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Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

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World Journal of Gastroenterology 2021年第14期27卷 1465-1482页

作者： Sarah A Malik Chencan Zhu Jinyu Li joseph f lacomb Paula I Denoya Igor Kravets Joshua D Miller Jie Yang Melissa Kramer W Richard McCombie Charles E Robertson Daniel N frank Ellen Li Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794United States Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource Stony Brook UniversityStony BrookNY 11794United States Department of Pathology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Surgery Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of family Population and Preventive MedicineStony Brook UniversityStony BrookNY 11794United States Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource Cold Spring HarborNY 11724United States Department of Medicine University of Colorado Anschutz Medical CampusAuroraCO 80045United States

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human ***-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)*** hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk *** To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection *** Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from *** 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on *** sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥*** PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach *** mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level *** confirmed increased fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics *** coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor *** expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race *** Recent adoption of additional preoperative antibiotics as sta

关键词： Colorectal cancer Antibiotics African Continental Ancestry Group Diabetes mellitus 16S rRNA gene RNA-sequencing

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Comparisons of oxbow lake fish assemblages in relation to bigheaded carp establishment in the lower White River, Arkansas

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Ecological Processes 2024年第1期13卷 188-205页

作者： Michael A.Eggleton Cody J.Salzmann joseph E.Kaiser Shannon C.f.Smith Department of Aquaculture and fisheries University of Arkansas at Pine Bluff Arkansas Game and fish Commission Virginia Institute of Marine Science

Background Since the late 1990s, bigheaded carps(largely silver carp [Hypophthalmichthys molitrix] but also bighead carp [H. nobilis]) have established throughout the lower Mississippi River basin. Using previously studied oxbow lakes in the lower White River basin, Arkansas, we compared current(2017, “post-carp” establishment) fish assemblages to historical(2002, “pre-carp” establishment) fish assemblages. fish assemblages were comprehensively assessed using multiple gears, including boat electrofishing, mini-fyke nets, and experimental small-mesh gill *** T-tests suggested that fish assemblage indices of richness, diversity, evenness, and dominance were often greater(P flected by boat electrofishing and experimental gill nets. However, all indices were generally similar(P > 0.05) between the pre-carp and post-carp period with fish assemblages depicted using mini-fyke nets. Nonmetric multidimensional scaling analyses indicated that fish assemblages differed structurally between pre-carp and post-carp periods. Assemblage differences were linked to both small and large abundance changes for more than 20 species. Abundances of gizzard shad(Dorosoma cepedianum), emerald shiner(Notropis atherinoides), pugnose minnow(Opsopoeodus emiliae), crappies(Pomoxis spp.), bluegill(Lepomis macrochirus), orangespotted sunfish(L. humilis), and yellow bass(Morone mississippiensis) declined between the pre-carp and postcarp periods. Conversely, abundances of weed shiner(N. texanus), pallid shiner(Hybopsis amnis), longear sunfish(L. megalotis), buffalofishes(Ictiobus spp.), and gars(Lepisosteus spp.) generally increased during the same *** Although not possible to conclude assemblage shifts were entirely related to bigheaded carps due to the absence of an appropriate reference system where carps did not establish, the wide establishment of these carps is one of the most pervasive changes to have occurred in the lower White

关键词： Bigheaded carp Silver carp Aquatic nuisance species fish assemblage Oxbow lake Large river

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Oxide-supported metal catalysts for anaerobic NAD+regeneration with concurrent hydrogen production

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Chinese Chemical Letters 2024年第2期35卷 263-267页

作者： Jianwei Li joseph W.H.Burnett Claudia Martinez Macias Russell f.Howe Xiaodong Wang Chemical Engineering School of EngineeringLancaster UniversityLancaster LA1 4YWUnited Kingdom Chemistry Department University of AberdeenAberdeen AB24 3UEUnited Kingdom

We report SiO_(2)-supported monometallic Pt,Pd,Au,Ni,Cu and Co catalysts for proton-driven NAD+regeneration,co-producing H_(2).All metals are fully selective to NAD+where the order of turnover frequencies(Pt>Pd>Cu>Au,Ni and Co)coincides with those otherwise observed in electrochemical hydrogen evolution *** has revealed that NADH is capable of converting the metal sites into a“cathode”without an external potential and the NADH to NAD+reaction involves transferring electron and hydrogen atom ***-deficient Ptδ+(on CeO_(2))enhances TOf and the heterogeneous Pt/CeO_(2) catalyst is recyclable without losing any activity/selectivity.

关键词： NAD+regeneration Heterogeneous catalyst Hydrogenase mimic Hydrogen binding energy Hydrogen production

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Treatment of Helicobacter pylori with potassium competitive acid blockers:A systematic review and meta-analysis

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World Journal of Gastroenterology 2024年第9期30卷 1213-1223页

作者： joseph Edwin Kanu Jonathan Soldera Post Graduate Program at Acute Medicine and Gastroenterology University of South WalesCardiff CF371DLUnited Kingdom

BACKGROUND Helicobacter pylori(***)infects over half the global population,causing gastrointestinal diseases like dyspepsia,gastritis,duodenitis,peptic ulcers,GMALT lymphoma,and gastric *** *** is crucial for treating and preventing these *** conventional proton pump inhibitor(PPI)-based triple therapy is effective,there’s growing interest in longer acid suppression *** competitive acid blocker(P-CAB)triple and dual therapy are new regimens for *** *** used in Asian populations,vonoprazan(VPZ)has been recently food and Drug Administration-approved for *** *** To assess the efficacy of regimens containing P-CABs in eradicating *** *** This study,following PRISMA 2020 guidelines,conducted a systematic review and meta-analysis by searching MEDLINE and Scopus libraries for randomized clinical trials(RCTs)or observational studies with the following command:[("Helicobacter pylori"OR"H pylori")AND("Treatment"OR"Therapy"OR"Eradication")AND("Vonaprazan"OR"Potassium-Competitive Acid Blocker"OR"P-CAB"OR"PCAB"OR"Revaprazan"OR"Linaprazan"OR"Soraprazan"OR"Tegoprazan")].Studies comparing the efficacy of P-CABs-based treatment to classical PPIs in eradicating *** were *** criteria included case reports,case series,unpublished trials,or conference *** variables encompassed age,diagnosis method,sample sizes,study duration,intervention and control,and *** eradication method were gathered by two independent ***-analysis was performed in R software,and forest plots were *** A total of 256 references were initially retrieved through the search ***,fifteen studies(7 RCTs,7 retrospective observational studies,and 1 comparative unique study)were included,comparing P-CAB triple therapy to PPI triple *** intention-to-treat analysis involved 8049 patients,with 4471 in the P-CAB intervention g

关键词： Helicobacter pylori infection Potassium competitive acid blockers Proton pump inhibitors Vonoprazan Amoxicillin

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Stability and Time-Step Constraints of Implicit-Explicit Runge-Kutta Methods for the Linearized Korteweg-de Vries Equation

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Communications on Applied Mathematics and Computation 2024年第1期6卷 658-687页

作者： joseph Hunter Zheng Sun Yulong Xing Department of Mathematics The Ohio State UniversityColumbusOH43210USA Department of Mathematics The University of AlabamaTuscaloosaAL35487USA

This paper provides a study on the stability and time-step constraints of solving the linearized Korteweg-de Vries(KdV)equation,using implicit-explicit(IMEX)Runge-Kutta(RK)time integration methods combined with either finite difference(fD)or local discontinuous Galerkin(DG)spatial *** analyze the stability of the fully discrete scheme,on a uniform mesh with periodic boundary conditions,using the fourier *** the linearized KdV equation,the IMEX schemes are stable under the standard Courant-friedrichs-Lewy(CfL)conditionτ≤λ***,λis the CfL number,τis the time-step size,and h is the spatial mesh *** study several IMEX schemes and characterize their CfL number as a function ofθ=d/h^(2)with d being the dispersion coefficient,which leads to several interesting *** also investigate the asymptotic behaviors of the CfL number for sufficiently refined meshes and derive the necessary conditions for the asymptotic stability of the IMEX-RK *** numerical experiments are provided in the paper to illustrate the performance of IMEX methods under different time-step constraints.

关键词： Linearized Korteweg-de Vries(KdV)equation Implicit-explicit(IMEX)Runge-Kutta(RK)method Stability Courant-friedrichs-Lewy(CfL)condition finite difference(fD)method Local discontinuous Galerkin(DG)method

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Monogenic diabetes in children:An underdiagnosed and poorly managed clinical dilemma

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World Journal of Diabetes 2024年第6期15卷 1051-1059页

作者： Saptarshi Bhattacharya joseph M Pappachan Department of Endocrinology Indraprastha Apollo HospitalsDelhi 110076India Department of Endocrinology and Metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom faculty of Biology Medicine and HealthThe University of ManchesterManchester M139PLUnited Kingdom

Monogenic diabetes,constituting 1%-2%of global diabetes cases,arises from single gene defects with distinctive inheritance *** over 50 associated genetic disorders,accurate diagnoses and management of monogenic diabetes remain inadequate,underscoring insufficient clinician *** disease spectrum encompasses maturity-onset diabetes of the young(MODY),characterized by distinct genetic mutations affecting insulin secretion,and neonatal diabetes mellitus(NDM)-a heterogeneous group of severe hyperglycemic disorders in *** diabetes,autoimmune monogenic diabetes,genetic insulin resistance and lipodystrophy syndromes further diversify the monogenic diabetes landscape.A tailored approach based on phenotypic and biochemical factors to identify candidates for genetic screening is recommended for suspected cases of *** diagnosis warrants immediate molecular genetic testing for infants under six *** these genetic defects presents a unique opportunity for precision *** research aimed to develop cost-effective genetic testing methods and gene-based therapy can facilitate appropriate identification and optimize clinical *** and study of new genes offer a valuable opportunity to gain deeper insights into pancreatic cell biology and the pathogenic mechanisms underlying common forms of *** clinical review published in the recent issue of World Journal of Diabetes is such an attempt to fill-in our knowledge gap about this enigmatic disease.

关键词： Monogenic diabetes Maturity-onset diabetes of the young Neonatal diabetes Mitochondrial diabetes Insulin resistance syndromes Genetic testing Next generation sequencing

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Periodontitis:An often-neglected complication of diabetes

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World Journal of Diabetes 2024年第3期15卷 318-325页

作者： Marina G Kudiyirickal joseph M Pappachan Primary Care Dental Practice The Smile ClinicPreston PR16PZUnited Kingdom Department of Endocrinology and Metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom faculty of Biology Medicine and HealthThe University of ManchesterManchester M139PLUnited Kingdom

The bidirectional association between type 2 diabetes mellitus(T2DM)and periodontitis is now well established,resulting in periodontal disease being considered as the 6th major complication of diabetes mellitus(DM)after cardiovascular disease,eye disease,neuropathy,nephropathy,and peripheral vascular *** can worsen the virulence and invasiveness of pathogenic oral microbial flora aggravating the local inflammation and infection in those with periodontal *** the other hand,the chemical and immunological mediators released into the circulation as part of periodontal inflammation worsen the systemic insulin resistance with worsening of *** if undiagnosed or left untreated can also result in eventual tooth loss.A study by Xu et al in the World Journal of Diabetes examined the predictive factors associated with periodontitis in Chinese patients with *** prevalence of periodontitis was found to be 75.7%in this *** on logistic regression analysis,the predictive factors for higher risk were low tooth brushing frequency[odds ratio(OR)=4.3],high triglycerides(TG;OR=3.31),high total cholesterol(TC;OR=2.87),higher glycated hemoglobin(HbA1c;OR=2.55),and higher age(OR=1.05)while higher education level was protective(OR=0.53).However,the most influential variables were HbA1c followed by age,TC,TG,low education level,brushing frequency,and sex on the random forest model(this model showed higher sensitivity for predicting the risk).A good understanding of the predictors for periodontitis in T2DM patients is important in prevention,early detection of susceptible patients,and intervention to improve periodontal health and enable long-term glycaemic control as observed by Xu et al.

关键词： Diabetes mellitus Periodontitis Predictive factors Cardiovascular disease Glycaemic control

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Advances in discovery of novel investigational agents for functional cure of chronic hepatitis B:A comprehensive review of phases II and III therapeutic agents

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World Journal of Hepatology 2024年第3期16卷 331-343页

作者： Robert Lam joseph K Lim Section of Digestive Diseases Yale University School of MedicineNew HavenCT 06520United States

Chronic hepatitis B virus(HBV)infection affects over 295 million people globally and an estimated 1.6 million people in the United *** is associated with significant morbidity and mortality due to cirrhosis,liver failure,and liver *** therapy with oral nucleos(t)ide analogues is associated with high rates of virologic suppression,which in turn has been associated with a decreased risk of liver ***,current antiviral regimens are limited by concerns with adverse effects,adherence,resistance,long-term treatment,and ongoing risk for liver *** investigational agents are currently in development and are targeted at achieving functional cure with sustained hepatitis B surface antigen(HBsAg)loss and suppression of HBV *** we review key evidence from phases II and III trials defining the efficacy and safety profiles for key investigational agents for functional cure of chronic hepatitis B,including core/capsid inhibitors,entry inhibitors,RNA interference(siRNA/ASO),HBsAg inhibitors,Toll-like receptor agonists,checkpoint inhibitors,and therapeutic vaccines.

关键词： Hepatitis B virus Treatment Clinical trials RNA interference Entry inhibitors Core inhibitors Immunomodulators

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Acoustofluidic scanning fluorescence nanoscopy with a large field of view

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Microsystems & Nanoengineering 2024年第3期10卷 159-167页

作者： Geonsoo Jin Neil Upreti joseph Rich Jianping Xia Chenglong Zhao Tony Jun Huang Thomas Lord Department of Mechanical Engineering and Materials Science Duke UniversityDurhamNC 27708USA Department of Biomedical Engineering Duke UniversityDurhamNC 27708USA The MITRE Corporation McLeanVA 22102USA

Large-field nanoscale fluorescence imaging is invaluable for many applications,such as imaging subcellular structures,visualizing protein interactions,and high-resolution tissue ***,conventional fluorescence microscopy requires a trade-off between resolution and field of view due to the nature of the optics used to form the *** overcome this barrier,we developed an acoustofluidic scanning fluorescence nanoscope that simultaneously achieves superior resolution,a large field of view,and strong fluorescent *** acoustofluidic scanning fluorescence nanoscope utilizes the superresolution capabilities of microspheres that are controlled by a programmable acoustofluidic device for rapid fluorescence enhancement and *** acoustofluidic scanning fluorescence nanoscope resolves structures that cannot be resolved with conventional fluorescence microscopes with the same objective lens and enhances the fluorescent signal by a factor of~5 without altering the field of view of the *** improved resolution realized with enhanced fluorescent signals and the large field of view achieved via acoustofluidic scanning fluorescence nanoscopy provides a powerful tool for versatile nanoscale fluorescence imaging for researchers in the fields of medicine,biology,biophysics,and biomedical engineering.

关键词： field resolution utilize

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Acute worsening of microvascular complications of diabetes mellitus during rapid glycemic control:The pathobiology and therapeutic implications

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World Journal of Diabetes 2024年第3期15卷 311-317页

作者： Dania Blaibel Cornelius James fernandez joseph M Pappachan Department of Endocrinology and Metabolism Lancashire Teaching Hospitals NHS TrustPreston PR29HTUnited Kingdom Department of Endocrinology and Metabolism Pilgrim HospitalUnited Lincolnshire Hospitals NHS TrustBoston PE219QSUnited Kingdom faculty of Science Manchester Metropolitan UniversityManchester M156BHUnited Kingdom faculty of Biology Medicine and HealthThe University of ManchesterManchester M139PLUnited Kingdom

While chronic hyperglycaemia resulting from poorly controlled diabetes mellitus(DM)is a well-known precursor to complications such as diabetic retinopathy,neuropathy(including autonomic neuropathy),and nephropathy,a paradoxical intensification of these complications can rarely occur with aggressive glycemic management resulting in a rapid reduction of glycated ***,acute onset or worsening of retinopathy and treatment induced neuropathy of diabetes are more common among these complications,rarely other problems such as albuminuria,diabetic kidney disease,Charcot’s neuroarthropathy,gastroparesis,and urinary bladder dysfunction are also *** World Journal of Diabetes recently published a rare case of all these complications,occurring in a young type 1 diabetic female intensely managed during pregnancy,as a case report by Huret et *** is essential to have a comprehensive understanding of the pathobiology,prevalence,predisposing factors,and management strategies for acute onset,or worsening of microvascular complications when rapid glycemic control is achieved,which serves to alleviate patient morbidity,enhance disease management compliance,and possibly to avoid medico-legal issues around this rare clinical *** editorial delves into the dynamics surrounding the acute exacerbation of microvascular complications in poorly controlled DM during rapid glycaemic control.

关键词： Diabetes mellitus Microvascular complications Diabetic retinopathy Treatment induced neuropathy of diabetes Diabetic nephropathy Charcot’s neuropathy

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