bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant fibrosis assessed by liver biopsy among Chinese bariatric surgery patients: A prospective cross-sectional study
Authors: Huang Yongsheng , Dong Shiliang , Wang Cunchuan , Dong Zhiyong , Chen Wenhui 
Published: January 2023

BackgroundFibrosis stages affect clinical prognoses related to nonalcoholic fatty liver disease (NAFLD). However, data on the prevalence and clinical features of significant fibrosis are scarce in Chinese bariatric surgery patients. We aimed to investigate the prevalence of significant fibrosis in bariatric surgery patients and to identify its predictors.MethodsWe prospectively enrolled the patients performing intra-operative liver biopsies during bariatric surgery from a bariatric surgery center in a university hospital between May 2020 and January 2022. Anthropometric characteristics, co-morbidities, laboratory data and pathology reports were collected and analyzed. The performance of non‐invasive models was evaluated.ResultsOf 373 patients, 68.9%% had non-alcoholic steatohepatitis (NASH) and 60.9% exhibited fibrosis. Significant fibrosis was present in 9.1% of patients, advanced fibrosis in 4.0%, and cirrhosis in 1.6%. Multivariate logistic regression showed that increasing age (odds ratio [OR], 1.06; p=0.003), presence of diabetes (OR, 2.62; p=0.019), elevated c- peptide (OR, 1.26; p=0.025) and elevated aspartate aminotransferase (AST) (OR, 1.02; p=0.004) were independent predictors of significant fibrosis. The non-invasive models, AST to Platelet ratio (APRI), Fibrosis‐4 (FIB-4), and Hepamet fibrosis scores (HFS) provided greater accuracy for predicting significant fibrosis, compared to the NAFLD Fibrosis Score (NFS) and BARD score.ConclusionMore than two-thirds of bariatric surgery patients had NASH and the prevalence of significant fibrosis was high. Elevated levels of AST and c- peptide, advanced age and diabetes indicated a higher risk of significant fibrosis. Non-invasive models, APRI, FIB-4 and HFS can be used to identify significant liver fibrosis in bariatric surgery patients.
Forest regeneration pathways in contrasting deforestation patterns of Amazonia
Authors: Alencar Lucas , Escada Maria Isabel Sobral , Camargo José Luís Campana 
Published: January 2023

Secondary vegetation is increasingly recognized as a key element for biodiversity conservation and carbon stocks in human-modified landscapes. Contrasting deforestation patterns should lead to distinct patterns of forest regeneration, but this relationship is yet to be unveiled for long-term studies. Using Landsat data from 1985–2015, we analyzed the surface area, spatial distribution, and age of secondary vegetation in Fishbone and Geometric patterns of deforestation. Additionally, we investigated to which extent secondary vegetation reduces forest patch isolation at the landscape level across time. We found the Fishbone pattern to consistently have more secondary vegetation over time than the Geometric pattern, despite having the same size of the deforested area. However, the Fishbone pattern showed more secondary vegetation area with less than 5 years old, while the Geometric pattern showed more area with secondary vegetation with more than 30 years old. Regarding spatial distribution, we found secondary vegetation to be more spread across the entire landscape at the Fishbone pattern and to consistently reduce forest patch isolation across time. This is congruent with the land use typically found in Geometric (industrial cropping and ranching) and Fishbone (fallow agriculture with small-scale ranching) patterns. These findings indicate that the Fishbone pattern of deforestation produces a more biodiversity-friendly landscape structure than the Geometric pattern. On the other hand, older secondary vegetation found in the Geometric deforestation pattern could indicate more carbon stocked in those landscapes. Future public policies of land use and occupation should consider better landscape planning and management to overcome this duality and create synergies between biodiversity conservation and secondary vegetation carbon stock.
Screening for diagnostic targets in tuberculosis and study on its pathogenic mechanism based on mRNA sequencing technology and miRNA-mRNA-pathway regulatory network
Authors: Yang Yue , Fu Yujuan , Sheng Siyu , Ji Chunlei , Pu Xinyi , Xu Guangyu 
Published: January 2023

PurposeTuberculosis is common infectious diseases, characterized by infectivity, concealment and chronicity, and the early diagnosis is helpful to block the spread of tuberculosis and reduce the resistance of Mycobacterium tuberculosis to anti-tuberculosis drugs. At present, there are obvious limitations in the application of clinical detection methods used for the early diagnosis of tuberculosis. RNA sequencing (RNA-Seq) has become an economical and accurate gene sequencing method for quantifying transcripts and detecting unknown RNA species.MethodsA peripheral blood mRNA sequencing was used to screen the differentially expressed genes between healthy people and tuberculosis patients. A protein-protein interaction (PPI) network of differentially expressed genes was constructed through Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. The potential diagnostic targets of tuberculosis were screened by the calculation of degree, betweenness and closeness in Cytoscape 3.9.1 software. Finally, the functional pathways and the molecular mechanism of tuberculosis were clarified in combination of the prediction results of key gene miRNAs, and by Gene Ontology (GO) enrichment analysis and the Kyoto Encyclopedia Genes and Genomes (KEGG) pathway annotation analysis.Results556 Differential genes of tuberculosis were screened out by mRNA sequencing. Six key genes (AKT1, TP53, EGF, ARF1, CD274 and PRKCZ) were screened as the potential diagnostic targets for tuberculosis by analyzing the PPI regulatory network and using three algorithms. Three pathways related to the pathogenesis of tuberculosis were identified by KEGG pathway analysis, and two key miRNAs (has-miR-150-5p and has-miR-25-3p) that might participate in the pathogenesis of tuberculosis were screened out by constructing a miRNA-mRNA pathway regulatory network.ConclusionSix key genes and two important miRNAs that could regulate them were screened out by mRNA sequencing. The 6 key genes and 2 important miRNAs may participate in the pathogenesis of infection and invasion of Mycobacterium tuberculosis through herpes simplex virus 1 infection, endocytosis and B cell receptor signaling pathways.
AFM negatively regulates the infiltration of monocytes to mediate sepsis-associated acute kidney injury
Authors: Guo Caiyun , Fan Youling , Cheng Jiurong , Deng Yingdong , Zhang Xiangsheng , Chen Yanna , Jing Huan , Li Wenjun , Liu Pei , Xie Jiaqi , Ning Wenjun , Chen Hongtao , Zhou Jun 
Published: January 2023

BackgroundSepsis is organ dysfunction due to the host’s deleterious response to infection, and the kidneys are one of the organs damaged in common sepsis. Sepsis-associated acute kidney injury (SA-AKI) increases the mortality in patients with sepsis. Although a substantial volume of research has improved the prevention and treatment of the disease, SA-SKI is still a significant clinical concern.PurposeAimed to use weighted gene co-expression network analysis (WGCNA) and immunoinfiltration analysis to study SA-AKI-related diagnostic markers and potential therapeutic targets.MethodsImmunoinfiltration analysis was performed on SA-AKI expression datasets from the Gene Expression Synthesis (GEO) database. A weighted gene co-expression network analysis (WGCNA) analysis was performed on immune invasion scores as trait data, and modules associated with immune cells of interest were identified as hub modules. Screening hub geneset in the hub module using protein-protein interaction (PPI) network analysis. The hub gene was identified as a target by intersecting with significantly different genes screened by differential expression analysis and validated using two external datasets. Finally, the correlation between the target gene, SA-AKI, and immune cells was verified experimentally.ResultsGreen modules associated with monocytes were identified using WGCNA and immune infiltration analysis. Differential expression analysis and PPI network analysis identified two hub genes (AFM and GSTA1). Further validation using additional AKI datasets GSE30718 and GSE44925 showed that AFM was significantly downregulated in AKI samples and correlated with the development of AKI. The correlation analysis of hub genes and immune cells showed that AFM was significantly associated with monocyte infiltration and hence, selected as a critical gene. In addition, Gene single-enrichment analysis (GSEA) and PPI analyses results showed that AFM was significantly related to the occurrence and development of SA-AKI.ConclusionsAFM is inversely correlated with the recruitment of monocytes and the release of various inflammatory factors in the kidneys of AKI. AFM can be a potential biomarker and therapeutic target for monocyte infiltration in sepsis-related AKI.
Protective role of colitis in inflammatory arthritis via propionate-producing Bacteroides in the gut
Authors: Shon Hoh-Jeong , Kim Yu-Mi , Kim Kyeong Seog , Choi Jin-Ouk , Cho Sang-Hyun , An Sujin , Park Se-Hyeon , Cho Yong-Joon , Park Joo-Hong , Seo Sang-Uk , Cho Joo-Youn , Kim Wan-Uk , Kim Donghyun 
Published: January 2023

ObjectivesTo investigate whether and how inflammatory disease in the intestine influences the development of arthritis, considering that organ-to-organ communication is associated with many physiological and pathological events.MethodsFirst, mice were given drinking water containing dextran sodium sulfate (DSS) and then subjected to inflammatory arthritis. We compared the phenotypic symptoms between the cohoused and separately-housed mice. Next, donor mice were divided into DSS-treated and untreated groups and then cohoused with recipient mice. Arthritis was then induced in the recipients. The fecal microbiome was analyzed by 16S rRNA amplicon sequencing. We obtained type strains of the candidate bacteria and generated propionate-deficient mutant bacteria. Short-chain fatty acids were measured in the bacterial culture supernatant, serum, feces, and cecum contents using gas chromatography-mass spectrometry. Mice fed with candidate and mutant bacteria were subjected to inflammatory arthritis.ResultsContrary to expectations, the mice treated with DSS exhibited fewer symptoms of inflammatory arthritis. Intriguingly, the gut microbiota contributes, at least in part, to the improvement of colitis-mediated arthritis. Among the altered microorganisms, Bacteroides vulgatus and its higher taxonomic ranks were enriched in the DSS-treated mice. B. vulgatus, B. caccae, and B. thetaiotaomicron exerted anti-arthritic effects. Propionate production deficiency further prevented the protective effect of B. thetaiotaomicron on arthritis.ConclusionsWe suggest a novel relationship between the gut and joints and an important role of the gut microbiota as communicators. Moreover, the propionate-producing Bacteroides species examined in this study may be a potential candidate for developing effective treatments for inflammatory arthritis.
Application of quantitative proteomics to discover biomarkers for tick resistance in cattle
Authors: Raza Ali , Schulz Benjamin L. , Nouwens Amanda , Naseem Muhammad Noman , Kamran Muhammad , Mantilla Valdivieso Emily F. , Kerr Edward D. , Constantinoiu Constantin , Jonsson Nicholas N. , James Peter , Tabor Ala E. 
Published: January 2023

IntroductionBreeding for tick resistance is a sustainable alternative to control cattle ticks due to widespread resistance to acaricidal drugs and the lack of a protective vaccine. The most accurate method used to characterise the phenotype for tick resistance in field studies is the standard tick count, but this is labour-intensive and can be hazardous to the operator. Efficient genetic selection requires reliable phenotyping or biomarker(s) for accurately identifying tick-resistant cattle. Although breed-specific genes associated with tick resistance have been identified, the mechanisms behind tick resistance have not yet been fully characterised.MethodsThis study applied quantitative proteomics to examine the differential abundance of serum and skin proteins using samples from naïve tick-resistant and -susceptible Brangus cattle at two-time points following tick exposure. The proteins were digested into peptides, followed by identification and quantification using sequential window acquisition of all theoretical fragment ion mass spectrometry.ResultsResistant naïve cattle had a suite of proteins associated with immune response, blood coagulation and wound healing that were significantly (adjusted P &lt; 10- 5) more abundant compared with susceptible naïve cattle. These proteins included complement factors (C3, C4, C4a), alpha-1-acid glycoprotein (AGP), beta-2-glycoprotein-1, keratins (KRT1 &amp; KRT3) and fibrinogens (alpha &amp; beta). The mass spectrometry findings were validated by identifying differences in the relative abundance of selected serum proteins with ELISA. The proteins showing a significantly different abundance in resistant cattle following early and prolonged tick exposures (compared to resistant naïve) were associated with immune response, blood coagulation, homeostasis, and wound healing. In contrast, susceptible cattle developed some of these responses only after prolonged tick exposure.DiscussionResistant cattle were able to transmigrate immune-response related proteins towards the tick bite sites, which may prevent tick feeding. Significantly differentially abundant proteins identified in this research in resistant naïve cattle may provide a rapid and efficient protective response to tick infestation. Physical barrier (skin integrity and wound healing) mechanisms and systemic immune responses were key contributors to resistance. Immune response-related proteins such as C4, C4a, AGP and CGN1 (naïve samples), CD14, GC and AGP (post-infestation) should be further investigated as potential biomarkers for tick resistance.
Physiological hypoxia improves growth and functional differentiation of human intestinal epithelial organoids
Authors: Walaas Gunnar Andreas , Gopalakrishnan Shreya , Bakke Ingunn , Skovdahl Helene Kolstad , Flatberg Arnar , Østvik Ann Elisabet , Sandvik Arne Kristian , Bruland Torunn 
Published: January 2023

BackgroundThe epithelium in the colonic mucosa is implicated in the pathophysiology of various diseases, including inflammatory bowel diseases and colorectal cancer. Intestinal epithelial organoids from the colon (colonoids) can be used for disease modeling and personalized drug screening. Colonoids are usually cultured at 18-21% oxygen without accounting for the physiological hypoxia in the colonic epithelium (3% to &lt;1% oxygen). We hypothesize that recapitulating the in vivo physiological oxygen environment (i.e., physioxia) will enhance the translational value of colonoids as pre-clinical models. Here we evaluate whether human colonoids can be established and cultured in physioxia and compare growth, differentiation, and immunological responses at 2% and 20% oxygen.MethodsGrowth from single cells to differentiated colonoids was monitored by brightfield images and evaluated with a linear mixed model. Cell composition was identified by immunofluorescence staining of cell markers and single-cell RNA-sequencing (scRNA-seq). Enrichment analysis was used to identify transcriptomic differences within cell populations. Pro-inflammatory stimuli induced chemokines and Neutrophil gelatinase-associated lipocalin (NGAL) release were analyzed by Multiplex profiling and ELISA. Direct response to a lower oxygen level was analyzed by enrichment analysis of bulk RNA sequencing data.ResultsColonoids established in a 2% oxygen environment acquired a significantly larger cell mass compared to a 20% oxygen environment. No differences in expression of cell markers for cells with proliferation potential (KI67 positive), goblet cells (MUC2 positive), absorptive cells (MUC2 negative, CK20 positive) and enteroendocrine cells (CGA positive) were found between colonoids cultured in 2% and 20% oxygen. However, the scRNA-seq analysis identified differences in the transcriptome within stem-, progenitor- and differentiated cell clusters. Both colonoids grown at 2% and 20% oxygen secreted CXCL2, CXCL5, CXCL10, CXCL12, CX3CL1 and CCL25, and NGAL upon TNF + poly(I:C) treatment, but there appeared to be a tendency towards lower pro-inflammatory response in 2% oxygen. Reducing the oxygen environment from 20% to 2% in differentiated colonoids altered the expression of genes related to differentiation, metabolism, mucus lining, and immune networks.ConclusionsOur results suggest that colonoids studies can and should be performed in physioxia when the resemblance to in vivo conditions is important.
Identification of a novel immune-related gene signature for prognosis and the tumor microenvironment in patients with uveal melanoma combining single-cell and bulk sequencing data
Authors: Wang Wanpeng , Zhao Han , Wang Sha 
Published: January 2023

IntroductionUveal melanoma (UVM) is the most invasive intraocular malignancy in adults with a poor prognosis. Growing evidence revealed that immune-related gene is related to tumorigenesis and prognosis. This study aimed to construct an immune-related prognostic signature for UVM and clarify the molecular and immune classification.MethodsBased on The Cancer Genome Atlas (TCGA) database, single-sample gene set enrichment (ssGSEA) and hierarchical clustering analysis were performed to identify the immune infiltration pattern of UVM and classify patients into two immunity clusters. Then, we proposed univariate and multivariate Cox regression analysis to identify immune-related genes that related to overall survival (OS) and validated in the Gene Expression Omnibus (GEO) external validation cohort. The molecular and immune classification in the immune-related gene prognostic signature defined subgroups were analyzed.ResultsThe immune-related gene prognostic signature was constructed based on S100A13, MMP9, and SEMA3B genes. The prognostic value of this risk model was validated in three bulk RNA sequencing datasets and one single-cell sequencing dataset. Patients in the low-risk group had better OS than those in the high-risk group. The receiver-operating characteristic (ROC) analysis revealed its strong predictive ability for UVM patients. Lower expression of immune checkpoint genes was presented in the low-risk group. Functional studies showed that S100A13 knockdown via siRNA inhibited UVM cell proliferation, migration, and invasion in vitro, with the increased expression of reactive oxygen species (ROS) related markers in UVM cell lines.DiscussionThe immune-related gene prognostic signature is an independent predictive factor for the survival of patients with UVM and provides new information about cancer immunotherapy in UVM.
Performance characteristics optimization of CRDI engine fuelled with a blend of sesame oil methyl ester and diesel fuel using response surface methodology approach
Authors: Kumar Manish , Gautam Raghvendra , Ansari Naushad Ahmad 
Published: January 2023

The primary aim of this experiment was to use response surface methodology (RSM) to optimize engine operating parameters for optimal performance and emission characteristics of a common rail direct injection (CRDI) diesel engine fuelled with sesame oil methyl ester (SOME)/diesel blends. The experiments were carried out on a water-cooled common rail direct injection engine with a 4-stroke, single-cylinder connected to an eddy current dynamometer. As input variables, the SOME% (0%–20%), fuel injection pressure (FIP) (500–600 bar), EGR rates (0%–14%), and engine load (0–12 kg) were used. The optimization method is utilized to maximize brake thermal efficiency (BTE) while minimizing BSFC, CO, HC, and NOx emissions. Experimental research data were used to create the RSM model through DoE (Design of experiments). The most relevant factors impacting the responses were identified using an ANOVA analysis. According to the optimization findings, the engine’s optimum working parameters were found to be a 20% SOME ratio, 577.5 bar FIP, 5.26% EGR rates, and 5.12 kg engine load. Under these operating circumstances, the optimal responses were determined to be 18.92% BTE, 0.3705 kg/kWh BSFC, 0.03190% vol. CO, 13 ppm HC, and 447.5 ppm NOx emission. At the same time, R2 values were 96.35%, 87.54%, 91.57%, 95.87%, and 93.73% for BTE, BSFC, CO, HC, and NOx respectively.
Tubridge flow diverter for the treatment of small and medium aneurysms
Authors: Xie Dajiang , Yang Heng , Zhao Li , Ye Xin , Yang Shuxu , Gao Chao , Tian Yanlong , Ni Wei , Gu Yuxiang 
Published: January 2023

BackgroundTubridge flow diverter is a widely used device aimed at reconstructing parent arteries and occluding complex aneurysms in China. The experience of Tubridge in treating small and medium aneurysms is still limited. In this study, we aimed to evaluate the safety and efficacy of the Tubridge flow diverter for the treatment of the two types of aneurysms.MethodsWe reviewed the clinical records of aneurysms treated with a Tubridge flow diverter between 2018 and 2021 in a national cerebrovascular disease center. Cases were divided into small and medium aneurysms according to aneurysm size. The therapeutic process, occlusion rate, and clinical outcome were compared.ResultsIn total, 57 patients and 77 aneurysms were identified. The patients were divided into two groups: small aneurysms (39 patients, 54 aneurysms) and medium aneurysms (18 patients, 23 aneurysms). There were 19 patients with tandem aneurysms (a total of 39 aneurysms) in the two groups, among which 15 patients (30 aneurysms) were in the small aneurysm group and four patients (nine aneurysms) were in the medium aneurysm group. The results show that the mean maximal diameter/neck in the small and medium aneurysms was 3.68/3.25 and 7.61/6.24 mm, respectively. In total, 57 Tubridge flow diverters were successfully implanted without unfolding failure, and there were six patients with new mild cerebral infarction in the small aneurysm group. The complete occlusion rate on the last angiographic follow-up was achieved in 88.46% of the small aneurysms group and 81.82% of the medium aneurysms group. The complete occlusion rate of patients with tandem aneurysms in the last angiographic follow-up was 86.67% (13/15) of the small aneurysms group and 50% (2/4) of the medium aneurysm group. Intracranial hemorrhage was nonencountered in the two groups.ConclusionOur preliminary experience suggests that the Tubridge flow diverter might be a safe and effective treatment for small and medium aneurysms along the internal carotid artery. Long stents may increase the risk of cerebral infarction. Adequate evidence is required to clarify the definite indications and complications in a multicenter randomized controlled trial with a long-term follow-up.