bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis reveals hypoxic response key genes and modules as well as adaptive mechanism of crucian carp (Carassius auratus) gill under hypoxic stress
Authors: Xing Mengchao , Rong Zhen , Zhao Xin , Gao Xiaowei , Hou Zhiguang , Zhang Lihan , Khor Waiho , Xu Yihuan , Chen Li , Wu Chengbin 
Published: February 2025

Fish gill tissue is a primary organ responsive to acute oxygen deprivation or dissolved oxygen (DO) fluctuations in aquatic environments. However, the adaptive mechanism of crucian carp to hypoxic stress remains largely unknown. Here, we investigated gill physiological and transcriptomic changes of crucian carp exposed to hypoxic conditions (dissolved oxygen concentration of 0.6 ± 0.3 mg/L) for different durations (0 d, 1 d, 2d, 3d, 4 d, and 5d). Transcriptomic analysis revealed that the hypoxia group (0.6 ± 0.3 mg/L DO) exhibited a reduction in interlamellar cell mass (ILCM) on the gill filaments, compared with the control group (6.6 ± 0.3 mg/L DO). With prolonged hypoxia stress, the epithelial cells in the gill lamellae became sparse at 3 d to 5 d, and gill vacuoles were increased. A total of 3,502 differentially expressed genes (DEGs) were identified, and 3 hypoxia-specific modules were screened through differential expression analysis, weighted gene co-expression network analysis (WGCNA), and Bayesian network analysis. The apoptosis, necroptosis, efferocytosis and FoxO signaling pathways were significantly enriched based on the KEGG enrichment pathway analysis. The VEGF pathway genes are significantly expressed, enhancing the generation of microvessels in the gill filaments, and improving the capacity to carry oxygen, thus enabling the crucian carp to adapt to hypoxia stress. Hypoxia activated glycolysis, enhanced anaerobic metabolism, promoted β-oxidation of fatty acids, providing energy and maintaining normal physiological metabolism, eventually improving antioxidant and immune capabilities in crucian carp. In summary, this study reveals the molecular mechanism by which crucian carp adapt to hypoxic stress. Our findings provide valuable references for promoting the healthy aquaculture of hypoxic-sensitive fish and breeding hypoxia-tolerant fish varieties.
Impact of religious fasting on ocular dryness: objective and subjective assessment
Authors: Alomari Amal F. , Issa Sara , Musleh Asma , Abusamak Mohammad , Bdair Omar , AlRyalat Saif Aldeen , Al-Wakfi Alanoud , Jaber Mohammed , Alloubani Ahmad , Sahawneh Haitham , El-Faouri Muhannd , Abdul Aziz Ayman , Al Bdour Muawyah 
Published: February 2025

BackgroundCertain religions require long hours of fasting, abstaining from fluid intake for durations extending up to 16 h. Lack of fluid intake may alter multiple physiological parameters, which can influence the ocular system. In this prospective study, we evaluated the effect of prolonged fasting on dry eye disease using both objective and subjective measures.MethodsWe included patients who fasted for at least 12 h a day for at least 2 weeks, including the testing day, and retested them at least 1 week after the fasting period had ended with no fasting on the testing day. At each visit, Non-Invasive Keratograph Break up time (NIKBUT) and Tear meniscus height (TM) were measured using the Oculus Keratograph 5 M. Ocular Surface Disease Index (OSDI) was evaluated at each timepoint to assess dryness symptoms subjectively.ResultsThis study included a total of 40 patients. NIKBUT values during the fasting times were higher than during the non-fasting times; however, the difference was statistically non-significant. There were no significant differences in TM and OSDI measurements between non-fasting and fasting periods (p &gt; 0.05). Lubricating eyedrop use was significantly lower in fasting patients.ConclusionOur study showed that prolonged fasting, including complete abstinence from fluid intake, did not lead to significant dryness, neither subjectively nor objectively. During fasting, patients used significantly fewer lubricating drops compared to non-fasting periods.
Predictive value of neutrophil to lymphocyte ratio for the clinical outcomes of acquired immune deficiency syndrome: a systematic review and meta-analysis
Authors: Guo Fuyu , Chen Jiamei , Zhang Hengkai 
Published: February 2025

ObjectiveThis study aimed to explore the predictive value of the neutrophil-to-lymphocyte ratio (NLR) for outcomes in Acquired Immune Deficiency Syndrome (AIDS) patients.MethodsPubMed, Embase, Cochrane, and Web of Science were conducted to search literature up to May 2024 and cohort and case–control studies were included. The primary outcomes were mortality and progression-free survival (PFS). Pooled odds ratios (ORs) or hazard ratios (HRs) with 95% confidence intervals (CIs) were calculated using a random-effects model. We conducted sensitivity analyses to assess result stability, reliability, and subgroup analyses to identify sources of heterogeneity using Review Manager 5.4.1. Egger’s tests were performed with Stata 15.1, and funnel plots were generated using Review Manager 5.4.1. Microsoft Excel was used for the initial data summarization.ResultsFourteen studies involving 30,752 AIDS patients were included. The pooled data showed higher NLR significantly associated with increased mortality (OR: 1.85, 95% CI: 1.43–2.41, p &lt; 0.00001) and shorter progression-free survival (PFS) (HR: 2.46, 95% CI: 1.32–4.59, p = 0.005). Subgroup analyses revealed that NLR’s predictive value was greater in studies with post-ART measurements. Sensitivity analyses show stable and reliable results. Egger’s test and funnel plot analysis revealed no significant publication bias.ConclusionNLR is a key prognostic biomarker for predicting mortality and progression-free survival (PFS) in AIDS patients. Incorporating NLR into predictive models may improve prognostic assessments and guide clinical decision-making.Systematic Review RegistrationPROSPERO (CRD42024532918: https://www.crd.york.ac.uk/PROSPERO).
Source attribution of human Campylobacter infection: a multi-country model in the European Union
Authors: Thystrup Cecilie , Brinch Maja Lykke , Henri Clementine , Mughini-Gras Lapo , Franz Eelco , Wieczorek Kinga , Gutierrez Montserrat , Prendergast Deirdre M. , Duffy Geraldine , Burgess Catherine M. , Bolton Declan , Alvarez Julio , Lopez-Chavarrias Vicente , Rosendal Thomas , Clemente Lurdes , Amaro Ana , Zomer Aldert L. , Grimstrup Joensen Katrine , Nielsen Eva Møller , Scavia Gaia , Skarżyńska Magdalena , Pinto Miguel , Oleastro Mónica , Cha Wonhee , Thépault Amandine , Rivoal Katell , Denis Martine , Chemaly Marianne , Hald Tine 
Published: February 2025

IntroductionInfections caused by Campylobacter spp. represent a severe threat to public health worldwide. National action plans have included source attribution studies as a way to quantify the contribution of specific sources and understand the dynamic of transmission of foodborne pathogens like Salmonella and Campylobacter. Such information is crucial for implementing targeted intervention. The aim of this study was to predict the sources of human campylobacteriosis cases across multiple countries using available whole-genome sequencing (WGS) data and explore the impact of data availability and sample size distribution in a multi-country source attribution model.MethodsWe constructed a machine-learning model using k-mer frequency patterns as input data to predict human campylobacteriosis cases per source. We then constructed a multi-country model based on data from all countries. Results using different sampling strategies were compared to assess the impact of unbalanced datasets on the prediction of the cases.ResultsThe results showed that the variety of sources sampled and the quantity of samples from each source impacted the performance of the model. Most cases were attributed to broilers or cattle for the individual and multi-country models. The proportion of cases that could be attributed with 70% probability to a source decreased when using the down-sampled data set (535 vs. 273 of 2627 cases). The baseline model showed a higher sensitivity compared to the down-sampled model, where samples per source were more evenly distributed. The proportion of cases attributed to non-domestic source was higher but varied depending on the sampling strategy. Both models showed that most cases could be attributed to domestic sources in each country (baseline: 248/273 cases, 91%; down-sampled: 361/535 cases, 67%;).DiscussionThe sample sizes per source and the variety of sources included in the model influence the accuracy of the model and consequently the uncertainty of the predicted estimates. The attribution estimates for sources with a high number of samples available tend to be overestimated, whereas the estimates for source with only a few samples tend to be underestimated. Reccomendations for future sampling strategies include to aim for a more balanced sample distribution to improve the overall accuracy and utility of source attribution efforts.
Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4
Authors: Xie Xiaofang , Zhai Yaxuan , Zhu Zhichen , Qian Feinan , Zhu Jie , Gao Qizhao , Du Hong 
Published: February 2025

ObjectivesThe aim of this study is to characterize the genomic features of ST6115 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring blaNDM-1 and blaIMP-4.MethodsThe genome sequences of one ST6115 Klebsiella pneumoniae (KP) strain and 12 ST17 KP strain were obtained through whole genome sequencing (WGS). Subsequently, a phylogenetic analysis was employed to ascertain the clonal relationship of these strains. The antimicrobial susceptibility testing (AST) was evaluated through the application of the minimum inhibitory concentration (MIC) methodology by the broth microdilution method. Annotation and analysis of the genome enabled the identification of the plasmid structure and the comparative analysis of the genetic background. Finally, the conjugation transfer experiment was conducted to assess the transferability of the plasmid pHD8428-NDM-IMP.ResultsA comparable phylogenetic analysis revealed that ST6115 HD8428 and the majority of ST17 strains (9/12) were clustered on the same clade, which suggests a close relationship between two ST types. Additionally, HD8428 showed particularly close genetic similarity to HD11490, with a single-nucleotide polymorphism (SNP) difference of only 273. The analysis of the antibiotic resistance genes carried by the 13 strains revealed that all strains carry extended-spectrum β-lactamase (ESBL) genes. AST revealed that HD8428 exhibited resistance to a diverse range of antibiotics. The blaNDM-1 and blaIMP-4 genes were identified as being located on the plasmid pHD8428-NDM-IMP. Further analysis demonstrated that the blaNDM-1 gene was present on ΔTn125, while the blaIMP-4 gene was located on In1377-2. The results of the conjugation experiment indicated that plasmid pHD8428-NDM-IMP may pose a risk for the transmission of antibiotic resistance in healthcare settings.ConclusionWe report a clinical ST6115 strain HD8428 and identify the coexistence of blaNDM-1 and blaIMP-4 in the IncHI5 type plasmid pHD8428-NDM-IMP. HD8428 was resistant to a wide range of antibiotics and harbored the transmissible plasmid pHD8428-NDM-IMP, which made it a potential threat to public health. Our study indicates that the healthcare system and services should remain vigilant regarding the spread and prevalence of ST6115.
Sex-specific associations between estimated glucose disposal rate and cognitive decline in middle-aged and older adults in China: a longitudinal cohort study
Authors: Luo Chun , Han Shuang , Shen Xiaoying , Wu Hao , Zhou Jianqing , Liu Bingyang 
Published: February 2025

BackgroundInsulin resistance (IR) is recognized as a potential modifiable risk factor for cognitive decline, but findings within Asian populations have been inconsistent. Given the high prevalence of dementia and its substantial economic burden in China, large-scale longitudinal studies are essential to elucidate the complex relationship between IR and cognitive function.MethodsThis longitudinal cohort study included 8,734 middle-aged and older adults (median age: 58 years; 53.6% females) from the China Health and Retirement Longitudinal Study (CHARLS), followed from 2011 to 2018. Estimated glucose disposal rate (eGDR) was used to assess IR and was calculated using waist circumference, hypertension status, and HbA1c levels. Participants were categorized into tertiles based on eGDR levels (Tertile 1: lowest; Tertile 3: highest). Cognitive function was calculated as the sum of episodic memory and executive function scores, which was then standardized to a Z-score. Linear mixed-effects models and dose-response analyses were performed to evaluate the association between baseline eGDR and cognitive changes in the total population and stratified by sex.ResultsHigher eGDR levels were significantly associated with slower global cognitive decline (Tertile 3 vs. Tertile 1: β = 0.007; 95% CI: 0.000–0.014; P = 0.047). This association was stronger in females (Tertile 3 vs. Tertile 1: β = 0.011; 95% CI: 0.002–0.021; P = 0.021), while no significant association was observed in males. Dose-response analyses indicated a linear positive relationship between baseline eGDR and global cognitive function in the total population and in females, but not in males. Similar patterns were found for episodic memory and executive function, with significant associations predominantly in females.ConclusionHigher eGDR was significantly associated with slower cognitive decline, particularly among women. These findings underscore the potential of eGDR as a marker for identifying and mitigating cognitive decline and highlight the importance of sex-specific strategies to address insulin resistance and promote cognitive health.
A multicenter analysis to identify the risk factors for stroke recurrence and mortality within 1 year
Authors: Alraddadi Eman A. , Alotaibi Hashim F. , Alatawi Yasser , Aljabri Ahmed , Alghamdi Ahmed A. , Alturki Fahad , Alamri Faisal F. 
Published: February 2025

BackgroundStroke recurrence is a serious and prevalent complication of ischemic stroke that warrants additional investigation.MethodsA hospital-based retrospective observational study included acute-subacute ischemic stroke adult patients. The primary aim was to determine the risk factors associated with recurrent stroke within 365 days. Additionally, a combined outcome consisting of any stroke recurrence or all-cause mortality within 365 days was considered secondary outcome. Univariate and multivariable Cox proportional-hazards models were used to examine the association of risk factors with stroke recurrence and composite death/stroke recurrence.ResultsOf 1,244 patients, 112 (9%) experienced stroke recurrence. The multivariable analysis identified risk factors for stroke recurrence including history of previous stroke (HR = 3.65, 95% CI:2.28–5.99, p = 0.0001), tissue plasminogen activator (tPA) treatment (HR = 2.84, 95% CI:1.57–4.86, p = 0.0003), seizure (HR = 1.96, 95% CI:1.14–3.22, p = 0.0105), and depression (HR = 2.26, 95% CI:1.33–3.69, p = 0.0016). Only previous stroke history (HR = 2.37, 95% CI:1.74–3.26, p = 0.0001) remained significantly associated with the combined outcome of stroke recurrence/death. Additional risk factors for the composite outcome included older age of patients (HR = 1.02, 95% CI:1.01–1.03, p = 0.0009), admission to the intensive care unit (ICU) (HR = 3.70, 95% CI:2.63–5.22, p = 0.0105), pneumonia (HR = 1.47, 95% CI:1.05–2.05, p = 0.0249), and brain edema (HR = 2.36, 95% CI:1.58–3.46, p = 0.0001).ConclusionKey findings include a stroke recurrence rate of 9.96% and a combined death/stroke recurrence rate of 21.83% within 365 days. Multivariable analysis confirmed that history of stroke, receiving tPA, experiencing seizures, and depression were significantly associated with stroke recurrence. Implementing additional preventive measures for individuals in these high-risk categories is essential. Further studies are needed to validate our findings.
Ocrelizumab-induced colitis—critical review and case series from a Romanian cohort of MS patients
Authors: Vodă Ileana Maria , Tiu Vlad Eugen , Răuță Luiza , Ciucur Paul , Mușuroi Andreea Ioana , Tomescu Alina Flavia , Humă Nicoleta Laura , Dobrițoiu Florin , Terecoasă Elena , Negreanu Lucian , Tiu Cristina 
Published: February 2025

BackgroundWidespread use of ocrelizumab, an anti-CD20 monoclonal antibody, for treating patients with multiple sclerosis (MS), has led to an increase in reported adverse events following real-world observation. Among these, drug-induced colitis is a rare, but severe side effect, prompting a recent FDA statement regarding this safety concern. Objectives: We analyzed a cohort of ocrelizumab treated patients in our MS center to evaluate the incidence of drug-induced colitis.MethodsWe present a critical review of the available literature on diagnosis and management of anti-CD20 induced colitis and display a case series of 3 suspected patients in our cohort.ResultsTwo patients met the full criteria for ocrelizumab-induced colitis, while a third partially met the criteria. Following symptomatic treatment and discontinuation of ocrelizumab, the patients showed favorable outcomes.ConclusionOcrelizumab-induced colitis is a rare, but severe adverse event. Its incidence may be higher than expected, reaching 1,95% in our cohort of MS patients. Further reporting of such cases is essential to broaden our understanding of this side effect.
Multimodal abnormalities of brain function in chronic low back pain: a systematic review and meta-analysis of neuroimaging studies
Authors: Chen Xingyao , Chen Nuo , Lai Peng , Sun Yiqi , Yu Jie , Xin Ming , Zhu Deliang , Liang Fanrong , Song Qian , Cheng Shirui , Li Zhengjie 
Published: February 2025

ObjectivesNeuroimaging investigations into chronic low back pain (CLBP) have detected functional abnormalities across a spectrum of brain regions, yet the findings have often been inconsistent. In this meta-analysis, we integrated the existing data, delineating a pattern of coherent results from the encompassed studies.MethodsA systematic search of neuroimaging studies investigating the brain activity differences between CLBP and Healthy controls (HCs) was conducted in seven databases up to December 22, 2024. An anisotropic effect-size signed differential mapping (AES-SDM)-based meta-analysis was carried out to report the results and perform a multimodal analysis.ResultsA total of 20 publications reporting on 24 experiments in this meta-analysis. The ReHo meta-analysis showed abnormal spontaneous activity of left inferior temporal gyrus (ITG), left superior frontal gyrus (SFG), right middle frontal gyrus (MFG), right precuneus, right fusiform gyrus and bilateral postcentral gyrus (PoCG) in CLBP patients. The ALFF meta-analysis demonstrated functional alterations in the right rolandic operculum (extending to the right insula and right IFG), left ITG, left middle occipital gyrus (MOG), left paracentral lobule, left PoCG and bilateral cuneus cortex in CLBP patients. The results of the functional group meta-analysis revealed that patients with CLBP displayed new decreased functional activity in the right thalamus, right precentral gyrus (PreCG) and right lingual gyrus.ConclusionPatients with CLBP exhibit extensive multimodal functional neuroimaging abnormalities, involving brain regions related to pain perception, emotional processing, cognitive functions, and both the visual and motor cortices. These meta-analysis findings might provide a valuable reference for the identification of potential therapeutic targets for CLBP in the brain.
Intratumoral and peritumoral radiomics using multi-phase contrast-enhanced CT for diagnosis of renal oncocytoma and chromophobe renal cell carcinoma: a multicenter retrospective study
Authors: Ye Yongsong , Weng Bei , Guo Yan , Huang Lesheng , Xie Shanghuang , Zhong Guimian , Feng Wenhui , Lin Wenxiang , Song Zhixuan , Wang Huanjun , Liu Tianzhu 
Published: February 2025

PurposeTo construct diagnostic models that distinguish renal oncocytoma (RO) from chromophobe renal cell carcinoma (CRCC) using intratumoral and peritumoral radiomic features from the corticomedullary phase (CMP) and nephrographic phase (NP) of computed tomography, and compare model results with manual and radiological results.MethodsThe RO and CRCC cases from five centers were split into a training set (70%) and a validation set (30%). CMP and NP intratumoral and peritumoral (1–3 mm) radiomic features were extracted. Segmentation was performed by radiologists and software. Features with high intraclass correlation coefficients (ICC&gt;0.75) were selected through univariate analysis, followed by the LASSO method to determine the final features for the SVM model. All images were assessed by two radiologists, and radiological reports were also examined. The diagnostic performances of the different methods were compared using several statistical methods.ResultsThe training set had 65 cases (29 RO, 36 CRCC) and the validation set had 27 cases (12 RO, 15 CRCC). All the training models had excellent performance (area under the curve [AUC]: 0.828–0.942); the AUC values of the validation models ranged from 0.900 (Model 4) to 0.600 (Model 2). CMP models (AUC: 0.811–0.900) generally outperformed NP and fusion models (AUC: 0.728–0.756). SVM models (sensitivity: 62.50–88.89%; specificity: 63.16–77.78%; accuracy: 62.96–81.48%) outperformed manual diagnosis (sensitivity: 46.74–70.59%; specificity: 41.67–46.34%; accuracy: 52.27–59.78%). The clinical reports alone had no diagnostic value.ConclusionCMP intratumoral and peritumoral radiomics models reliably distinguished RO from CRCC.
Prognostic value of circulating Chromogranin A in prostate cancer: a systematic review and meta-analysis
Authors: Tang Xiaoying , Liu Zhenyu , Song Liangdong , Zhu Huixuan , Su Shuai , Wang Delin 
Published: February 2025

BackgroundThere are discrepancies between the results of different studies regarding the prognostic role of circulating Chromogranin A (CgA) in prostate cancer. Therefore, we conducted a meta-analysis of the available findings to explore the value of circulating Chromogranin A in the prognosis of prostate cancer.MethodsWe systematically searched the PubMed, Embase, Web of Science, Cochrane Library, and Clinical Trials databases for studies on the relationship between CgA and survival outcomes in prostate cancer from inception until December 2024, and we focused on articles detecting circulating CgA, with the primary endpoints of the studies being overall survival (OS), and progression-free survival (PFS).ResultsOf the 2049 articles retrieved, 10 articles met our inclusion criteria, involving a total of 1445 patients. Elevated circulating CgA was associated with poorer OS (HR=1.82, 95% CI: 1.38–2.41; p&lt;0.001) and PFS (HR=2.04, 95% CI: 1.42–2.94; p&lt;0.001). However, no correlation was found between post-treatment circulating CgA changes and OS (HR=0.95, 95% CI: 0.66–1.37; p=0.767).ConclusionCirculating CgA is a predictive marker of poor survival outcomes in prostate cancer However, the sample size of the current study is small and larger studies are needed to further validate this in the future.