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Pretreating and normalizing metabolomics data for statistical analysis

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Genes & Diseases 2024年第3期11卷 188-205页

作者： Jun Sun Yinglin Xia division of gastroenterology and hepatology Department of MedicineDepartment of Microbiology/ImmunologyUIC Cancer CenterUniversity of Illinois ChicagoJesse Brown VA Medical Center Chicago(537)ChicagoIL 60612USA division of gastroenterology and hepatology Department of MedicineUniversity of Illinois ChicagoChicagoIL 60612USA

Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological *** is emerging as a powerful tool generally for pre-cision ***,integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and ***,metabo-lomics data are very ***/pretreating and normalizing procedures on metabolomics data are usually required before statistical *** this review article,we comprehensively review various methods that are used to preprocess and pretreat metabolo-mics data,including MS-based data and NMR-based data preprocessing,dealing with zero and/or missing values and detecting outliers,data normalization,data centering and scaling,data *** discuss the advantages and limitations of each *** choice for a suitable preprocessing method is determined by the biological hypothesis,the characteristics of the data set,and the selected statistical data analysis *** then provide the perspective of their applications in the microbiome and metabolome research.

关键词： Data centering and scaling Data normalization Data transformation Missing values MS-Baseddata preprocessing NMRData preprocessing Outliers Preprocessing/pretreatment

Hepatic recompensation according to Baveno VII criteria via transjugular intrahepatic portosystemic shunt

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World Journal of gastroenterology 2024年第12期30卷 1777-1779页

作者： Hossam Eldin Shaaban Abeer Abdellatef Hussein Hassan Okasha Department of Internal Medicine and gastroenterology NHTMRICairo 11796Egypt Department of Internal Medicine Division of Gastroenterology and HepatologyKasr Al-Aini School of MedicineCairo UniversityCairo 11562Egypt

Transjugular intrahepatic portosystemic shunt is a therapeutic modality done through interventional *** is aimed to decrease portal pressure in special situations for patients with decompensated liver disease with portal *** represents a potential addition to the therapeutic modalities that could achieve hepatic recompensation in those patients based on Baveno VII criteria.

关键词： Decompensated liver cirrhosis Hepatic recompensation Baveno VII Portal hypertension

Bowel function and inflammation: Is motility the other side of the coin?

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World Journal of gastroenterology 2024年第14期30卷 1963-1967页

作者： Alba Panarese division of gastroenterology and Digestive Endoscopy Department of Medical SciencesCentral Hospital-Azienda OspedalieraTaranto 74123Italy

Digestion and intestinal absorption allow the body to sustain itself and are the emblematic functions of the *** the flip side,functions also arise from its role as an interface with the ***,the gut houses microorganisms,collectively known as the gut microbiota,which interact with the host,and is the site of complex immune *** role in human pathology is complex and scientific evidence is progressively elucidating the functions of the gut,especially regarding the pathogenesis of chronic intestinal diseases and inflammatory conditions affecting various organs and *** editorial aims to highlight and relate the factors involved in the pathogenesis of intestinal and systemic inflammation.

关键词： Motility Inflammation Pathogenesis Vitamin D Microbiota Gut Chronic intestinal pseudo-obstruction

Exploiting open source omics data to advance pancreas research

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胰腺病学杂志(英文) 2024年第1期7卷 21-27页

作者： Swaminathan Gayathri Saito Toshie Husain Sohail Z. division of gastroenterology Hepatology and Nutrition Department of Pediatrics Stanford University School of Medicine Stanford CA

The "omics" revolution has transformed the biomedical research landscape by equipping scientists with the ability to interrogate complex biological phenomenon and disease processes at an unprecedented level. The volume of "big" data generated by the different omics studies such as genomics, transcriptomics, proteomics, and metabolomics has led to the concurrent development of computational tools to enable in silico analysis and aid data deconvolution. Considering the intensive resources and high costs required to generate and analyze big data, there has been centralized, collaborative efforts to make the data and analysis tools freely available as "Open Source," to benefit the wider research community. Pancreatology research studies have contributed to this "big data rush" and have additionally benefitted from utilizing the open source data as evidenced by the increasing number of new research findings and publications that stem from such data. In this review, we briefly introduce the evolution of open source omics data, data types, the "FAIR" guiding principles for data management and reuse, and centralized platforms that enable free and fair data accessibility, availability, and provide tools for omics data analysis. We illustrate, through the case study of our own experience in mining pancreatitis omics data, the power of repurposing open source data to answer translationally relevant questions in pancreas research.

关键词： Gene expression Omics Open source data Pancreatitis

Advancements in hemostatic strategies for managing upper gastrointestinal bleeding: A comprehensive review

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World Journal of gastroenterology 2024年第15期30卷 2087-2090页

作者： Ah Young Lee Joo Young Cho division of gastroenterology Department of Internal MedicineCha Gangnam Medical CenterCha University College of MedicineSeoul 06135Korea

Upper gastrointestinal(GI)hemorrhage presents a substantial clinical *** management typically involves resuscitation and endoscopy within 24 h,although the benefit of very early endoscopy(<12 h)for high-risk patients is *** goals include stopping acute bleeding,preventing rebleeding,and using a multimodal approach encompassing endoscopic,pharmacological,angiographic,and surgical *** agents such as vasopressin,prostaglandins,and proton pump inhibitors are effective,but the increase in antithrombotic use has increased GI bleeding *** hemostasis,particularly for nonvariceal bleeding,employs techniques such as electrocoagu-lation and heater probes,with concerns over tissue injury from monopolar *** methods such as Hemospray and Endoclot show promise in creating mechanical tamponades but have ***,the first-line therapy includes thermal probes and hemoclips,with over-the-scope clips emerging for larger ulcer *** gold probe,combining bipolar electrocoagulation and injection,offers targeted coagulation but has faced device-related *** advancements involve combining techniques and improving endoscopic imaging,with studies exploring combined approaches showing *** research is crucial for developing standardized and effective hemorrhage management strategies.

关键词： Upper gastrointestinal bleeding Hemostasis Endoscopy Probe Spray Clip

Interleukin-10 suppresses lipid metabolism-mediated intestinal inflammation

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Life Metabolism 2024年第3期3卷 3-5页

作者： Tristram A.J.Ryan Ivan Zanoni division of Immunology and division of gastroenterology Boston Children’s Hospital and Harvard Medical SchoolBostonMA 02115United States

In a recent paper published in Nature,York et *** that the anti-inflammatory cytokine interleukin(IL)-10 regulates sphingolipid metabolism to limit NF-κB-mediated *** of Il10 in mice,or genetic mutation of IL10 in humans,predisposes to inflammatory bowel disease,which may be overcome by restoring homeostatic sphingolipid metabolism.

关键词： metabolism inflammation al.

Trends in colorectal cancer incidence according to an increase in the number of colonoscopy cases in Korea

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World Journal of Gastrointestinal Oncology 2024年第1期16卷 51-60页

作者： Ga Hee Kim Yeong Chan Lee Tae Jun Kim Sung Noh Hong Dong Kyung Chang Young-Ho Kim Dong-Hoon Yang Chang Mo Moon Kyunga Kim Hyun Gun Kim Eun-Ran Kim division of gastroenterology Department of Internal MedicineAsan Medical CenterUniversity of Ulsan College of MedicineSeoul 05505South Korea Department of Digital Health Samsung Advanced Institute for Health Science and TechnologySungkyunkwan University School of MedicineSeoul 06351South Korea division of gastroenterology Department of Internal MedicineSamsung Medical CenterSungkyunkwan University School of MedicineSeoul 06351South Korea division of gastroenterology Department of Internal MedicineEwha Womans UniversitySeoul 07985South Korea Biomedical Statistics Center Samsung Medical CenterSeoul 06351South Korea division of gastroenterology Department of Internal MedicineSoonchunhyang University College of MedicineSeoul 04401South Korea

BACKGROUND The incidence of colorectal cancer(CRC)and preinvasive CRC(e.g.,early colon cancer and advanced adenoma)is gradually increasing in several *** To evaluate the trend in incidence of CRC and preinvasive CRC according to the increase in the number of colonoscopies performed in *** This retrospective cohort study enrolled Korean patients from 2002 to 2020 to evaluate the incidence of CRC and preinvasive CRC,and assess the numbers of diagnostic colonoscopies and colonoscopic ***-related complications by age group were also *** The incidence of CRC showed a rapid increase,then decreased after 2012 in the 50-75 year-age *** the study period,the rate of incidence of preinvasive CRC increased at a similar level in patients under 50 and 50-75 years of *** 2009,the increase has been rapid,showing a pattern similar to the increase in *** rate of colonoscopic polypectomy in patients aged under 50 was similar to the rate in patients over 75 years of age after *** rate of complications after colonoscopy and related deaths within 3 mo was high for those over 75 years of *** The diagnosis of preinvasive CRC increased with the increase in the number of colonoscopies *** the risk of colonoscopy-related hospitalization and death is high in the elderly,if early lesions at risk of developing CRC are diagnosed and treated under or at the age of 75,colonoscopy-related complications can be reduced for those aged 76 years or over.

关键词： Colorectal cancer Preinvasive colorectal cancer Colorectal polypectomy Colonoscopy

MicroRNAs in hepatocellular carcinoma treatment:Charting the path forward

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World Journal of gastroenterology 2024年第11期30卷 1470-1474页

作者： Hong T Lin Antonio F Alvarez Castaneda Somashekar G Krishna Khalid Mumtaz division of gastroenterology Hepatology and NutritionDepartment of MedicineThe Ohio State University Wexner Medical CenterColumbusOH 43210United States

MicroRNAs(miRNAs)are recognized for their involvement in the regulation of gene expression and exhibit significant potential in both the prognostic assessment and treatment of hepatocellular carcinoma(HCC).HCC,like other tumors,seldom occurs in isolation;instead,it evolves within a microenvironment featuring oncogenic and tumor-suppressive *** combined with suitable delivery vehicles,miRNA technology provides the capability to directly engage with these elements,thereby hindering tumor formation and *** research in this domain holds the promise of enabling a more efficacious and multi-modal treatment approach for HCC in the near future.

关键词： hepatocellular carcinoma Tumor microenvironment MicroRNA Mesenchymal stem cell Exosome

Autophagy in hepatic progenitor cells modulates exosomal miRNAs to inhibit liver fibrosis in schistosomiasis

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Frontiers of Medicine 2024年第3期18卷 538-557页

作者： Yue Yuan Jiaxuan Li Xun Lu Min Chen Huifang Liang Xiao-ping Chen Xin Long Bixiang Zhang Song Gong Xiaowei Huang Jianping Zhao Qian Chen division of gastroenterology Department of Internal Medicine at Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Hepatic Surgery Center Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Hubei Key Laboratory of hepato–Pancreato–Biliary Diseases Wuhan430030China Department of Trauma Surgery Tongji Trauma CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China

Schistosoma infection is one of the major causes of liver *** roles of hepatic progenitor cells(HPCs)in the pathogenesis of liver fibrosis have been ***,the precise mechanism underlying the role of HPCs in liver fibrosis in schistosomiasis remains *** study examined how autophagy in HPCs affects schistosomiasis-induced liver fibrosis by modulating exosomal *** activation of HPCs was verified by immunohistochemistry(IHC)and immunofluorescence(IF)staining in fibrotic liver from patients and mice with Schistosoma japonicum *** coculturing HPCs with hepatic stellate cells(HSCs)and assessing the autophagy level in HPCs by proteomic analysis and in vitro phenotypic assays,we found that impaired autophagy degradation in these activated HPCs was mediated by lysosomal *** autophagy by the autophagy inhibitor chloroquine(CQ)significantly diminished liver fibrosis and granuloma formation in ***-infected ***-secreted extracellular vehicles(EVs)were further isolated and studied by miRNA ***-1306-3p,miR-493-3p,and miR-34a-5p were identified,and their distribution into EVs was inhibited due to impaired autophagy in HPCs,which contributed to suppressing HSC *** conclusion,we showed that the altered autophagy process upon HPC activation may prevent liver fibrosis by modulating exosomal miRNA release and inhibiting HSC activation in *** the autophagy degradation process may be a therapeutic strategy for liver fibrosis during Schistosoma infection.

关键词： schistosomiasis hepatic progenitor cell autophagy extracellular vesicle fibrosis miRNA