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Evaluation of bacterial biomarkers to aid in challenging inflammatory bowel diseases diagnostics and subtype classification

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World journal of Gastrointestinal Pathophysiology 2020年第3期11卷 64-77页

作者： Mireia Lopez-Siles Xavier Aldeguer Miriam Sabat-Mir Mariona Serra-Pagès Sylvia H Duncan harry j flint L jesús Garcia-Gil Margarita Martinez-Medina Laboratory of Molecular Microbiology Biology DepartmentUniversitat de GironaGirona 17003Spain Department of Gastroenterology Hospital Universitari Dr.Josep TruetaGirona 17007Spain Department of Gastroenterology Hospital Santa CaterinaSalt 17190Spain GoodGut SL Girona 17003Spain Microbiology Group Rowett Institute of Nutrition and HealthUniversity of AberdeenAberdeen AB252ZDUnited Kingdom

BACKGROUND The challenges for inflammatory bowel disease(IBD)diagnostics are to discriminate it from gut conditions with similar symptoms such as irritable bowel syndrome(IBS),to distinguish IBD subtypes,to predict disease progression,and to establish the risk to develop colorectal cancer(CRC).Alterations in gut microbiota have been proposed as a source of information to assist in IBD *** prausnitzii(***),its phylogroups,and Escherichia coli(***)have been reported as potential biomarkers,but their performance in challenging IBD diagnostic situations remains *** hypothesize that bacterial biomarkers based in these species may help to discriminate these conditions of complex *** To evaluate the usefulness of indices calculated from the quantification of these species as biomarkers to aid in IBD *** A retrospective study of 131 subjects(31 controls(H);45 Crohn’s disease(CD),25 ulcerative colitis(UC),10 IBS,and 20 CRC patients)was performed to assess the usefulness of bacterial biomarkers in ***,the performance of biomarkers in faeces was studied in 29 stool samples(19 CD,10 UC).Relative abundances of total ***(FP),its phylogroups(PHGI and PHGII),and ***(E)quantification were determined by *** were combined to calculate the FP-E index,the PHGI–E index and the PHGII-E *** accuracy to discriminate among conditions was measured by the area under the receiver operating characteristic curve(AUC).RESULTS In biopsies,FP-E index was good for discriminating IBS from CD(AUC=0.752)while PHGII-E index was suitable for discriminating IBS from UC(AUC=0.632).The FP-E index would be the choice to discriminate IBD from CRC,especially from all UC subtypes(AUC≥0.875),regardless of the activity status of the *** between UC patients that had the longest disease duration and those with CRC featured slightly lower AUC *** differentiation in IB

关键词： Crohn’s disease Ulcerative colitis Inflammatory bowel disease Diagnostic tests Faecalibacterium prausnitzii Escherichia coli Irritable bowel syndrome Colorectal cancer

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Bile acids,gut microbiota,and therapeutic insights in hepatocellular carcinoma

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Cancer Biology & Medicine 2024年第2期21卷 144-162页

作者： Yang Song harry CH Lau Xiang Zhang jun Yu Institute of Digestive Disease and Department of Medicine and Therapeutics State Key Laboratory of Digestive DiseaseLi Ka Shing Institute of Health SciencesCUHK Shenzhen Research InstituteThe Chinese University of Hong KongHong KongChina Department of Gastroenterology Zhongshan Hospital Xiamen UniversityXiamen 361004China

Hepatocellular carcinoma(HCC)is a prevalent and aggressive liver *** interplay between bile acids(BAs)and the gut microbiota has emerged as a critical factor in HCC development and *** normal conditions,BA metabolism is tightly regulated through a bidirectional interplay between gut microorganisms and *** gut microbiota plays a critical role in BA metabolism,and BAs are endogenous signaling molecules that help maintain liver and intestinal *** note,dysbiotic changes in the gut microbiota during pathogenesis and cancer development can disrupt BA homeostasis,thereby leading to liver inflammation and fibrosis,and ultimately contributing to HCC ***,understanding the intricate interplay between BAs and the gut microbiota is crucial for elucidating the mechanisms underlying *** this review,we comprehensively explore the roles and functions of BA metabolism,with a focus on the interactions between BAs and gut microorganisms in ***,therapeutic strategies targeting BA metabolism and the gut microbiota are discussed,including the use of BA agonists/antagonists,probiotic/prebiotic and dietary interventions,fecal microbiota transplantation,and engineered *** summary,understanding the complex BA-microbiota crosstalk can provide valuable insights into HCC development and facilitate the development of innovative therapeutic approaches for liver malignancy.

关键词： Bile acid gut microbiota hepatocellular carcinoma therapeutics microbiota modulation

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Significance of using isolated footing technique for resi- dential construction on expansive soils

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Frontiers of Structural and Civil Engineering 2017年第1期11卷 123-129页

作者： harry FAR Deacon flint Centre for Built Infrastructure Research School of Civil and Environmental Engineering University of Technology Sydney (UTS)Australia

Expansive soils cause problems with the founding of lightly loaded structures in many parts of the world. Foundation design for expansive soils is one of the most discussed and problematic issues in Australia as expansive soils were responsible for billions of dollars＇ worth of damage to man-made structures such as buildings and roads. Several studies and reports indicate that one of the most common and least recognized problems causing severe structural damage to houses lies in expansive soils. In this study, a critical review has been carried out on the current Australian standards for building on expansive soils and they are compared with some techniques that are not included in the current Australian standards for residential slabs and footings. Based on the results of this review, the most effective and economical method has been proposed for construction of footings on all site classifications without restriction to 75mm of characteristic movement. In addition, it has become apparent that as design procedures for footings resting on sites with extreme characteristic movements are not included in the current Australian standards, there is a strong need for well-developed and simplified standard design procedures for characteristic soil movement of greater than 75mm to be included into the Australian Standards.

关键词： expansive soils residential slabs isolated footings Australian Standards

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Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis

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Ecological Processes 2012年第1期1卷 109-123页

作者： Lorraine E flint Alan L flint U.S.Geological Survey Placer Hall6000 J St.SacramentoCA 95819USA

Introduction:Evaluating the environmental impacts of climate change on water resources and biological components of the landscape is an integral part of hydrologic and ecological investigations,and the resultant land and resource management in the twenty-first *** of both climate and simulated hydrologic parameters on ecological processes are relevant at scales that reflect the heterogeneity and complexity of *** present,simulations of climate change available from global climate models[GCMs]require downscaling for hydrologic or ecological ***:Using statistically downscaled future climate projections developed using constructed analogues,a methodology was developed to further downscale the projections spatially using a gradient-inverse-distancesquared approach for application to hydrologic modeling at 270-m spatial ***:This paper illustrates a methodology to downscale and bias-correct national GCMs to subkilometer scales that are applicable to fine-scale environmental *** scenarios were chosen to bracket the range of future emissions put forth by the Intergovernmental Panel on Climate ***-scale applications of downscaled datasets of ecological and hydrologic correlations to variation in climate are ***:The methodology,which includes a sequence of rigorous analyses and calculations,is intended to reduce the addition of uncertainty to the climate data as a result of the downscaling while providing the fine-scale climate information necessary for ecological *** results in new but consistent data sets for the US at 4 km,the southwest US at 270 m,and California at 90 m and illustrates the utility of fine-scale downscaling to analyses of ecological processes influenced by topographic complexity.

关键词： downscaling climate change spatial scale scenarios

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Fine-scale hydrologic modeling for regional landscape applications:the California Basin Characterization Model development and performance

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Ecological Processes 2013年第1期2卷 254-274页

作者： Lorraine E flint Alan L flint james H Thorne Ryan Boynton Water Resources Discipline U.S.Geological SurveyPlacer Hall6000 J StreetSacramentoCA 95819-6129USA Information Center for the Environment University of CaliforniaDavisCA95616USA

Introduction:Resource managers need spatially explicit models of hydrologic response to changes in key climatic drivers across variable landscape *** demonstrate the utility of a Basin Characterization Model for California(CA-BCM)to integrate high-resolution data on physical watershed characteristics with historical or projected climate data to predict watershed-specific hydrologic ***:The CA-BCM applies a monthly regional water-balance model to simulate hydrologic responses to climate at the spatial resolution of a 270-m *** model has been calibrated using a total of 159 relatively unimpaired watersheds for the California ***:As a result of calibration,predicted basin discharge closely matches measured data for validation *** CA-BCM recharge and runoff estimates,combined with estimates of snowpack and timing of snowmelt,provide a basis for assessing variations in water *** important output variable,climatic water deficit,integrates the combined effects of temperature and rainfall on site-specific soil moisture,a factor that plants may respond to more directly than air temperature and precipitation *** outputs are calculated for each grid cell,allowing results to be summarized for a variety of planning units including hillslopes,watersheds,ecoregions,or political ***:The ability to confidently calculate hydrologic outputs at fine spatial scales provides a new suite of hydrologic predictor variables that can be used for a variety of purposes,such as projections of changes in water availability,environmental demand,or distribution of plants and *** we present the framework of the CA-BCM model for the California hydrologic region,a test of model performance on 159 watersheds,summary results for the region for the 1981–2010 time period,and changes since the 1951–1980 time period.

关键词： Water balance Basin models Watershed hydrology Climate change Downscaling Basin characterization model

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Characterizing drought in California:new drought indices and scenario-testing in support of resource management

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Ecological Processes 2018年第1期7卷 1-13页

作者： Lorraine E.flint Alan L.flint john Mendoza julie Kalansky F.M.Ralph U.S.Geological Survey 6000 J.StSacramentoCA 95819USA Sonoma County Water Agency 404 Aviation Dr.Santa RosaCA 95403USA Scripps Institution of Oceanography 9500 Gilman Dr.La JollaCA 92093USA

Introduction:California’s recent drought(2012–2016)has implications throughout the state for natural resource management and adaptation planning and has generated many discussions about drought characterization and *** study characterizes drought conditions with two indices describing deficits in natural water supply and increases in landscape stress developed on the basis of water balance modeling,at a fine spatial scale to assess the variation in conditions across the entire state,and provides an in-depth evaluation for the Russian River basin in northern California to address local resource management by developing extreme drought scenarios for consideration in planning and ***:We employed the USGS Basin Characterization Model to characterize drought on the basis of water supply(a measure of recharge plus runoff)and landscape stress(climatic water deficit).These were applied to the state and to the Russian River basin where antecedent soil moisture conditions were evaluated and extreme drought scenarios were developed and run through a water management and reservoir operations model to further explore impacts on water ***:Drought indices indicated that as of the end of water year 2016 when reservoirs were full,additional water supply and landscape replenishment of up to three average years of precipitation in some locations was needed to return to normal *** soil conditions in the Russian River were determined to contribute to very different water supply results for different years and were necessary to understand to anticipate proper watershed response to *** drought scenarios manifested very different kinds of drought and recovery and characterization helps to guide the management response to ***:These scenarios and indices illustrate how droughts differ with regard to water supply and landscape stress and how long warm droughts recover much more slowly than short very dry dro

关键词： California drought Russian River Water supply Basin Characterization Model

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Telaprevir/boceprevir era: From bench to bed and back

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World journal of Gastroenterology 2012年第43期18卷 6183-6188页

作者： Maikel P Peppelenbosch harry LA janssen Robert j de Knegt Department of Gastroenterology and Hepatology Erasmus MC-University Medical Center 3015 CE Rotterdam The Netherlands

Hepatitis C virus (HCV) infects approximately 200 million people worldwide. Interferon-based therapies have dominated over the past two decades. However, the overall response rates remain suboptimal. Thanks to the tremendous effort from both academia and industry, two serine protease inhibitors telaprevir and boceprevir for treating chronic hepatitis C have finally reached the clinic. Although these compounds are only approved for combination use with interferon and ribavirin in genotype 1 HCV infected chronic patients, the management of HCV patients however is now evolving incredibly. Here, we overviewed a series of landmark studies, regarding the clinical development of telaprevir and boceprevir. We discussed the mechanism-of-action of telaprevir/boceprevir and their potential application in HCV-positive liver transplantation patients. We further emphasized some emerging concerns with perspective of further development in this field.

关键词： Telaprevir Boceprevir Mechanism-of-action Clinical efficacy Liver transplantation patient Interferon Ribavirin

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Cross-scale modeling of surface temperature and tree seedling establishment in mountain landscapes

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Ecological Processes 2013年第1期2卷 313-327页

作者： john R Dingman Lynn C Sweet Ian McCullough Frank W Davis Alan flint janet Franklin Lorraine E flint Earth Research Institute University of California Santa BarbaraSanta BarbaraCA 93106USA U.S.Geological Survey California Water Science CenterSacramentoCA 95819USA Bren School of Environmental Science&Management University of California Santa BarbaraSanta BarbaraCA93106USA School of Geographical Sciences and Urban Planning Arizona State UniversityTempeAZ85287USA

Introduction:Estimating surface temperature from above-ground field measurements is important for understanding the complex landscape patterns of plant seedling survival and establishment,processes which occur at heights of only several ***,future climate models predict temperature at 2 m above ground,leaving ground-surface microclimate not well ***:Using a network of field temperature sensors and climate models,a ground-surface temperature method was used to estimate microclimate variability of minimum and maximum *** lapse rates were derived from field temperature sensors and distributed across the landscape capturing differences in solar radiation and cold air drainages modeled at a 30-m spatial ***:The surface temperature estimation method used for this analysis successfully estimated minimum surface temperatures on north-facing,south-facing,valley,and ridgeline topographic settings,and when compared to measured temperatures yielded an R2 of 0.88,0.80,0.88,and 0.80,*** surface temperatures generally had slightly more spatial variability than minimum surface temperatures,resulting in R2 values of 0.86,0.77,0.72,and 0.79 for north-facing,south-facing,valley,and ridgeline topographic ***-Poisson regressions predicting recruitment of Quercus kelloggii(black oak)seedlings from temperature variables were significantly improved using these estimates of surface temperature compared to air temperature modeled at 2 ***:Predicting minimum and maximum ground-surface temperatures using a downscaled climate model coupled with temperature lapse rates estimated from field measurements provides a method for modeling temperature effects on plant *** methods could be applied to improve projections of species’range shifts under climate *** of complex topography can provide intricate microclimates that may allow species to redistribute locally as climate

关键词： Black oak Climate change Generalized linear models Microclimate Topography Spatial scale Surface temperature

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Variation in the plant-mediated methane transport and its importance for methane emission from intact wetland peat mesocosms

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journal of Plant Ecology 2013年第4期6卷 298-304页

作者： Gurbir S.Bhullar Peter j.Edwards harry Olde Venterink Institute of Integrative Biology ETH ZurichUniversitätstrasse 168092 ZurichSwitzerland

Aims and Methods Vascular plants are known to influence the production,transport and oxidation of methane in wetland soils,but these processes are not well *** plants grown in intact peat cores,we compared the influence upon methane emissions of 20 forb and graminoid species from European *** measured plant-mediated transport of methane(conduit or chimney effect)using a novel agar-sealing technique that prevented methane exchange from the bare soil to the *** Findings the plant-mediated transport(chimney effect)represented between 30%and almost 100%of the total methane flux,with graminoids exhibiting greater internal transport than *** general,plants with less dense root tissues and a relatively larger root volume exhibited a larger chimney *** species(12 out of 20)signif-icantly reduced methane emissions compared to bare soil and only one species,Succisa pratensis,increased *** suggest that characterising vegetation in terms of plant functional traits and plant processes offers an effective method for estimating methane emis-sions from ***,we found no correlation between the magnitude of the chimney effect and the overall influence of different plant species on methane *** introducing a useful tool to study plant-mediated transport,this work suggests that characterising vegetation in terms of functional traits could improve estimates of methane emissions from wetlands,which in turn could help in designing mitigation strategies.

关键词： functional group graminoid forb agar-sealing conduit gas transportreceived

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Machine learning ensemble model prediction of northward shift in potato cyst nematodes(Globodera rostochiensis and ***)distribution under climate change conditions

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journal of Integrative Agriculture 2024年第10期23卷 3576-3591页

作者： Yitong He Guanjin Wang Yonglin Ren Shan Gao Dong Chu Simon j.McKirdy Shandong Engineering Research Centre for Environment-friendly Agricultural Pest Management College of Plant Health andMedicineQingdao Agricultural UniversityQingdao 266109China harry Butler Institute Murdoch UniversityMurdochWA 6150Australia School of Information Technology Murdoch UniversityPerthWA 6150Australia Hebei Dahaituo National Nature Reserve Management Centre Chicheng 075500China

Potato cyst nematodes(PCNs)are a significant threat to potato production,having caused substantial damage in many *** the future distribution of PCN species is crucial to implementing effective biosecurity strategies,especially given the impact of climate change on pest species invasion and *** learning(ML),specifically ensemble models,has emerged as a powerful tool in predicting species distributions due to its ability to learn and make predictions based on complex data ***,this research utilised advanced machine learning techniques to predict the distribution of PCN species under climate change conditions,providing the initial element for invasion risk *** first used Global Climate Models to generate homogeneous climate predictors to mitigate the variation among ***,five machine learning models were employed to build two groups of ensembles,single-algorithm ensembles(ESA)and multi-algorithm ensembles(EMA),and compared their *** this research,the EMA did not always perform better than the ESA,and the ESA of Artificial Neural Network gave the highest performance while being *** results indicated that the distribution range of PCNs would shift northward with a decrease in tropical zones and an increase in northern ***,the total area of suitable regions will not change significantly,occupying 16-20%of the total land surface(18%under current conditions).This research alerts policymakers and practitioners to the risk of PCNs’incursion into new ***,this ML process offers the capability to track changes in the distribution of various species and provides scientifically grounded evidence for formulating long-term biosecurity plans for their control.

关键词： invasive species distribution future climates homogeneous climate predictors single-algorithm ensembles multi-algorithm ensembles artificial neural network

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