bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the late Cenozoic structural deformation and tectonic stress field of the Qiabuqia region, Gonghe Basin, northeastern Qinghai–Tibetan Plateau
Authors: Yang Zhang , Qingda Feng , Fucheng Li , Linyou Zhang , Chao Zhang , Senqi Zhang , Dunpeng Li , Zhen Yan , Jian Song , Lei Fu , Zhaoxuan Niu 
Published: January 2023

In addition to overall uplift of the Qiabuqia region during the Late Cenozoic, three deformation stages can be identified in the northeastern Qinghai–Tibet Plateau. Specifically, these deformation stages were recognized in areas east of the Gonghe Basin that surrounds Waliguan Mountain and include: 1) Late Miocene to Late Pliocene deformation—dominated by thrust napping with dextral strike-slipping; 2) Early Pleistocene to late middle period of Pleistocene deformation—fault structures were dominated by the dextral strike-slipping with thrust napping; and 3) end of Late Pleistocene to Middle Holocene deformation—thrust napping slowed down and finally braked, while the shallow surface began to loosen and extend at Qiabuqia region’s rear-edge. DR4 borehole drilling data indicate that the Xiangshuihe Formation’s buried depth is ∼1,000 m. The Xianshuihe Formation’s top section is characterized by normal fault–type (NF) tectonic stress, while the maximum principal tectonic stress (σ1) is perpendicular and the minimum principal tectonic stress (σ3) is horizontal. In contrast, the deep basement is characterized by thrust fault (TF) and strike-slip (SS) tectonic stress, while the σ1 is in the NE-SW direction, ranging from 20.1° to 75.3° with an average of 40.0°. Based on the aforementioned observations, it can be inferred that there are three sets of hidden faults in the basement of the Qiabuqia region: 1) the NW–NNW trending compressional–torsional faults; 2) the NE trending tensional–torsional faults; and 3) the NWW trending compressional–torsional faults. The findings in this study can potentially offer a robust geological basis for exploring and utilizing hot, dry rock resources within the Gonghe Basin.
Global trends in polycystic ovary syndrome research: A 10-year bibliometric analysis
Authors: Shi Na , Ma Hong-bo 
Published: January 2023

BackgroundPolycystic ovary syndrome (PCOS) is one of the most common reproductive metabolic disorders in women, significantly affecting the biological functionalities of ovaries. This disease has garnered enormous interest from researchers. However, there is a lack of a comprehensive research concerning assessing the current status and future trends in PCOS field. This study uses bibliometric tools to comprehensively analyze the PCOS-related research progress based on the literature in the past decade.MethodsThe reported PCOS literature in the past decade is downloaded from the Web of Science database. The bibliometric software is applied to analyze the co-authorship, co-citation, and co-occurrence status.ResultsA total of 9936 publications imported into bibliometric tools for analysis show a sharp increase in the annual citations. The USA is dominant in terms of contribution in the field of PCOS, while China is making a significant contribution to the advancement of this field. Monash University is the most prolific institution with the highest H-index value. The contribution of University of Adelaide must be acknowledged. Legro RS and Teede HJ are the most active and influential authors in recent times, while Azziz R is the most contributed pioneer in this field. The Journal of Clinical Endocrinology &amp; Metabolism is the most active journal with the highest number of publications and citations. The pathogenesis of PCOS had been a long-term forefront of research. In recent years, the health management in PCOS prevention and long-term complications was attracting more and more attention. The keywords like “gut microbiota”, “microRNAs”, “apoptosis”, “Myo-inositol”, “TNF-alpha”, “androgen receptor”, and “Vitamin D-deficient” are considered the latest research topics.ConclusionThe study comprehensively analyzes the current status and global trends in the PCOS field, providing a significant reference for researchers to explore this field effectively.
Living on the edge – An overview of invertebrates from groundwater habitats prone to extreme environmental conditions
Authors: Pop Maria Mirabela , Di Lorenzo Tiziana , Iepure Sanda 
Published: January 2023

Groundwater ecosystems from cold polar and circumpolar regions, hot springs, as well as those developed in salt, gypsum or in volcanic rocks are one of the environments considered to exhibit extreme environmental conditions such as low (below 0°C) or high (over 45°C) temperatures, hypersaline waters, or with elevated content of toxic gases like hydrogen sulfide or methane. They represent the “unseen ecosystem beneath our feet” and are inhabited by a large diversity of organisms, persisting and flourishing under severe environmental conditions that are usually hostile to the majority of organisms. These types of groundwater ecosystems are remarkable “evolutionary hotspots” that witnessed the adaptive radiation of morphologically and ecologically diverse species, whereas the organisms living here are good models to understand the evolutionary processes and historical factors involved in speciation and adaptation to severe environmental conditions. Here, we provide an overview of the groundwater invertebrates living in continental groundwater habitats prone to extreme environmental conditions in one or more physico-chemical parameters. Invertebrates are represented by a wide variety of taxonomic groups, however dominated by crustaceans that show specific adaptations mostly metabolic, physiologic, and behavioral. Symbiotic associations among bacteria and invertebrates are also discussed enlightening this biological interaction as a potential adaptation of different groundwater invertebrates to cope with severe environmental conditions. Given the high pressures that anthropogenic activities pose on groundwater habitats worldwide, we predict that several of these highly specialized organisms will be prone to extinction in the near future. Finally, we highlight the knowledge gaps and future research approaches in these particular groundwater ecosystems by using integrative-omic studies besides the molecular approach to shed light on genetic variation and phenotypic plasticity at species and populational levels.GRAPHICAL ABSTRACT
DNA methylation and mRNA expression of glutathione S-transferase alpha 4 are associated with intracranial aneurysms in a gender-dependent manner
Authors: Xu Tianqi , Yu Xi , Zhou Shenjun , Wu Yiwen , Deng Xinpeng , Wu Yuefei , Wang Shiyi , Gao Xiang , Nie Sheng , Zhou Chenhui , Sun Jie , Huang Yi 
Published: January 2023

Objective: We performed a case-control study to investigate the correlation between DNA methylation and mRNA expression of the glutathione S-transferase alpha 4 (GSTA4) gene and the risk of intracranial aneurysm (IA) in the Chinese Han population.Methods: After propensity score matching, 44 pairs of cases and controls were collected in this study. Fasting blood samples were collected for DNA and RNA extraction within 24 h of admission. Nine CpG dinucleotides were selected from the GSTA4 promoter region for DNA methylation pyrosequencing. mRNA expression of GSTA4 was measured by quantitative real-time polymerase chain reaction (RT-qPCR). In vitro cell experiments were conducted to verify the association between 5-aza-2′-deoxycytidine induced DNA hypomethylation and GSTA4 mRNA expression.Results: The mean methylation level of GSTA4 was much lower in IA patients, especially in IA patients, especially in unruptured IA (UIA), than that in controls (IA vs. Control, p &lt; .001; ruptured IA (RIA) vs. Control, p = .005; UIA vs. Control, p &lt; .001). With sex stratification, we further found that the association between GSTA4 methylation and IA risk presented only in women (mean methylation level: IA vs. Control, p &lt; .001; RIA vs. Control, p = .009; UIA vs. Control, p &lt; .001). GSTA4 mRNA expression was significantly higher in the IA group than in the control group (p &lt; .01) and negatively correlated with DNA methylation in all individuals (r = −.746, p &lt; .001). DNA hypomethylation can increase GSTA4 mRNA expression in human primary artery smooth muscle cells. The receiver operating characteristic (ROC) curve showed that GSTA4 mean methylation (AUC = .80, p &lt; .001) was a reliable predictor of women intracranial aneurysm, among which CpG 1 exhibited the best predictive value (AUC = .89, p &lt; .001). In addition, GSTA4 expression levels could also predict the risk of IA in women (AUC = .87, p = .005).Conclusion: Decreased DNA methylation and increased mRNA expression of the GSTA4 gene are associated with the risk of IA in women.
DeteX: A highly accurate software for detecting SNV and InDel in single and paired NGS data in cancer research
Authors: Cui Yunlong , Li Hongfeng , Liu Pengfei , Wang Hailong , Zhang Zhenzhen , Qu Hongzhu , Tian Caijuan , Fang Xiangdong 
Published: January 2023

Graphical AbstractSoftware running process and output results.
Effect of early postnatal supplementation of newborns with probiotic strain E. coli O83:K24:H31 on allergy incidence, dendritic cells, and microbiota
Authors: Súkeníková Lenka , Černý Viktor , Thon Tomáš , Roubalová Radka , Jirásková Zákostelská Zuzana , Novotná Olga , Petrásková Petra , Boráková Kristýna , Kocourková Ingrid , Lodinová-Žádníková Rája , Musil Zdeněk , Kolářová Libuše , Prokešová Ludmila , Valenta Zdeněk , Hrdý Jiří 
Published: January 2023

IntroductionProbiotic administration seems to be a rational approach to promote maturation of the neonatal immune system. Mutual interaction of the microbiota with the host immune system is critical for the setting of appropriate immune responses including a tolerogenic one and thevmaintenance of homeostasis. On the other hand, our knowledge on the modes of actions of probiotics is still scarce.MethodsIn our study, probiotic strain Escherichia coli O83:K24:H31 (EcO83) was administered to neonates of allergic mothers (AMs; neonates with increased risk for allergy development) within 48 h after the delivery, and the impact of this early postnatal supplementation on allergy incidence and selected immune markers has been analyzed 10 years after the primary EcO83 administration.ResultsWe have observed decreased allergy incidence in 10-year-old children supplemented with EcO83 (13 of 52 children were allergic) in comparison with non-supplemented children of AMs (16 of 42 children were allergic). The early postnatal EcO83 supplementation appeared to limit the allergy in the high-risk group (children of AMs) compared to that in the low-risk group (children of healthy mothers). Dendritic cells (DCs) in the peripheral blood of EcO83-supplemented children do not differ significantly in cell surface presence of CD83. The immunomodulatory capacity of EcO83 on DCs was tested in vitro as well. Both directly isolated myeloid and in vitro monocyte-derived DCs from cord blood increased CD83 expression together with interleukin (IL)-10 secretion after EcO83 stimulation. The effect of early postnatal EcO83 supplementation on the microbiota composition of 10-year-old children was characterized by next-generation sequencing, and we have not observed significant changes in the microbiota composition of EcO83-supplemented and non-supplemented children at the age of 10 years.ConclusionsEarly postnatal EcO83 supplementation appears to lower allergy incidence in children of AMs. It seems that the beneficial effect of EcO83 is mediated via modulation of DC functional capacities without impacting the microbiota composition. Larger-scale studies will be necessary to confirm these preliminary findings.
Immunity against Delta and Omicron variants elicited by homologous inactivated vaccine booster in kidney transplant recipients
Authors: Zhang Lei , Yang Jiaqing , Lai Changchun , Wan Li , Xiong Shilong , Kong Weiya , Liu Zijian , Yu Pei , Chen Mingxiao , Mai Weikang , Khan Shahzad Akbar , Deng Min , Chen Lu , Lei Yu , Zhou Qiang , Yu Nan , Li Pingchao , Chen Zheng , Ji Tianxing 
Published: January 2023

BackgroundA third mRNA vaccine booster is recommended to improve immunity against SARS-CoV-2 in kidney transplant recipients (KTRs). However, the immunity against SARS-CoV-2 Ancestral strain and Delta and Omicron variants elicited by the third dose of inactivated booster vaccine in KTRs remains unknown.MethodsThe blood parameters related to blood cells count, hepatic function, kidney function, heart injury and immunity were explored clinically from laboratory examinations. SARS-CoV-2 specific antibody IgG titer was detected using an enzyme-linked immunosorbent assay. Cellular immunity was analyzed using interferon-γ enzyme-linked immunospot assay.ResultsThe results showed that there were no severe adverse effects and apparent changes of clinical laboratory biomarkers in KTRs and healthy volunteers (HVs) after homologous inactivated vaccine booster. A third dose of inactivated vaccine booster significantly increased anti-Ancestral-spike-trimer-IgG and anti-Ancestral-receptor binding domain (RBD)-IgG titers in KTRs and HVs compared with the second vaccination. However, the anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG titers were significantly lower than anti-Ancestral-RBD-IgG titer in KTRs and HVs after the third dose. Notably, only 25.6% (10/39) and 10.3% (4/39) of KTRs had seropositivity for anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG after booster, which were significantly lower than HVs (anti-Delta-RBD-IgG: 100%, anti-Omicron-RBD-IgG: 77.8%). Ancestral strain nucleocapsid protein and spike specific T cell frequency after booster was not significantly increased in KTRs compared with the second dose, significantly lower than that in HVs. Moreover, 33.3% (12/36), 14.3% (3/21) and 14.3% (3/21) of KTRs were positive for the Ancestral strain and Delta and Omicron spike-specific T cells, which were significantly lower than HVs (Ancestral: 80.8%, Delta: 53.8%, and Omicron: 57.7%).ConclusionsA third dose of inactivated booster vaccine may significantly increase humoral immunity against the Ancestral strain in KTRs, while humoral and cellular immunity against the Delta and Omicron variants were still poor in KTRs.
Partially replacing cyclophosphamide with bendamustine in combination with cyclosporine A improves survival and reduces xenogeneic graft-versus-host-disease
Authors: Gilman Kristy E. , Cracchiolo Megan J. , Matiatos Andrew P. , Davini Dan W. , Simpson Richard J. , Katsanis Emmanuel 
Published: January 2023

IntroductionThe use of allogeneic hematopoietic cell transplantation (allo-HCT) for treating hematological disorders is increasing, but the development of graft-versus-host disease (GvHD) remains a major cause of morbidity and mortality. The use of post-transplant cyclophosphamide (CY) has significantly improved outcomes following allo-HCT, but complications of viral reactivation due to delayed immune reconstitution or relapse remain. Other laboratories are evaluating the potential benefit of lowering the dose of CY given post-transplant, whereas our laboratory has been focusing on whether partially replacing CY with another DNA alkylating agent, bendamustine (BEN) may be advantageous in improving outcomes with allo-HCT.MethodsHere, we utilized a xenogeneic GvHD (xGvHD) model in which immunodeficient NSG mice are infused with human peripheral blood mononuclear cells (PBMCs).ResultsWe show that a lower dose of CY (25 mg/kg) given on days +3 and +4 or CY (75 mg/kg) given on only day +3 post-PBMC infusion is not sufficient for improving survival from xGvHD, but can be improved with the addition of BEN (15 mg/kg) on day +4 to day +3 CY (75 mg/kg). CY/BEN treated mice when combined with cyclosporine A (CSA) (10mg/kg daily from days +5 to +18 and thrice weekly thereafter), had improved outcomes over CY/CY +CSA treated mice. Infiltration of GvHD target organs was reduced in both CY/CY and CY/BEN treatment groups versus those receiving no treatment. CY/CY +CSA mice exhibited more severe xGvHD at day 10, marked by decreased serum albumin and increased intestinal permeability. CY/BEN treated mice had reductions in naïve, effector memory and Th17 polarized T cells. RNAseq analysis of splenocytes isolated from CY/CY and CY/BEN treated animals revealed increased gene set enrichment in multiple KEGG pathways related to cell migration, proliferation/differentiation, and inflammatory pathways, among others with CY/BEN treatment.ConclusionTogether, we illustrate that the use of CY/BEN is safe and shows similar control of xGvHD to CY/CY, but when combined with CSA, survival with CY/BEN is significantly prolonged compared to CY/CY.
Association of preoperative prognostic nutritional index with risk of postoperative delirium: A systematic review and meta-analysis
Authors: Hung Kuo-Chuan , Chiu Chong-Chi , Hsu Chih-Wei , Ho Chun-Ning , Ko Ching-Chung , Chen I-Wen , Sun Cheuk-Kwan 
Published: January 2023

Study objectiveTo assess the association between prognostic nutritional index (PNI) and risk of postoperative delirium (POD) in adult patients.MethodsMEDLINE, Google scholar, EMBASE, and Cochrane library databases were searched from inception till April 2022. The primary outcome was the association between PNI and the risk of POD, while the secondary outcomes were correlations of other prognostic factors with POD risk. The correlation between PNI and the incidence of POD was assessed with three approaches: Difference in preoperative PNI between POD and non-POD groups (Model 1) as well as the association of PNI as a continuous parameter (Model 2) or as a binary variable (i.e., low vs. high using a PNI cut-off value of 50) (Model 3) with POD risk.ResultsAnalysis of nine observational studies published from 2010 to 2021 recruiting 3,743 patients showed a POD incidence of 6.4–35%. Our meta-analysis demonstrated a lower PNI among patients in the POD group (MD: −3.78, 95% CI: −4.85 to −2.71, p &lt; 0.0001, I2 = 54.2%) compared to the non-POD group (Model 1). Pooled results revealed a negative association between PNI and POD risk for both Model 2 (OR: 0.91, 95% CI: 0.86–0.97, p = 0.002, I2 = 71%) and Model 3 (OR: 1.68, 95% CI: 1.26–2.23, p &lt; 0.0001, I2 = 0%). Besides, while our results supported an age-dependent increase in POD risk, other factors including body-mass index, surgical time, health status, hypertension, diabetes mellitus, and male gender were non-significant predictors of POD.ConclusionOur results demonstrated a negative association between PNI and POD, which warrant further large-scale studies for validation.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42022323809.
Development and validation of risk-adjusted quality indicators for the long-term outcome of acute sepsis care in German hospitals based on health claims data
Authors: Wedekind Lisa , Fleischmann-Struzek Carolin , Rose Norman , Spoden Melissa , Günster Christian , Schlattmann Peter , Scherag André , Reinhart Konrad , Schwarzkopf Daniel 
Published: January 2023

BackgroundMethods for assessing long-term outcome quality of acute care for sepsis are lacking. We investigated a method for measuring long-term outcome quality based on health claims data in Germany.Materials and methodsAnalyses were based on data of the largest German health insurer, covering 32% of the population. Cases (aged 15 years and older) with ICD-10-codes for severe sepsis or septic shock according to sepsis-1-definitions hospitalized in 2014 were included. Short-term outcome was assessed by 90-day mortality; long-term outcome was assessed by a composite endpoint defined by 1-year mortality or increased dependency on chronic care. Risk factors were identified by logistic regressions with backward selection. Hierarchical generalized linear models were used to correct for clustering of cases in hospitals. Predictive validity of the models was assessed by internal validation using bootstrap-sampling. Risk-standardized mortality rates (RSMR) were calculated with and without reliability adjustment and their univariate and bivariate distributions were described.ResultsAmong 35,552 included patients, 53.2% died within 90 days after admission; 39.8% of 90-day survivors died within the first year or had an increased dependency on chronic care. Both risk-models showed a sufficient predictive validity regarding discrimination [AUC = 0.748 (95% CI: 0.742; 0.752) for 90-day mortality; AUC = 0.675 (95% CI: 0.665; 0.685) for the 1-year composite outcome, respectively], calibration (Brier Score of 0.203 and 0.220; calibration slope of 1.094 and 0.978), and explained variance (R2 = 0.242 and R2 = 0.111). Because of a small case-volume per hospital, applying reliability adjustment to the RSMR led to a great decrease in variability across hospitals [from median (1st quartile, 3rd quartile) 54.2% (44.3%, 65.5%) to 53.2% (50.7%, 55.9%) for 90-day mortality; from 39.2% (27.8%, 51.1%) to 39.9% (39.5%, 40.4%) for the 1-year composite endpoint]. There was no substantial correlation between the two endpoints at hospital level (observed rates: ρ = 0, p = 0.99; RSMR: ρ = 0.017, p = 0.56; reliability-adjusted RSMR: ρ = 0.067; p = 0.026).ConclusionQuality assurance and epidemiological surveillance of sepsis care should include indicators of long-term mortality and morbidity. Claims-based risk-adjustment models for quality indicators of acute sepsis care showed satisfactory predictive validity. To increase reliability of measurement, data sources should cover the full population and hospitals need to improve ICD-10-coding of sepsis.
Radiomics to predict the mortality of patients with rheumatoid arthritis-associated interstitial lung disease: A proof-of-concept study
Authors: Venerito Vincenzo , Manfredi Andreina , Lopalco Giuseppe , Lavista Marlea , Cassone Giulia , Scardapane Arnaldo , Sebastiani Marco , Iannone Florenzo 
Published: January 2023

ObjectivesPatients with rheumatoid arthritis (RA) and interstitial lung disease (ILD) have increased mortality compared to the general population and factors capable of predicting RA-ILD long-term clinical outcomes are lacking. In oncology, radiomics allows the quantification of tumour phenotype by analysing the characteristics of medical images. Using specific software, it is possible to segment organs on high-resolution computed tomography (HRCT) images and extract many features that may uncover disease characteristics that are not detected by the naked eye. We aimed to investigate whether features from whole lung radiomic analysis of HRCT may alone predict mortality in RA-ILD patients.MethodsHigh-resolution computed tomographies of RA patients from January 2012 to March 2022 were analyzed. The time between the first available HRCT and the last follow-up visit or ILD-related death was recorded. We performed a volumetric analysis in 3D Slicer, automatically segmenting the whole lungs and trachea via the Lung CT Analyzer. A LASSO-Cox model was carried out by considering ILD-related death as the outcome variable and extracting radiomic features as exposure variables.ResultsWe retrieved the HRCTs of 30 RA-ILD patients. The median survival time (interquartile range) was 48 months (36–120 months). Thirteen out of 30 (43.33%) patients died during the observation period. Whole line segmentation was fast and reliable. The model included either the median grey level intensity within the whole lung segmentation [high-resolution (HR) 9.35, 95% CI 1.56–55.86] as a positive predictor of death and the 10th percentile of the number of included voxels (HR 0.20, 95% CI 0.05–0.84), the voxel-based pre-processing information (HR 0.23, 95% CI 0.06–0.82) and the flatness (HR 0.42, 95% CI 0.18–0.98), negatively correlating to mortality. The correlation of grey level values to their respective voxels (HR 1.52 95% CI 0.82–2.83) was also retained as a confounder.ConclusionRadiomic analysis may predict RA-ILD patients’ mortality and may promote HRCT as a digital biomarker regardless of the clinical characteristics of the disease.