Song Wenyan , Haixia Jin , Yao Guidong 
Published: October 2024

BackgroundSecond-trimester abortion is a critical issue in infertile women with polycystic ovary syndrome (PCOS) treated with assisted reproductive technology (ART), cervical incompetence (CI) may play a role. Although previous studies have revealed an association between PCOS and CI in women undergoing ART with fresh embryo transfer, the associated risk factors in frozen embryo transfer cycles are still unknown. The primary objective of this study is to examine the impact of CI on the occurrence of second-trimester abortion in women with PCOS undergoing frozen embryo transfer.MethodsThis retrospective cohort study included patients who underwent frozen-thawed embryo transfer and experienced second-trimester abortion between January 2012 and January 2020 from the Reproductive Medical Center of the First Affiliated Hospital of Zhengzhou University. Logit-transformed propensity score matching (PSM) was used to assess covariates. Patients were classified into the PCOS and non-PCOS groups. The PCOS group was further divided into two subgroups: the CI group and non-CI group.ResultsAfter case matching with PSM, 278 patients were included: 139 each in the PCOS group and non-PCOS groups. More miscarriages were attributed to CI in the PCOS group compared with the control group (20.14% vs. 10.07%). Subsequently, in the PCOS group, CI and non-CI subgroup analyses revealed a higher transfer cleavage-stage embryo incidence in the CI group than in the blastocysts group (p=0.001). Moreover, the between-group miscarriage-related gestational age varied significantly (p=0.039). Binary logistic regression analysis revealed that cleavage embryo transfer (p= 0.047) was associated with increased CI risk in the PCOS group, besides, increasing the number of transferred embryos did not impact the occurrence of CI in patients with PCOS.ConclusionCI independently predicted a higher risk of second-trimester abortion in patients with PCOS during the frozen embryo transfer cycle. What’s more, increasing the number of transferred embryos did not affect the incidence of CI in the PCOS group.
Impact of thyroid hormones on predicting the occurrence of persistent inflammation, immunosuppression, and catabolism syndrome in patients with sepsis
Authors: Zhang Ling , Tan Ruoming , Pan Tingting , Qu Hongping 
Published: October 2024

BackgroundThe prevalence of persistent inflammation, immunosuppression, and catabolism syndrome (PICS) has an upward trend in sepsis patients and can be associated with poor outcomes. Thyroid hormones are expected to be correlated with inflammation, immunity, and metabolism. Thus, the purpose of this study was to evaluate the effect of thyroid hormones on the occurrence of PICS and then further explore the optimal level of them in sepsis.MethodsThis retrospective observational study used the online database Medical Information Mart for Intensive Care (MIMIC)-IV. Univariate and multivariate logistic regression analyses were employed to determine correlations between thyroid hormone levels and PICS. A combination of independent PICS development factors was established with accuracy assessed using the area under the receiver operating characteristic curve (AUC-ROC).ResultsPatients were divided into PICS (n=205) and non-PICS (n=671) groups. The third quartiles of triiodothyronine (T3) (60-80ng/dl) and thyroxine (T4) (5.5-6.8ug/dl) had the lowest PICS incidence and the adjusted odds ratio (OR) was 0.33 (T3, p=0.009) and 0.39 (T4, p=0.006), respectively, compared with the first quartiles of T3 and T4. For patients with a pre-existing T3 deficiency, severe deficiency (T3 &lt;60ng/dl) and a high Sequential Organ Failure Assessment (SOFA) score were significantly related to PICS incidence. The AUC for these combined parameters in predicting PICS occurrence was 0.748 (all patients) and 0.861 (patients without thyroid disease).ConclusionsA mild T3 deficiency (60-80ng/dl) was significantly associated with the lowest risk-adjusted PICS occurrence in patients with sepsis. A severe T3 deficiency (&lt;60ng/dl) and a high SOFA score were independent risk factors for PICS occurrence.
Hydrochemical variation characteristics and driving factors of surface water in arid Areas—a case study of Beichuan River in Northwest China
Authors: Jinbing Xing , Long Wang , Jie Zhao , Tianlun Zhai 
Published: October 2024

Examining the chemical properties of river water and the controlling factors is crucial for devising efficacious strategies in water resources management and ecological conservation. This study investigates the hydrochemical characteristics and driving factors of the Beichuan River in the arid region of Northwest China. Surface water samples were collected during wet and dry seasons, and analyzed using hydrochemical diagrams, mathematical statistics, and principal component analysis (PCA). The results show that the pH value of Beichuan River is generally weakly alkaline, the main hydrochemical types are HCO3-Ca, and the average TDS are 224 mg/L and 236 mg/L respectively, which are higher than the world average level (115 mg/L). The seasonal variation of hydrochemical components is mainly controlled by rainfall, showing that the concentrations of Na+, Cl− and NO3− in the wet season are higher than those in the dry season, while the concentrations of other chemical components show an opposite trend, while the spatial variation is mainly controlled by human activities, and the concentrations of hydrochemical components show a gradual increasing trend from upstream to downstream, especially Na+, Mg2+, Cl− and NO3−. Rock weathering is the key natural factor controlling the Hydrochemical Composition of Beichuan River. Na+ and Cl− are mainly from the dissolution of silicate, Ca2+ and Mg2+ are mainly from the weathering of carbonate rocks and silicate, and SO42- is mainly from the dissolution of evaporite. It is noted that human activities, especially domestic sewage and agricultural runoff, contribute significantly to NO3− in the water body. PCA identified rock weathering and agricultural runoff as major wet-season factors, while domestic sewage predominantly affects the dry season. This study can provide a scientific basis for the rational development of water resources and ecological environment protection in arid areas.
epiArt: a graphical HLA eplet amino acid repertoire translation reveals the need for an epitope driven revision of allele group nomenclature
Authors: Doxiadis Ilias , Lehmann Claudia , Lachmann Nils , Loeffler-Wirth Henry 
Published: October 2024

IntroductionThe immune response after transplantation depends on recipient/donor HLA allele mismatches. To enhance our understanding of the relations of HLA alleles in terms of amino-acid polymorphisms and shared epitopes, we assessed pairwise sequence difference between HLA-alleles.MethodsWe translated amino-acid sequences of confirmed eplets into an atlas of HLA class I and II antigens, followed by visualization of the pairwise allele distances by means of antigen-specific disparity graphs in differential amino-acid space. We obtained an overview of relationships of all alleles of an antigen, corresponding similarity/dissimilarity structures, outliers, alleles with similarity to different antigen groups. Additionally, we calculated prevalence of the amino-acids for each polymorphic sequence position and visualized them in amino-acid motif plots of all alleles belonging to an antigen.ResultsOur visualizations show strongly varying intra-group heterogeneity of HLA class I and II alleles, as well as shared inter-group and inter-locus eplets and epitopes, indicating a benefit of epitope-based transplant matching: Single allele recipient/donor mismatches potentially refer to identical eplets, or to a set of multiple mismatched eplets.DiscussionThis data reveals inconsistencies in the HLA group nomenclature and consequently adds a new level of quality to allocation, motivating the definition of tolerable or taboo mismatches.
Differences in distribution and characteristics of microplastics in sediments of the south-eastern part of the Gulf of Trieste
Authors: Jamšek Jena , Prosen Helena , Bajt Oliver 
Published: October 2024

IntroductionThe Gulf of Trieste is prone to the accumulation of various pollutants and microplastics due to its geomorphological and hydrological characteristics. However, the distribution and sources of microplastics in this semi-enclosed area are poorly studied. The aim of our study was to determine the distribution and chemical composition of MP particles in the sediments of the Gulf of Trieste.MethodsIn this study, we collected 24 surface sediment samples using a Van Veen grab. Microplastics were extracted by density separation using NaCl. The size, shape, and color of the extracted microplastics were determined using an optical microscope, and the composition of the polymers was determined by Fourier transform infrared spectroscopy.Results and discussionThe highest concentrations of up to 125 microplastic particles per 100 g dry sediment were found in coastal areas. Concentrations in the open sea were much lower, with an average of 3 particles per 100 g of sediment. Most of the microplastic was fibrous, made of polypropylene, 100–300 µm in size, and blue. This is the first study showing that microplastics are present in the sediments of the south-eastern part of the Gulf of Trieste. The findings suggest that microplastics exhibit a tendency to be retained within the sediment, leading to their accumulation primarily in a narrow coastal area rather than dispersing offshore. Our results will contribute to a better knowledge of the distribution and possible sources of plastics and microplastics in the Gulf of Trieste and even beyond in similar semi-enclosed marine areas.
A clinical study on the relationship between chronic rhinosinusitis and bronchial asthma
Authors: Kang Jing , Yong Hui , Zhang Zhijuan , Liu Jing , Gao Xiaoping , Shao Hui , Hou Li 
Published: October 2024

ObjectiveTo investigate the correlation between chronic rhinosinusitis (CRS) and bronchial asthma, focusing on the CRS without nasal polyps (CRSsNP) and CRS with nasal polyps (CRSwNP), as well as their impact on lung function.MethodsA total of 141 patients diagnosed with chronic nasal-sinus inflammation were included in this study. Clinical data, including medical histories, nasal endoscopy scores, CT scores, symptom scores, and quality of life assessments, were collected.ResultsAmong the patients with CRSsNP, 23.8% had concomitant bronchial asthma. The incidence of asthma was significantly associated with the severity of sinus involvement in CRSsNP patients (p = 0.049). Pulmonary function impairment was correlated with the severity of sinus inflammation in CRSsNP patients (p = 0.019). Quality of life was significantly affected in patients with concomitant asthma and CRSsNP or CRSwNP.ConclusionChronic rhinosinusitis, both with and without nasal polyps, is closely correlated with bronchial asthma. Pulmonary function impairment is associated with the extent of inflammatory lesions in CRSsNP. Although CRSwNP does not significantly affect pulmonary function, the treatment of sinus diseases can contribute to the control of asthma.
Computed tomography image quality in patients with primary hepatocellular carcinoma: intraindividual comparison of contrast agent concentrations
Authors: Peng Fei , Luo Chaotian , Ning Xiaojing , Xiao Fangyan , Guan Kaiming , Tang Cheng , Huang Fuling , Liang Junli , Peng Peng 
Published: October 2024

ObjectiveThis study aimed to assess the impact of the different concentrations of iodine contrast agents used on the quality of computed tomography (CT) images obtained intraindividually in hepatocellular carcinoma patients.MethodsIn this retrospective study, data from a cohort of 29 patients diagnosed with primary hepatocellular carcinoma who had undergone two preoperative CT-enhanced examinations within a 3-month timeframe were analyzed. Each patient was randomly assigned to receive either a low-concentration contrast agent (300 mg I/mL iohexol) or a high-concentration contrast agent (350 mg I/mL iohexol) for the first scan and the alternative contrast agent for the second scan. CT images of different liver regions of each patient were compared between low-and high-concentration scans using their before-and-after control design. Subjective image quality scores for portal vein images were also assessed.ResultsThe findings of this study indicate that patients in the high-concentration group presented significantly elevated CT values across various anatomical regions, including the liver parenchyma, abdominal aorta, and hepatic portal vein, compared to those in the low-concentration group (p &lt; 0.05). Moreover, the high-concentration group demonstrated superior subjective image ratings (p &lt; 0.05). Nevertheless, there was no statistically significant difference in the CT values observed in liver cancer parenchyma scans at different phases between the two groups (p &gt; 0.05).ConclusionIn summary, using a high-concentration iodine contrast agent is efficient in enhancing the visual clarity of the liver parenchyma, the aorta, and the portal vein in individuals diagnosed with primary hepatocellular carcinoma.
MED-ChatGPT CoPilot: a ChatGPT medical assistant for case mining and adjunctive therapy
Authors: Liu Wei , Kan Hongxing , Jiang Yanfei , Geng Yingbao , Nie Yiqi , Yang Mingguang 
Published: October 2024

BackgroundThe large-scale language model, GPT-4-1106-preview, supports text of up to 128 k characters, which has enhanced the capability of processing vast quantities of text. This model can perform efficient and accurate text data mining without the need for retraining, aided by prompt engineering.MethodThe research approach includes prompt engineering and text vectorization processing. In this study, prompt engineering is applied to assist ChatGPT in text mining. Subsequently, the mined results are vectorized and incorporated into a local knowledge base. After cleansing 306 medical papers, data extraction was performed using ChatGPT. Following a validation and filtering process, 241 medical case data entries were obtained, leading to the construction of a local medical knowledge base. Additionally, drawing upon the Langchain framework and utilizing the local knowledge base in conjunction with ChatGPT, we successfully developed a fast and reliable chatbot. This chatbot is capable of providing recommended diagnostic and treatment information for various diseases.ResultsThe performance of the designed ChatGPT model, which was enhanced by data from the local knowledge base, exceeded that of the original model by 7.90% on a set of medical questions.ConclusionChatGPT, assisted by prompt engineering, demonstrates effective data mining capabilities for large-scale medical texts. In the future, we plan to incorporate a richer array of medical case data, expand the scale of the knowledge base, and enhance ChatGPT’s performance in the medical field.