bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gut microbiota regulates diabetic retinopathy in adult rats
Authors: Hou Jueyu , Lv Zhongping , Wang Yujiao , Chen Danian 
Published: January 2025

IntroductionDiabetic retinopathy (DR) is the most common complication of diabetes. Neuronal apoptosis, activated microglia, and microvascular changes are early features of DR. The gut microbiota is critical for the maturation and activation of microglia in the brain, and DR patients exhibit gut dysbiosis. However, the effect of the gut microbiota on retinal microglia under normal or diabetic conditions is still unclear.MethodsType 2 diabetes (T2D) was established in male adult Brown Norway (BN) rats, and they were treated with gavage of broad-spectrum antibiotic (ABX) suspension. Retinal fundus fluorescein angiography was performed to observe the dynamic growth process and leakage of blood vessels. Retro-orbital injection of FITC-Dextran was performed to observe the changes in blood-retinal barriers. After treatment with ABX and diabetes lasting for more than 6 months, 16S RNA sequencing of stool samples was performed to determine changes in the gut microbiome and mass spectrometry was used to analyze metabolome changes. IBA1, IB4, and Brn3 staining were performed on adult rats’ retinal wholemount or sections to observe the changes in microglia, blood vessels and the number of ganglion cells.ResultsLong-term (6 months) T2D caused gut dysbiosis with increased average taxa numbers. We showed that broad-spectrum antibiotics (ABXs) gavage can reduce the average number of gut microbiota taxa and retinal microglia in adult male BN rats with or without T2D. Interestingly, adult male BN rats with T2D for more than 6 months showed a loss of retinal ganglion cells (RGCs) without significant changes in retinal microglia or retinal vascular vessels. However, ABX gavage reduced retinal microglia and alleviated RGC damage in these T2D rats.ConclusionOur data suggests that ABX gavage-induced gut dysbiosis can reduce retinal microglia in adult rats and alleviate RGC loss in long-term T2D rats. Targeting the gut microbiota may be a future therapeutic strategy for DR management.
Genome analysis of colistin-resistant Salmonella isolates from human sources in Guizhou of southwestern China, 2019–2023
Authors: Wu Jingtong , Wen Yongxian , You Lv , Wei Xiaoyu , Wang Junhua , Zhu Ge , Li Shijun 
Published: January 2025

BackgroundColistin is commonly used as a last-resort antibiotic for multidrug resistance (MDR) bacterial infections. The emergence of colistin-resistant (CL-R) Salmonella has become a significant public health concern. However, the prevalence of CL-R Salmonella in Guizhou province remains unknown. Therefore, it is necessary to monitor CL-R Salmonella in Guizhou and systematically elucidate their characteristics-related resistance, virulence, and molecular epidemiology to develop effective public health strategies against resistant pathogens.MethodsThe CL-R Salmonella isolates were identified from 933 Salmonella isolates by antimicrobial resistance testing. To further evaluate the molecular epidemiology, the CL-R Salmonella isolates underwent whole-genome sequencing (WGS) analysis followed by bioinformatic analysis.ResultsA total of 43 CL-R isolates (4.6%) were identified from 933 Salmonella isolates, of which 39 isolates being MDR (resistance to three or more classes of antimicrobials). WGS analysis revealed 34 antibiotic resistance genes (ARGs), and point mutations in the gyrA gene (D87Y and D87G) were identified in all 43 CL-R isolates. Only one isolate carried the mcr-1.1 gene, a known colistin resistance. All CL-R isolates were found to carry multidrug efflux pumps. Furthermore, the most common resistance gene was aac(6′)-ly (40 out of 43), followed by blaTEM-1 (39 out of 43). The majority of CL-R isolates contained the virulence factor spvB and a notable diversity in other virulence factors with varied functions. Core genome multilocus sequence typing (cgMLST) revealed that 43 CL-R Salmonella isolates were divided into 19 cgSTs, with cgST179151 (10 out of 43) being the most prevalent. Additionally, the CL-R Salmonella isolates exhibited genetic similarities with human Salmonella isolates from Poland, Canada, and Zhejiang province. Among the 42 CL-R isolates lacking markers for CL-R, 12 single-nucleotide variations (SNVs) were observed in 24 isolates using genome-wide association study (GWAS) analysis, which was possibly associated with colistin resistance.ConclusionThis study revealed that the majority of CL-R Salmonella isolates in Guizhou province exhibited MDR, with complex resistance mechanisms, representing a significant public health challenge. The genetic similarities between isolates from Guizhou and other regions suggested the possibility of international transmission or shared reservoirs of resistance. These results highlighted the urgent need for enhanced surveillance and effective public health strategies to address the risks posed by these pathogens in Guizhou.
Cellular and immune landscape of chronic liver diseases: insights from immunophenotyping
Authors: Soleimani Shaghayegh , Albayrak Ozgur , Somay Kayra , Yang Hong , Yigit Buket , Ulukan Burge , Atak Dila , Akyildiz Murat , Gursoy Metehan , Demirtas Elif , Mardinoglu Adil , Vural Atay , Dayangac Murat , Zeybel Mujdat 
Published: January 2025

BackgroundChronic liver disease due to alcohol-related liver disease and chronic viral hepatitis pose a substantial burden on healthcare systems. Chronic liver disease may predispose to hepatocellular carcinoma, for which therapeutic options are limited. This study aimed to explore the immune cell characteristics of the clinical conditions.MethodsExplant liver samples were collected from 25 patients for bulk RNA sequencing and flow cytometry analysis. Immune cell populations were characterized by flow cytometry from isolated hepatic and peripheral mononuclear cells.ResultsSignificant differences in immune cell characteristics were observed among patients with three clinical conditions. Viral hepatitis and peri-tumor samples exhibited higher hepatic B cell counts compared to alcohol-related liver disease. Additionally, chronic liver disease patients showed higher levels of CD57+ T cells, suggestive of T cell differentiation. Differential expression analysis identified several genes associated with immune regulation, including downregulation of CD27 and upregulation of granzyme B in ARLD, consistent with a highly differentiated phenotype. LAG3 and PDCD1 were upregulated in peri-tumor samples. The NK cell count was lower in peri-tumor liver specimens compared to ARLD, and an upregulation of TIGIT, an inhibitory marker, was observed in those peri-tumor specimens.ConclusionThis study contributes to the understanding of immune dynamics in chronic liver disease among different etiologies. B lymphocytes are relatively reduced in alcohol-related liver disease compared to other groups, and T cells exhibit a more differentiated subtype. The peritumor microenvironment in HCC suggests a relatively diminished presence of NK cells and a potential tendency toward increased inhibitory characteristics.
Extracranial carotid plaque calcification and its association with risk factors for cerebrovascular events: insights from the ANTIQUE study
Authors: Pakizer David , Šalounová Dana , Školoudík David 
Published: January 2025

IntroductionExtracranial carotid calcification is a common marker of advanced atherosclerosis. However, its impact on stroke risk is not consistent across studies, and examining the type of calcification and the presence of systemic diseases might be helpful. We aimed to investigate extracranial carotid calcification and its association with risk factors for ischemic cerebrovascular diseases.Materials and methodsAmong 1,863 consecutive patients in the Atherosclerotic Plaque Characteristics Associated with a Progression Rate of the Plaque and a Risk of Stroke in Patients with the Carotid Bifurcation Plaque Study (ANTIQUE), 132 symptomatic or asymptomatic patients (177 carotid plaques) with &gt;30% carotid stenosis examined through computed tomography (CT) and magnetic resonance imaging (MRI) were included. Statistical data were assessed using the χ2-test, Fisher’s exact test, t-test, and Mann–Whitney test to investigate the calcification risk factors.ResultsCompared to the absence of calcifications, spotty calcifications were associated with male sex [odds ratio (OR): 3.72, 95% confidence interval (CI): 1.06–13.05], while large calcifications were associated with older patients (OR: 1.60 per 5 years of age, 95% CI: 1.20–2.13). Large calcifications were also strongly associated with coronary heart disease (OR: 4.07, 95% CI: 1.15–14.44) and atrial fibrillation (p = 0.025). In comparison between only spotty and large calcifications, spotty calcifications were associated with male sex (OR: 3.72, 95% CI: 1.06–13.05), smoking (p = 0.020) in more significant quantities (p = 0.014), and lipid plaque (p &lt; 0.001), while large calcifications with contralateral stenosis degree (p = 0.044). No significant relationship was found between cerebrovascular events and the type of calcification.ConclusionAlthough the presence and type of extracranial carotid calcification were not related to ipsilateral ischemic events, large calcifications were strongly associated with coronary heart disease and atrial fibrillation.Clinical trial registrationClinicalTrials.gov, identifier NCT02360137.
PilotCareTrans Net: an EEG data-driven transformer for pilot health monitoring
Authors: Zhao Kun , Guo Xueying 
Published: January 2025

IntroductionIn high-stakes environments such as aviation, monitoring cognitive, and mental health is crucial, with electroencephalogram (EEG) data emerging as a keytool for this purpose. However traditional methods like linear models Long Short-Term Memory (LSTM), and Gated Recurrent Unit (GRU) architectures often struggle to capture the complex, non-linear temporal dependencies in EEG signals. These approaches typically fail to integrate multi-scale features effectively, resulting in suboptimal health intervention decisions, especially in dynamic, high-pressure environments like pilot training.MethodsTo overcome these challenges, this study introduces PilotCareTrans Net, a novel Transformer-based model designed for health intervention decision-making in aviation students. The model incorporates dynamic attention mechanisms, temporal convolutional layers, and multi-scale feature integration, enabling it to capture intricate temporal dynamics in EEG data more effectively. PilotCareTrans Net was evaluated on multiple public EEG datasets, including MODA, STEW, SJTUEmotion EEG, and Sleep-EDF, where it outperformed state-of-the-art models in key metrics.Results and discussionThe experimental results demonstrate the model's ability to not only enhance prediction accuracy but also reduce computational complexity, making it suitable for real-time applications in resource-constrained settings. These findings indicate that PilotCareTrans Net holds significant potential for improving cognitive health monitoring and intervention strategies in aviation, thereby contributing to enhanced safety and performance in critical environments.
Association between vitamin levels and geriatric hip fractures: A cross-sectional study
Authors: He Qifei , Zhang Chun , Xie Wei , Deng Zhaoqiang , Yang Shiwei , Li Xia , Sun Wei 
Published: January 2025

ObjectivesGeriatric hip fractures, known as osteoporotic fractures, are associated with nutritional deficiencies such as vitamin D (VitD). However, the relationship between other vitamins besides VitD and fracture is still lacking. Therefore, we intended to identify various vitamin levels and deficiencies in elderly patients with hip fractures and compared those with healthy elderly individuals.MethodsA total of 210 geriatric hip fracture continuous patients and 402 healthy elderly individuals aged ≥65 years old and with complete serum vitamin records were enrolled in this study. The levels of serum VitA, VitB1, VitB2, VitB3, VitB5, VitB6, VitB9, VitE, VitK1, and 25-hydroxyvitamin D (25-HO-VitD) and nutritional markers, such as prognostic nutritional index (PNI), were compared between geriatric hip fracture patients and healthy control. The correlation between vitamin level and the nutritional markers was explored. A multiple linear regression analysis was conducted to assess the association between vitamin levels and hip fracture.ResultsThe levels of VitA, VitB1, VitB3, VitB5, VitB9, 25-HO-VitD, 25-HO-VitD3, E, and K1 were all lower in the hip fracture group (p &lt; 0.05). More than 80% of older persons suffered 25-HO-VitD deficiency in both healthy and fracture groups. A positive correlation between levels of VitA and nutritional markers existed in the fracture and healthy groups. In regression analysis, the association strength between standardized vitamin levels and fracture was the most significant in VitB9 (β = −0.94; 95%CI, −1.15 to −0.73; p &lt; 0.001), VitA (β = −0.83; 95%CI, −1.04 to −0.61; p &lt; 0.001), and VitK1 (β = −0.80; 95%CI, −1.02 to −0.58; p &lt; 0.001), with no significant statistic difference found in VitB2, VitB9, 25-HO-VitD2, and 25-HO-VitD3.ConclusionVitamin D deficiency is common in elderly people with or without fracture. The levels of VitA, VitB9, and VitK1, instead of VitD, were much lower in fracture patients than in the healthy control, even controlling age and gender. VitA is a potential target for hip fracture prevention.
Ultrasound-assisted extraction of polyphenols from Lonicera japonica leaves and their α-glucosidase inhibition
Authors: Li Gang , Bao Chunming , Zhang Hao , Bai Lu 
Published: January 2025

IntroductionThe search for natural bioactive compounds that act as α-glucosidase inhibitors is a central focus in diabetes treatment research.MethodsThis study utilized ultrasonic-assisted extraction to optimize the extraction of polyphenols from honeysuckle leaves through response surface methodology (RSM). Enzyme inhibition and fluorescence quenching experiments were conducted to examine the inhibitory activity and binding behavior of the extracted polyphenols.ResultsThe results indicated that the optimal conditions for polyphenol extraction were as follows: ethanol concentration, 64%, liquid–solid ratio, 45 mL/g, ultrasonic power, 700 W, ultrasonic time, 6 min. Under these conditions, the yield of polyphenols from honeysuckle leaves was 9.16 ± 0.19%, which closely aligns with the predicted value of 9.18%. The total phenolic content of the polyphenol extracts was 20.6 ± 0.67%, with chlorogenic acid and luteoloside contents measuring 5.65 ± 0.40% and 2.51 ± 0.14%, respectively. The inhibitory effect of polyphenol extracts (IC50, 0.14 ± 0.01 mg/mL) on α-glucosidase was better than that of chlorogenic acid (IC50, 0.55 ± 0.02 mg/mL). Fluorescence quenching experiments indicated that the polyphenol extracts interact with α-glucosidase, resulting in alterations to the microenvironment of amino acid residues.DiscussionThis interaction can reduce the binding affinity between the substrate and α-glucosidase, thereby contributing to the objective of lowering postprandial hyperglycemia. Our research results can provide reference for the development and utilization of honeysuckle leaves.
Transcriptome profiling revealed multiple circadian rhythm-related genes associated with common gynecological cancers
Authors: Peng Lan , Jiang Meiping , Li Kangming , Yu Shuhui , Zhao Chunfang , Zhang Lan , Li Lan 
Published: January 2025

BackgroundStudies have shown that more than half of the human genome expression is affected by circadian rhythms, which includes genes involved in cell cycle control, DNA repair and apoptosis that are critical in cancer biology. However, the roles of circadian rhythm-related genes (CRRGs) in cervical cancer (CC) and other common gynecologic cancers remain unclear.MethodsThe transcriptome data and clinical information related to CC and other common gynecologic cancers were extracted from the UCSC Xena and Gene Expression Omnibus (GEO) databases. In this study, the differentially expressed CRRGs of CC (target genes) were obtained, and the functional enrichment analysis of these target genes was performed by “clusterProfiler”. Then, the biomarkers of CC were screened out to construct the survival risk model (risk score). Moreover, function and tumor micro-environment (TME) analyses in different risk groups were performed for further study of the potential mechanism of CC. Furthermore, the prognostic value and function analyses of biomarkers in three common gynecologic cancers were performed to reveal the potential agreement or heterogeneity regulations.ResultsA total of 19 target genes were associated with pyrimidine metabolism. The survival risk model was constructed with six biomarkers, including APOBEC3B, CDA, HELLS, RHOB, SLC15A3, and UPP1. Among these, APOBEC3B, HELLS, and SLC15A3 were identified as positive factors, while CDA, RHOB, and UPP1 were identified as negative factors in CC. It is notable that multiple immune-related signaling pathways were associated with the clinical risk of CC, and the immunotherapy sensitivity was worse in the high-risk group. In addition, we found that most of biomarkers had the prognostic values in other common gynecologic cancers. It was notable that the mechanisms by which these biomarkers influence gynecologic cancers were associated with extracellular matrix (ECM) receptor interaction, focal adhesion, etc.ConclusionThis study identified six circadian rhythm-related biomarkers, including APOBEC3B, CDA, HELLS, RHOB, SLC15A3, and UPP1, which were associated with the prognosis of CC. The mechanisms by which these biomarkers influence gynecologic cancers were associated with ECM receptor interaction, focal adhesion, and other functions. These findings might help to deepen the understanding of the agreement or heterogeneity of CRRGs in the pathological processes of common gynecologic cancers.
Patients with colorectal cancer combined with HIV had a worse overall survival after surgery: a meta-analysis
Authors: Yang Wen-Wen , Zhou Xiong , He Gan 
Published: January 2025

PurposeThe purpose of this current study was to find out whether human immunodeficiency virus (HIV) affected overall survival (OS) of colorectal cancer (CRC) patients after surgery.MethodsPubMed, Embase, the Cochrane Library, and CNKI were searched from inception to March 27, 2023 to find eligible studies. Eligible studies included CRC patients grouped by HIV status (HIV-positive and HIV-negative). Stata SE 16 was used for data analysis.ResultsA total of eight studies involving 2180 patients were enrolled in this study. After data analysis, there were significant differences in sex (OR=0.69, 95% CI=0.49 to 0.98, I2 = 22.6%, P=0.04&lt;0.1), tumor grade (OR=6.61, 95% CI=2.36 to 18.49, I2 = 0.00%, P=0.00&lt;0.1), and tumor location (OR=2.19, 95% CI=1.74 to 2.77, I2 = 0.04%, P=0.00&lt;0.1) between the HIV and non-HIV groups. Furthermore, we found that HIV was associated with worse OS in CRC patients after surgery (HR=3.12, 95% CI=2.07 to 4.69, I2 = 52.51%, P=0.00&lt;0.1).ConclusionThis study highlights that HIV is associated with significantly poorer OS in CRC patients after surgery, emphasizing the need for tailored postoperative management strategies for this vulnerable population. Future research should explore underlying mechanisms and potential interventions to improve outcomes for HIV-positive CRC patients.
Immunotherapy as a neoadjuvant preoperative treatment for locally advanced pulmonary sarcomatoid carcinoma: a case report of clinical efficacy
Authors: Li Hanhan , Chen Ruilian , Guo Wei , Xiang Shang , Huang Jiayang , Chen Hanrui 
Published: January 2025

BackgroundPulmonary sarcomatoid carcinoma (PSC) is a rare subtype of non-small cell lung cancer (NSCLC) with a generally poor prognosis. Studies have shown that the survival rate for advanced-stage patients is less than 5%, with a median overall survival (OS) of less than 6.5 months.Case reportHerein, we report a case of locally advanced PSC in a 56-year-old male patient who received platinum-based double-drug therapy combined with anti-angiogenic drugs, followed by immunotherapy as the first-line systemic treatment. After undergoing eight cycles of neoadjuvant therapy, the opportunity for surgery arose. Postoperative pathology confirmed that the neoadjuvant chemotherapy in this regimen achieved pathological complete remission (pCR). At present, the patient maintains a good quality of life, continues with immunotherapy for consolidation and prevention of recurrence, and has reached a survival period of 10 months.ConclusionFor patients with locally advanced PSC who do not have significant genetic mutations, the use of immunotherapy as a first-line neoadjuvant and adjuvant therapy may hold promise for achieving a pCR. Further research into this treatment protocol is warranted.
Machine learning based predictive model and genetic mutation landscape for high-grade colorectal neuroendocrine carcinoma: a SEER database analysis with external validation
Authors: Wu Ruixin , Chen Sihao , He Yi , Li Ya , Mu Song , Jin Aishun 
Published: January 2025

BackgroundHigh-grade colorectal neuroendocrine carcinoma (HCNEC) is a rare but aggressive subset of neuroendocrine tumors. This study was designed to construct a risk model based on comprehensive clinical and mutational genomics data to facilitate clinical decision making.MethodsA retrospective analysis was conducted using data from the Surveillance, Epidemiology, and End Results (SEER) database, spanning 2000 to 2019. The external validation cohort was sourced from two tertiary hospitals in Southwest China. Independent factors influencing both overall survival (OS) and cancer-specific survival (CSS) were identified using LASSO, Random Forest, and XGBoost regression techniques. Molecular data with the most common mutations in CNEC were extracted from the Catalogue of Somatic Mutations in Cancer (COSMIC) database.ResultsIn this prognostic analysis, the data from 714 participants with HCNEC were evaluated. The median OS for the cohort was 10 months, whereas CSS was 11 months. Six variables (M stage, LODDS, Nodes positive, Surgery, Radiotherapy, and Chemotherapy) were screened as key prognostic indicators. The machine learning model showed reliable performance across multiple evaluation dimensions. The most common mutations of CNEC identified in the COSMIC database were TP53, KRAS, and APC.ConclusionsIn this study, a refined machine learning predictive model was developed to assess the prognosis of HCNEC accurately and we briefly analyzed its genomic features, which might offer a valuable tool to address existing clinical challenges.