bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the molecular nexus between Omicron infection and acute kidney injury: a bioinformatics approach
Authors: Wang Li , Chen Anning , Zhang Lantian , Zhang Junwei , Wei Shuqi , Chen Yangxiao , Hu Mingliang , Mo Yihao , Li Sha , Zeng Min , Li Huafeng , Liang Caixing , Ren Yi , Xu Liting , Liang Wenhua , Zhu Xuejiao , Wang Xiaokai , Sun Donglin 
Published: July 2024

BackgroundThe ongoing global health crisis of COVID-19, and particularly the challenges posed by recurrent infections of the Omicron variant, have significantly strained healthcare systems worldwide. There is a growing body of evidence indicating an increased susceptibility to Omicron infection in patients suffering from Acute Kidney Injury (AKI). However, the intricate molecular interplay between AKI and Omicron variant of COVID-19 remains largely enigmatic.MethodsThis study employed a comprehensive analysis of human RNA sequencing (RNA-seq) and microarray datasets to identify differentially expressed genes (DEGs) associated with Omicron infection in the context of AKI. We engaged in functional enrichment assessments, an examination of Protein-Protein Interaction (PPI) networks, and advanced network analysis to elucidate the cellular signaling pathways involved, identify critical hub genes, and determine the relevant controlling transcription factors and microRNAs. Additionally, we explored protein-drug interactions to highlight potential pharmacological interventions.ResultsOur investigation revealed significant DEGs and cellular signaling pathways implicated in both Omicron infection and AKI. We identified pivotal hub genes, including EIF2AK2, PLSCR1, GBP1, TNFSF10, C1QB, and BST2, and their associated regulatory transcription factors and microRNAs. Notably, in the murine AKI model, there was a marked reduction in EIF2AK2 expression, in contrast to significant elevations in PLSCR1, C1QB, and BST2. EIF2AK2 exhibited an inverse relationship with the primary AKI mediator, Kim-1, whereas PLSCR1 and C1QB demonstrated strong positive correlations with it. Moreover, we identified potential therapeutic agents such as Suloctidil, Apocarotenal, 3′-Azido-3′-deoxythymidine, among others. Our findings also highlighted a correlation between the identified hub genes and diseases like myocardial ischemia, schizophrenia, and liver cirrhosis. To further validate the credibility of our data, we employed an independent validation dataset to verify the hub genes. Notably, the expression patterns of PLSCR1, GBP1, BST2, and C1QB were consistent with our research findings, reaffirming the reliability of our results.ConclusionOur bioinformatics analysis has provided initial insights into the shared genetic landscape between Omicron COVID-19 infections and AKI, identifying potential therapeutic targets and drugs. This preliminary investigation lays the foundation for further research, with the hope of contributing to the development of innovative treatment strategies for these complex medical conditions.
Assessing the role of antioxidant and pro-oxidant balance in mediating the relationship between vitamin K intake and depressive symptoms in adults
Authors: Wang Lujie , Huang Shuling , Feng Zhiyi , Xiao Jianyun , Luo Gaoquan , Zhang Yuan 
Published: July 2024

BackgroundGrowing evidence suggests a link between vitamin K (VK) intake and depression, although the underlying mechanisms remain unclear. We aimed to investigate whether oxidative balance scores (OBS) mediate the association between VK intake and depression in participants from the National Health and Nutrition Examination Survey (NHANES) 2007–2018.MethodsWe analyzed data from 30,408 individuals. Dietary VK intake served as the independent variable, depression symptoms as the outcome variable, and OBS as the mediator. Multivariable logistic regression and restricted cubic splines assessed the associations. Mediation analysis was conducted to evaluate the potential mediating role of OBS.ResultsHigher dietary VK intake was associated with lower depression risk in the multivariate model. Compared to the lowest log2 VK quartile, those in the higher quartiles had significantly lower depression odds (Q3: OR 0.66, 95% CI 0.55–0.78; Q4: OR 0.64, 95% CI 0.52–0.78). Additionally, a 1-unit increase in log2 VK intake was associated with a 15% decrease in depression odds (OR 0.85, 95% CI 0.81–0.90). Restricted cubic splines revealed a non-linear relationship between log2 VK and depression (p for non-linearity &lt;0.001). Notably, OBS mediated 26.09% (p &lt; 0.001) of the association between log2 VK and depression.ConclusionHigher VK intake is associated with reduced depression risk, potentially mediated by oxidative balance. Further research is warranted to confirm causality and elucidate the underlying mechanisms.
Association between dietary fiber to carbohydrate ratio and risk of dental caries in diabetic patients: an analysis of the National Health and Nutrition Examination Survey 2015–2020
Authors: Liang Xue , Lu Hongbing , Lin Ping , Huang Xiaojing 
Published: July 2024

AimPeople with diabetes mellitus have a higher risk of dental caries than the general population. Diet is one of the most important factors affecting the risk of dental caries. This study aimed to evaluate the effect of dietary fiber to carbohydrate ratio (FCR) on the risk of dental caries in diabetic patients.MethodsData of this cross-sectional study were extracted from the 2015–2020 cycle of the National Health and Nutrition Examination Survey (NHANES) database. FCR levels were divided into two categories based on the median (0.13). The outcomes were untreated dental caries and dental caries experience. The associations of FCR with untreated dental caries and dental caries experience were assessed using multivariable logistic regression analysis and reported as odds ratio (OR) and 95% confidence interval (CI). Stratified analyses were performed according to age (&lt;65 and ≥ 65 years), gender (female and male), hypertension (yes and no), and the ratio of family income to poverty (PIR, &lt;1 and ≥ 1).ResultsA total of 2,412 patients diagnosed with diabetes were included, of whom 728 (30.18%) had untreated dental caries and 2,104 (87.23%) had dental caries experience. Patients with FCR ≥0.13 were correlated with lower odds of untreated dental caries (OR = 0.72, 95%CI: 0.52–0.99) and dental caries experience (OR = 0.63, 95%CI: 0.42–0.93) compared to patients with FCR &lt;0.13. Stratified analyses demonstrated that patients with FCR ≥0.13 were found to be related to lower odds of untreated dental caries in those aged &lt;65 years (OR = 0.64, 95%CI: 0.42–0.97), female (OR = 0.57, 95%CI: 0.35–0.93), with hypertension (OR = 0.66, 95%CI: 0.45–0.96), and PIR ≥1 (OR = 0.64, 95%CI: 0.42–0.99). Similar results to untreated dental caries were observed in the analysis of dental caries experience (p &lt; 0.05).ConclusionHigh levels of FCR may be associated with a lower risk of dental caries in patients with diabetes. Increasing the proportion of dietary fiber intake among diabetic patients may help prevent the occurrence of dental caries.
Case report: Liver PEComa after kidney transplantation in recipient with tuberous sclerosis complex
Authors: Dymkowski Marcin , Kalman Paulina , Niecikowski Piotr , Koperski Łukasz , Kosieradzki Maciej 
Published: July 2024

IntroductionPerivascular epithelioid cell tumors (PEComa) are rare tumors of mesenchymal origin that exhibit perivascular epithelioid cell phenotype. One of its most common localizations is uterus, whereas only a few studies reported PEComa localization as liver. There is a correlation between the presence of PEComa and tuberous sclerosis complex (TSC). TSC is a rare disease which leads to the development of mostly non-cancerous tumors in various organs. We would like to present a case of a kidney transplant recipient with a PEComa detected post-transplant in the liver.Case reportA 27-year-old patient, 3 years after kidney transplantation (KTx) due to chronic renal failure in the course of autosomal dominant polycystic kidney disease and concomitant TSC, was admitted to the Clinic and Department of General and Transplant Surgery for abnormal findings in computed tomography (CT). A CT scan was conducted for oncological follow-up after a kidney transplant (KTx) because before the transplantation, a small cystic lesion measuring 7 mm in diameter was removed from the donor kidney and diagnosed as papillary renal cell carcinoma (PRCC). Two tumors in the liver were detected - one 27mm in diameter in segment VII/VIII and the other 8mm in diameter in segment II/III. Because of typical radiological signs hepatocellular carcinoma was suspected, but the serum level of alpha fetoprotein was within normal limits and liver function was preserved. The intraoperative biopsy and the radiofrequency ablation (RFA) of the larger tumor were performed three months later. In the histopathological examination benign PEComa (HMB45 +, Melan A +) was detected.ConclusionThe oncological surveillance made it possible to detect liver lesion in early stage and in 3,5-year follow-up no sign of recurrence of PEComa was found. This case is the second to show RFA as treatment method of liver PEComa and first in kidney transplant recipient.
Ovarian steroid cell tumors, not otherwise specified: three case reports and literature review
Authors: Sun Yue , Tian Lina , Meng Chao , Liu Guoyan 
Published: July 2024

ObjectiveTo provide a reference for the diagnosis and treatment of ovarian steroid cell tumors, not otherwise specified (SCTs-NOS).MethodsWe retrospectively analyzed the clinicopathological data of three patients with SCTs-NOS admitted to the Tianjin Medical University General Hospital from 2012 to 2022 and reviewed literature reports related to this disease.ResultsA total of 3 cases in our center and 70 cases searched in literature reports were included. The age at diagnosis ranged from 3 to 93 years (median, 34 years). The common clinical manifestations were hirsutism, acne, deepened voice, clitoromegaly, amenorrhea, and excessive weight gain. Tumor sizes ranged from 1.2 to 45 cm, with an average diameter of 6.5cm. Most of SCTs-NOS were benign, but some of them exhibited malignant behavior. Surgery was the main treatment and close follow-up was required. The follow up time of 73 cases ranged from 3 to 132 months (median, 21.3 months). Disease recurrence or progression occurred in 14 cases (19.2%). Three of the 73 patients had a successful pregnancy.ConclusionSCTs-NOS usually occur in women of reproductive age, which are mainly manifested as androgen excess symptoms. Surgery is an appropriate treatment for SCTs-NOS and should be individualized. Final diagnosis depends on pathology. SCTs-NOS have malignant potential, and the treatments for patients with malignant tumors and disease recurrence or progression were cytoreductive surgery, adjuvant chemotherapy, and gonadotrophin-releasing hormone agonists (GnRHa) therapy.
Integration of PSAd and multiparametric MRI to forecast biopsy outcomes in biopsy-naïve patients with PSA 4~20 ng/ml
Authors: Ren Lei , Chen Yanling , Liu Zixiong , Huang Guankai , Wang Weifeng , Yang Xu , Bai Baohua , Guo Yan , Ling Jian , Mao Xiaopeng 
Published: July 2024

IntroductionThis study aims to investigate whether the transrectal ultrasound-guided combined biopsy (CB) improves the detection rates of prostate cancer (PCa) and clinically significant PCa (csPCa) in biopsy-naïve patients. We also aimed to compare the Prostate Imaging Reporting and Data System (PI-RADS v2.1) score, ADC values, and PSA density (PSAd) in predicting csPCa by the combined prostate biopsy.MethodsThis retrospective and single-center study included 389 biopsy-naïve patients with PSA level 4~20 ng/ml, of whom 197 underwent prebiopsy mpMRI of the prostate. The mpMRI-based scores (PI-RADS v2.1 scores and ADC values) and clinical parameters were collected and evaluated by logistic regression analyses. Multivariable models based on the mpMRI-based scores and clinical parameters were developed by the logistic regression analyses to forecast biopsy outcomes of CB in biopsy-naïve patients. The ROC curves measured by the AUC values, calibration plots, and DCA were performed to assess multivariable models.ResultsThe CB can detect more csPCa compared with TRUSB (32.0% vs. 53%). The Spearman correlation revealed that Gleason scores of the prostate biopsy significantly correlated with PI-RADS scores and ADC values. The multivariate logistic regression confirmed that PI-RADS scores 4, 5, and prostate volume were important predictors of csPCa. The PI-RADS+ADC+PSAd (PAP) model had the highest AUCs of 0.913 for predicting csPCa in biopsy-naïve patients with PSA level 4~20 ng/ml. When the biopsy risk threshold of the PAP model was greater than or equal to 0.10, 51% of patients could avoid an unnecessary biopsy, and only 5% of patients with csPCa were missed.ConclusionThe prebiopsy mpMRI and the combined prostate biopsy have a high CDR of csPCa in biopsy-naïve patients. A multivariable model based on the mpMRI-based scores and PSAd could provide a reference for clinicians in forecasting biopsy outcomes in biopsy-naïve patients with PSA 4~20 ng/ml and make a more comprehensive assessment during the decision-making of the prostate biopsy.
Preoperative magnetic resonance imaging-radiomics in cervical cancer: a systematic review and meta-analysis
Authors: Wu Linyong , Li Songhua , Li Shaofeng , Lin Yan , Wei Dayou 
Published: July 2024

BackgroundThe purpose of this systematic review and meta-analysis is to evaluate the potential significance of radiomics, derived from preoperative magnetic resonance imaging (MRI), in detecting deep stromal invasion (DOI), lymphatic vascular space invasion (LVSI) and lymph node metastasis (LNM) in cervical cancer (CC).MethodsA rigorous and systematic evaluation was conducted on radiomics studies pertaining to CC, published in the PubMed database prior to March 2024. The area under the curve (AUC), sensitivity, and specificity of each study were separately extracted to evaluate the performance of preoperative MRI radiomics in predicting DOI, LVSI, and LNM of CC.ResultsA total of 4, 7, and 12 studies were included in the meta-analysis of DOI, LVSI, and LNM, respectively. The overall AUC, sensitivity, and specificity of preoperative MRI models in predicting DOI, LVSI, and LNM were 0.90, 0.83 (95% confidence interval [CI], 0.75-0.89) and 0.83 (95% CI, 0.74-0.90); 0.85, 0.80 (95% CI, 0.73-0.86) and 0.75 (95% CI, 0.66-0.82); 0.86, 0.79 (95% CI, 0.74-0.83) and 0.80 (95% CI, 0.77-0.83), respectively.ConclusionMRI radiomics has demonstrated considerable potential in predicting DOI, LVSI, and LNM in CC, positioning it as a valuable tool for preoperative precision evaluation in CC patients.
Characteristics of gut microbiome in patients with pediatric solid tumor
Authors: Du Xiaoran , Cui Xu , Fan Rongrong , Pan Juntao , Cui Xichun 
Published: July 2024

BackgroundPediatric solid tumors are a common malignant disease in children, and more and more studies have proved that there is an inseparable relationship between adult tumors and intestinal microbiome, but the changes in the intestinal microbiota of pediatric solid tumor (PST) patients have been scarcely examined. This study aims to examine the differences in the intestinal microbiota features between patients diagnosed with PST and healthy controls (HCs).MethodsTo elucidate the unique characteristics of the gut microbiota in pediatric patients with solid tumors, we recruited 23 PST patients and 20 HCs. A total of 43 stool samples were gathered, and then 16S rRNA sequencing was performed.ResultsWe noticed a noticeable pattern of elevated diversity in the gut microbiota within the PST groups. The differences in microbial communities among two groups were remarkable, regarding the analysis at the class level, the abundance of Bacilli was markedly increased in PST patients compared to HCs (P &lt; 0.05), regarding the analysis at the genus level, The presence of Enterococcus was significantly higher in PST cases compared to HCs (P &lt; 0.01), while Lachnospiraceae unclassified, Lachnospira, Haemophilus and Colidextribacter in PST cases, the abundance was significantly reduced. (P &lt; 0.05), 6 genera, including Bacilli, Lactobacillales, Enterococcaceae and Morganella, showed a significant enrichment compared to healthy controls, while 10 genera, including Bilophila, Colidextribacter, Pasteurellales, Haemophilus, Lachnospiraceae unclassified, Lachnospira and Fusobacteriales, were significant reduction in the PST groups.ConclusionOur research conducted the characterization analysis of the gut microbiota in PST patients for the first time. More importantly, there are some notable differences in the gut microbiota between PST patients and healthy controls, which we believe is an interesting finding.
Infant with diffuse large B-cell lymphoma identified postmortem with homozygous founder Slavic RAG1 variant: a case report and literature review
Authors: Volodashchik Tatiana P. , Polyakova Ekaterina A. , Mikhaleuskaya Taisia M. , Sakovich Inga S. , Kupchinskaya Aleksandra N. , Dubrouski Aliaxandr Ch. , Belevtsev Mikhail V. , Dasso Joseph F. , Varabyou Dzmitry S. , Notarangelo Luigi D. , Walter Jolan E. , Sharapova Svetlana O. 
Published: July 2024

Background and aimsThere is an increased risk of lymphomas in inborn errors of immunity (IEI); however, germline genetic testing is rarely used in oncological patients, even in those with early onset of cancer. Our study focuses on a child with a recombination-activating gene 1 (RAG1) deficiency who was identified through a screening program for Slavic founder genetic variants among patients who died with malignancy at an early age in Belarus.ResultsWe identified one homozygous founder RAG1 variant out of 24 available DNA samples from 71 patients who developed lymphoma aged &lt;3 years from the Belarusian cancer registry between 1986 and 2023. Our patient had an episode of pneumonia at 3 months of age and was hospitalized for respiratory distress, candida-positive lung disease, and lymphadenopathy at 14 months of age. The diagnosis of Epstein–Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) was established. The patient had a normal lymphocyte count that decreased over time. One month after chemotherapy initiation, the patient died due to sepsis and multiple organ failure without a genetic diagnosis. In a retrospective analysis, T-cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs) were undetectable in peripheral blood.ConclusionsA targeted screening program designed to detect a Slavic founder variant in the RAG1 gene among children revealed a 14-month-old Belarusian male infant with low TREC levels who died of EBV-driven DLBCL and complications of chemotherapy including infections. This case highlights how patients with IEI and recurrent infections may develop serious non-infectious complications, such as fatal malignancy. It also emphasizes the importance of early identification, such as newborn screening for severe combined immune deficiency. Earlier diagnosis of RAG deficiency could have prompted hematopoietic stem cell transplant well before the DLBCL occurrence. This likely would impact the onset and/or management strategies for the cancer.
Relationship between cathepsins and cardiovascular diseases: a Mendelian randomized study
Authors: Li Qiaoqiao , Zhou Zhongzheng , Xu Teng , Gao Xueping , Lou Yake , Chen Zijun , Zhang Muzi , Fang Qinghua , Tan Jie , Huang Jing 
Published: July 2024

Background: Cardiovascular diseases (CVDs) are the leading age-related disorders worldwide, with their prevalence increasing annually. Cathepsins are protein-degrading enzymes essential for processes such as intracellular protein breakdown, apoptosis, and immune responses. Recent studies suggest a potential link between cathepsins and CVDs, yet the exact causal relationship remains to be elucidated. To address this, we propose using Mendelian randomization (MR) to explore the causal relationships between cathepsins and CVDs.Methods: We obtained single nucleotide polymorphism (SNP) data for cathepsins from the INTERVAL study, a publicly accessible genome-wide association study (GWAS) dataset. Outcome SNP data were sourced from seven distinct GWAS datasets, ensuring a comprehensive analysis across multiple cardiovascular outcomes. For MR analysis, we primarily employed the inverse variance weighted (IVW) method, known for its efficiency when all SNPs are valid instruments. This was supplemented by the weighted median and MR-Egger methods to provide robustness against potential violations of MR assumptions, such as pleiotropy. The IVW method offers precision and efficiency, the weighted median method adds robustness against invalid instruments, and the MR-Egger method helps identify and correct for pleiotropic biases. Cochran’s Q test was utilized to assess heterogeneity, and sensitivity analyses were conducted using MR-PRESSO and the leave-one-out approach.Results: The strength of the associations between exposure and outcome was measured using odds ratios (ORs), and results were presented with 95% confidence intervals (CIs). The cathepsin E increases the risk of myocardial infarction (MI) (OR = 1.053%, 95% CI: 1.007–1.101, p = 0.024) and ischemic stroke (IS) (OR = 1.06%, 95% CI: 1.019–1.103, p = 0.004). Conversely, cathepsin L2 decreases the risk of chronic heart failure (CHF) (OR = 0.922%, 95% CI: 0.859–0.99, p = 0.025) and atrial fibrillation (AF) (OR = 0.956%, 95% CI: 0.918–0.996, p = 0.033). Cathepsin O was associated with an increased risk of IS (OR = 1.054%, 95% CI: 1.008–1.102, p = 0.021) and AF (OR = 1.058%, 95% CI: 1.02–1.098, p = 0.002).Conclusion: Our MR analysis reveals that cathepsin E is a risk factor for MI and IS, cathepsin L2 offers protective effects against CHF and AF, and cathepsin O increases the risk for IS and AF.