bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of extreme debris flow-induced paleodamming events on the sedimentological evolution of the middle Yarlung Tsangpo River reaches since the late Pleistocene, Tibet
Authors: Wang Huiying , Wang Ping , Hu Gang , Yuan Renmao , Ge Yukui , Xu Bo , Shi Lingfan 
Published: January 2023

As extreme surface processes, long-term river damming and outburst events can impact sediment supply and transportation in valleys and therefore significantly change the landscape. Lacustrine sediments were identified in the wide Xigaze Valley, in the middle reaches of the Yarlung Tsangpo River in Tibet, an area which has been considered to have been a paleodammed lake. However, the evolutionary process and damming mechanisms associated with this paleolake, and any subsequent impact on sedimentation within the valley, remain unclear. Here, we present a detailed geomorphological and sedimentary analysis of the proposed paleolake area, based on a study of a prominent valley fill found along a section of the Yarlung Tsangpo River and its tributary that flows into it from the south, the Menchu River. This section stretches from Xigaze to Dazhuka. Sedimentary facies analysis of two stratigraphic sections in Renbu Town showed that at least two paleolakes caused by debris flow related to glaciers developed in the Xigaze Valley and that the paleodam was located near the outlet of the Dazhuka Gorge. Chronological constraints suggest that the first damming event occurred between ∼48.6 and 33.7 ka in Marine Isotope Stage (MIS) 3 and had a minimum lake surface elevation of ∼3,820 m. The second damming occurred between ∼24.3 and 12.7 ka during the Last Glacial Maximum (LGM), producing a lake surface elevation of at least ∼3,760 m. During the development of the paleolakes in the Xigaze Valley, several small-scale damming and outburst events happened in the upper and middle reaches of the Menchu River, resulting in fluviolacustrine and outburst flood sediments accumulating in the main stream of the Yarlung Tsangpo River and forming thick-fill terraces. We presumed that the paleolakes in the middle reaches of the Yarlung Tsangpo River gradually drained as a result of continuous overflow undercutting instead of outburst flood events, thereby allowing fluvial aggradation of the upper reaches of the paleodam.
Warming increases the relative change in the turnover rate of decadally cycling soil carbon in microbial biomass carbon and soil respiration
Authors: Liu Dan , Zhang Wenling , Xiong Chunmei , Nie Qingyu 
Published: January 2023

Decadally cycling soil carbon (dSOC) is the main component of the terrestrial soil carbon (C) pool. The response of dSOC to warming largely determines the feedback between climate warming and the C cycle. However, there is a lack of investigations about the effect of warming on the relative change in turnover rate (RCT) of dSOC and annually cycling SOC (aSOC) in dissolved organic carbon (DOC), microbial biomass carbon (MBC) and CO2. We clarified this issue by incubating two C3-C4 vegetation switch soils (23 years switch, HA soil and 55 years switch, GG soil) at 20°C and 30°C in the recently improved continuous airflow CO2 trapping system for 1 year. Warming increased the contribution of dSOC (C3-C) by 21℅ (soil HA) and 8℅ (soil GG) in MBC, and 38℅ (soil HA) and 15℅ (soil GG) in CO2, while only 2%–3℅ increase in DOC at the final stage of the incubation. Furthermore, warming increased the RCT in MBC and CO2 by 5.3- and 4.1-fold, respectively, but had no significant influence on the RCT in DOC, indicating that soil microbes may be an important engine to accelerate dSOC-derived CO2 emission in a warming world.
Study on the influence of confining pressure and unloading damage on the bursting liability characteristics of coal
Authors: Du Taotao , Pan Junfeng , Xia Yongxue , Sun Ruda 
Published: January 2023

The research on the bursting liability of coal under confining pressure and unloading damage is critical in creating prevention mechanisms for coal mass rock bursts in deep underground mines. Cyclic loading and unloading tests of variable stress with a lower limit were performed under multistage confining pressure and different amplitude unloading to explore their influence on the impact tendency of the coal bodies. Meanwhile, the characteristic parameter analysis of acoustic emissions was used to evaluate the failure. The results revealed that the accumulated number and energy of acoustic emission events gradually decreased with increasing the confining pressure. The coal specimen became denser, and the failure mode gradually transitioned from brittle to ductile. With the increase in unloading amplitude, the cumulative number of acoustic emission events in the coal specimens decreases, the damage degree to the coal body increases, the peak load decreases, and the failure mode transitions from ductile to brittle. The increase in confining pressure results in an increase in the input energy and the elastic strain energy, while the increase in the unloading range of the coal body leads to a decrease in the input energy and elastic strain energy. In addition, after the confining pressures of 3 MPa, 6 MPa, and 9 MPa, the residual elastic energy index of the coal specimens increases by 21.76%, 42.92%, and 71.69%, respectively, compared with the room pressure conditions. The residual elastic energy index decreases by 21.11% and 55.38% for the unloading amplitude of 3 MPa and 6 MPa, respectively, compared with the unloaded coal specimen, indicating that the impact tendency of the coal body is enhanced by the confining pressure conditions.
Local symptoms of Hashimoto’s thyroiditis: A systematic review
Authors: Yuan Jiaojiao , Qi Shuo , Zhang Xufan , Lai Hezheng , Li Xinyi , Xiaoheng Chen , Li Zhe , Yao Simiao , Ding Zhiguo 
Published: January 2023

ObjectiveHashimoto’s thyroiditis (HT) is the most common type of thyroid disease and can cause many different manifestations. The local symptoms of HT are an under-studied area of research. Therefore, the purpose of this study was to investigate the local symptoms of HT and their prevalence.MethodsA systematic review was performed to find articles in PubMed that discuss the local symptoms of HT. Relevant vocabulary terms and key terms included: autoimmune thyroid disease (AITD), hyperthyroidism, hypothyroidism, neck, throat, pharynx, airway, esophagus, breathe, swallow, globus, sleep apnea, symptoms, and quality of life. Two investigators independently screened the eligible studies.ResultsA total of 54 articles fulfilled the inclusion criteria. Of these, 25 were clinical studies, 24 were case reports, and five were reviews. These clinical studies and case reports included a total of 2660 HT patients. There were eight local symptoms related to HT: neck pain (0.02%~16%), voice changes (7%~30%), throat discomfort (20%~43.7%), shortness of breath (28%~50%), dysphagia (29%), goiter-related symptoms (69.44%), sleep apnea, and generally defined compressive symptoms. Due to the use of different outcome measures among all the studies, a meta-analysis of the data could not be performed.ConclusionGoiter symptoms, which are an item on the ThyPRO scales, are the most frequent local symptoms in HT patients, and include neck pain, voice changes, throat discomfort, and dysphagia. These local symptoms should be identified in the clinic and included in the early diagnosis and management of HT, as well as evaluated further to understand their relevance in the pathogenesis of HT.
The effect of Kuntai capsule on ovarian function in cisplatin-induced premature ovarian insufficiency rats
Authors: Luo Suiyu , Ruan Xiangyan , Mueck Alfred O. 
Published: January 2023

ObjectiveThis study aims to evaluate the effect of Kuntai capsule on ovarian function in cisplatin-induced premature ovarian insufficiency rats and to explore the mechanism of Kuntai capsule on the ovarian function of rats.MethodsSeventy-four female Sprague-Dawley rats were used for this study. Eight of the rats were randomly assigned to the Control group. The remaining sixty-six rats were utilized to establish the POI model via Cisplatin and then randomly divided into four groups: the model Control group, the Estradiol group, and groups treated with low and high doses of Kuntai capsule. For the 28-day administration, the Control and model Control groups were intragastrically administered with 2.0 mL of 0.9% sodium chloride daily, the Estradiol group with 2.0 mL of Estradiol suspension (0.2mg/kg/d), and the low dose Kuntai capsule group and the high dose Kuntai capsule group with 2.0 mL of Kuntai capsule suspension (0.6g/kg/d, 1.8g/kg/d, respectively). Sex hormone levels, estrous cycle, and ovarian coefficient of the five groups were compared, histological sections analyzed follicle counts, and the protein expressions of growth differentiation factor 9, light chain 3 A-II, and Beclin 1 in the ovarian tissue were detected by Western blotting.ResultsAfter the 28-day administration, the serum Estradiol and Follicle-Stimulating Hormone levels of the group treated with low dose of Kuntai capsule were not significantly different from the Control group, the serum anti-Müllerian Hormone level of the group treated with high dose of Kuntai capsule was significantly higher than the Estradiol group. The estrous cycle of the group treated with low dose of Kuntai capsule was significantly lower than the model Control group. Regarding ovarian coefficient, resting and growing follicles, growth differentiation factor 9, light chain 3 A-II, and Beclin 1 expression, both Kuntai capsule groups outperformed the model Control group with the statistical difference (P&lt;0.05).ConclusionKuntai capsule can improve the estrous cycle and ovarian coefficient of rats with premature ovarian insufficiency, maintain the number of resting and growing follicles, and up-regulate the protein expression of growth differentiation factor 9, light chain 3 A-II, and Beclin 1 of rats’ ovaries.
Impact of metabolic control on all-cause mortality in a nationwide cohort of patients with diabetes from Colombia
Authors: Mendivil Carlos O. , Amaya-Montoya Mateo , Hernández-Vargas Juliana Alexandra , Ramírez-García Nathaly , Herrera-Parra Lina Johana , Guatibonza-García Valentina , Romero-Díaz Camila , Pérez-Londoño Agustín , Acuña-Merchán Lizbeth 
Published: January 2023

ObjectiveThe magnitude of the mortality benefit conferred by good integral metabolic control in diabetes in not sufficiently known, especially among Latin American patients. We prospectively studied the association between sustained control of blood glucose (HbA1c&lt;7%), systolic blood pressure (SBP) (&lt;130 mmHg) and LDL (LDLc, &lt;100mg/dL) and non-HDL (non-HDLc, &lt;130 mg/dL) cholesterol, and death from any cause among all adult patients with diagnosed diabetes in Colombia.MethodsWe retrospectively analyzed data from a nationwide, centralized, mandatory registry of all patients with diagnosed diabetes assisted by the Colombian health system between July 1, 2015, and June 30, 2019. We estimated the associations of sustained achievement of each goal, and of the joint triple goal (HbA1c + SBP + LDLc) with all-cause death. Associations were assessed after adjustment for sex, age, race, insurance type and BMI in multivariable logistic models.ResultsWe studied 1 352 846 people with diabetes. Sustained SBP (OR 0.42 [0.41-0.43]), HbA1c (OR 0.25 [0.24-0.26]) and LDLc (OR 0.28 [0.27-0.29]) control had strong negative associations with death. Moreover, among the 5.4% of participants who achieved joint, sustained metabolic control, the OR for death was 0.19 (0.18-0.21). Importantly, the impact of sustained, joint metabolic control was significantly smaller for patients of black race compared to other races (OR 0.31 [0.23-0.43] versus 0.18 [0.17-0.20], p-value for interaction &lt;0.001), mostly at the expense of a smaller impact of LDLc control. The results were similar across body-mass index categories.ConclusionsSustained and simultaneous metabolic control was associated with remarkably lower odds of death.
Elafin is related to immune infiltration and could predict the poor prognosis in ovarian cancer
Authors: Lu Weiyu , Xie Biao , Tan Guangqing , Dai Wanying , Ren Jingyi , Pervaz Sadaf , Li Kun , Li Fangfang , Wang Yingxiong , Wang Meijiao 
Published: January 2023

BackgroundOvarian cancer (OC) is the most lethal gynecologic malignancy, yet the clinical results for OC patients are still variable. Therefore, we examined how elafin expression affects the patients’ prognoses and immunotherapy responses in OC, which may facilitate treatment selection and improve prognosis.MethodsThe elafin mRNA expression profile was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus. Elafin’s prognostic potential and its relationship with clinical variables were investigated using Kaplan–Meier survival curves, time-dependent receiver operating characteristic curves as well as univariate and multivariate Cox regression models. As validation, protein expression in the tumor and adjacent tissues of OC patients was investigated by using immunohistochemistry (IHC). Comprehensive analyses were then conducted to explore the correlation between immune infiltration and elafin expression.ResultsA higher mRNA expression of elafin was associated with an unfavorable prognosis in TCGA cohort and was validated in GSE31245 and IHC. Moreover, elafin was indicated as an independent risk factor for OC. A significantly higher protein expression of elafin was detected in the adjacent tissues of OC patients with shorter overall survival (OS). The immune-related pathways were mainly enriched in the high-elafin-mRNA-expression group. However, the mRNA expression of elafin was favorably correlated with indicators of the immune filtration and immunotherapy response, which also proved better immunotherapy outcomes.ConclusionThe high elafin expression was associated with an unfavorable OS, while it also indicated better immunotherapy responses. Thus, the detection of elafin is beneficial to diagnosis and treatment selection.
The association of BTLA gene polymorphisms with non-small lung cancer risk in smokers and never-smokers
Authors: Andrzejczak Anna , Partyka Anna , Wiśniewski Andrzej , Porębska Irena , Pawełczyk Konrad , Ptaszkowski Kuba , Kuśnierczyk Piotr , Jasek Monika , Karabon Lidia 
Published: January 2023

IntroductionLung cancer is the predominant cause of death among cancer patients and non-small cell lung cancer (NSCLC) is the most common type. Cigarette smoking is the prevailing risk factor for NSCLC, nevertheless, this cancer is also diagnosed in never-smokers. B and T lymphocyte attenuator (BTLA) belongs to immunological checkpoints which are key regulatory molecules of the immune response. A growing body of evidence highlights the important role of BTLA in cancer. In our previous studies, we showed a significant association between BTLA gene variants and susceptibility to chronic lymphoblastic leukemia and renal cell carcinoma in the Polish population. The present study aimed to analyze the impact of BTLA polymorphic variants on the susceptibility to NSCLC and NSCLC patients’ overall survival (OS).MethodsUsing TaqMan probes we genotyped seven BTLA single-nucleotide polymorphisms (SNPs): rs2705511, rs1982809, rs9288952, rs9288953, rs1844089, rs11921669 and rs2633582 with the use of ViiA 7 Real-Time PCR System.ResultsWe found that rs1982809 within BTLA is associated with NSCLC risk, where carriers of rs1982809G allele (AG+GG genotypes) were more frequent in patients compared to controls. In subgroup analyses, we also noticed that rs1982809G carriers are significantly overrepresented in never-smokers, but not in smokers compared to controls. Additionally, the global distribution of the haplotypes differed between the never-smokers and smokers, where haplotypes A G G C A, C G A C G, and C G A T G were more frequent in never-smoking patients. Furthermore, the presence rs1982809G (AG+GG genotypes) allele as well as the presence of rs9288953T allele (CT+TT genotypes) increased NSCLC risk in females’ patients. After stratification by histological type, we noticed that rs1982809G and rs2705511C carriers were more frequent among adenocarcinoma patients. Moreover, rs1982809G and rs2705511C correlated with the more advanced stages of NSCLC (stage II and III), but not with stage IV. Furthermore, we showed that rs2705511 and rs1982809 significantly modified OS, while rs9288952 tend to be associated with patients’ survival.ConclusionOur results indicate that BTLA polymorphic variants may be considered low penetrating risk factors for NSCLC especially in never-smokers, and in females, and are associated with OS of NSCLC patients.
The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies
Authors: Goll Johannes B. , Bosinger Steven E. , Jensen Travis L. , Walum Hasse , Grimes Tyler , Tharp Gregory K. , Natrajan Muktha S. , Blazevic Azra , Head Richard D. , Gelber Casey E. , Steenbergen Kristen J. , Patel Nirav B. , Sanz Patrick , Rouphael Nadine G. , Anderson Evan J. , Mulligan Mark J. , Hoft Daniel F. 
Published: January 2023

IntroductionOver the last decade, the field of systems vaccinology has emerged, in which high throughput transcriptomics and other omics assays are used to probe changes of the innate and adaptive immune system in response to vaccination. The goal of this study was to benchmark key technical and analytical parameters of RNA sequencing (RNA-seq) in the context of a multi-site, double-blind randomized vaccine clinical trial.MethodsWe collected longitudinal peripheral blood mononuclear cell (PBMC) samples from 10 subjects before and after vaccination with a live attenuated Francisella tularensis vaccine and performed RNA-Seq at two different sites using aliquots from the same sample to generate two replicate datasets (5 time points for 50 samples each). We evaluated the impact of (i) filtering lowly-expressed genes, (ii) using external RNA controls, (iii) fold change and false discovery rate (FDR) filtering, (iv) read length, and (v) sequencing depth on differential expressed genes (DEGs) concordance between replicate datasets. Using synthetic mRNA spike-ins, we developed a method for empirically establishing minimal read-count thresholds for maintaining fold change accuracy on a per-experiment basis. We defined a reference PBMC transcriptome by pooling sequence data and established the impact of sequencing depth and gene filtering on transcriptome representation. Lastly, we modeled statistical power to detect DEGs for a range of sample sizes, effect sizes, and sequencing depths.Results and DiscussionOur results showed that (i) filtering lowly-expressed genes is recommended to improve fold-change accuracy and inter-site agreement, if possible guided by mRNA spike-ins (ii) read length did not have a major impact on DEG detection, (iii) applying fold-change cutoffs for DEG detection reduced inter-set agreement and should be used with caution, if at all, (iv) reduction in sequencing depth had a minimal impact on statistical power but reduced the identifiable fraction of the PBMC transcriptome, (v) after sample size, effect size (i.e. the magnitude of fold change) was the most important driver of statistical power to detect DEG. The results from this study provide RNA sequencing benchmarks and guidelines for planning future similar vaccine studies.
A nomogram based on HBeAg, AST, and age to predict non-minimal liver inflammation in CHB patients with ALT <80 U/L
Authors: Zhang Lu , Bi Xiaoyue , Chen Xiaoxue , Zhang Luxue , Xiong Qiqiu , Cao Weihua , Lin Yanjie , Yang Liu , Jiang Tingting , Deng Wen , Wang Shiyu , Wu Shuling , Liu Ruyu , Gao Yuanjiao , Shen Ge , Chang Min , Hao Hongxiao , Xu Mengjiao , Hu Leiping , Lu Yao , Li Minghui , Xie Yao 
Published: January 2023

ObjectivePrecise assessment of liver inflammation in untreated hepatitis B e antigen (HBeAg)-positive patients with chronic hepatitis B virus (HBV) infection can determine when to initiate antiviral therapy. The aim of this study was to develop and validate a nomogram model for the prediction of non-minimal liver inflammation based on liver pathological injuries combined with age and alanine aminotransferase (ALT), aspartate aminotransferase (AST), hepatitis B surface antigen (HBsAg), HBeAg, and HBV DNA quantification.MethodsWe retrospectively included 735 HBeAg-positive chronic hepatitis B (CHB) patients with ALT &lt; 80 U/L as the primary cohort and prospectively enrolled 196 patients as the validation cohort. Multivariate logistic regression analysis identified independent impact factors. A nomogram to predict significant liver inflammation was developed and validated.ResultsMultivariate logistic regression analysis showed that HBeAg, AST, and age were independent risk factors for predicting non-minimal liver inflammation in untreated CHB patients. The final formula for predicting non-minimal liver inflammation was Logit(P) = −1.99 − 0.68 × Log10HBeAg + 0.04 × Age + 0.06 × AST. A nomogram for the prediction of non-minimal liver inflammation was established based on the results from the multivariate analysis. The predicted probability of the model being consistent with the actual probability was validated by the calibration curves, showing the best agreement in both the primary and validation cohorts. The C-index was 0.767 (95%CI = 0.734–0.802) in the primary cohort and 0.749 (95%CI = 0.681–0.817) in the prospective validation cohort.ConclusionsThe nomogram based on HBeAg, AST, and age might help predict non-minimal liver inflammation in HBeAg-positive CHB patients with ALT &lt; 80 U/L, which is practical and easy to use for clinicians.
Identification of gene signatures associated with ulcerative colitis and the association with immune infiltrates in colon cancer
Authors: Pan Zhaoji , Lin Hao , Fu Yanyan , Zeng Fanpeng , Gu Feng , Niu Guoping , Fang Jian , Gu Bing 
Published: January 2023

BackgroundInflammatory bowel diseases, including ulcerative colitis (UC) and Crohn’s disease, are some of the most common inflammatory disorders of the gastrointestinal tract. The dysfunction of the immune system in the intestines is suggested to be the underlying cause of the pathogenesis of UC. However, the mechanisms regulating these dysfunctional immune cells and inflammatory phenotypes are still unclear.MethodsThe differential expression analysis on microarray datasets were performed including GSE24287, GSE87466, GSE102133, and GSE107499, including 376 samples. “Gene Ontology” and “Kyoto Encyclopedia of Genes and Genomes” pathway enrichment analyses were conducted to identify the common differentially expressed genes (DEGs) in these datasets and explore their underlying biological mechanisms. Further algorithms like “Cell-type Identification by Estimating Relative Subsets of RNA Transcripts” were used to determine the infiltration status of immune cells in patients with UC. “Cytoscape” and “Gene Set Enrichment Analysis” were used to screen for hub genes and to investigate their biological mechanisms. The Tumor Immune Estimation Resource database was used to study the correlation between hub genes and infiltrating immune cells in patients with UC. A total of three hub genes, CCL3, MMP3, and TIMP1, were identified using Cytoscape.ResultsA positive correlation was observed between these hub genes and patients with active UC. These genes served as a biomarker for active UC. Moreover, a decrease in CCL3, MMP3, and TIMP1 expression was observed in the mucosa of the intestine of patients with active UC who responded to Golimumab therapy. In addition, results show a significant positive correlation between CCL3, MMP3, and TIMP1 expression and different immune cell types including dendritic cells, macrophages, CD8+ T cells, and neutrophils in patients with colon cancer. Moreover, CCL3, MMP3, and TIMP1 expression were strongly correlated with different immune cell markers.ConclusionStudy results show the involvement of hub genes like CCL3, MMP3, and TIMP1 in the pathogenesis of UC. These genes could serve as a novel pharmacological regulator of UC. These could be used as a therapeutic target for treating patients with UC and may serve as biomarkers for immune cell infiltration in colon cancer.