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deCS:A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues

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Genomics, Proteomics & Bioinformatics 2023年第2期21卷 370-384页

作者： Guangsheng Pei Fangfang Yan Lukas m.simon Yulin Dai Peilin Jia Zhongming Zhao Center for Precision Health School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTX 77030USA Therapeutic Innovation Center Baylor College of MedicineHoustonTX 77030USA Human Genetics Center School of Public HealthThe University of Texas Health Science Center at HoustonHoustonTX 77030USA mD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences HoustonTX 77030USA Department of Biomedical Informatics Vanderbilt University Medical CenterNashvilleTN 37203USA CAS Key Laboratory of Genomic and Precision medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China

Single-cell RNA sequencing(scRNA-seq)is revolutionizing the study of complex and dynamic cellular ***,cell type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation,which is cumbersome and *** increasing number of scRNA-seq datasets,as well as numerous published genetic studies,has motivated us to build a comprehensive human cell type reference ***,we present decoding Cell type Specificity(deCS),an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker *** used deCS to annotate scRNAseq data from various tissue types and systematically evaluated the annotation accuracy under different conditions,including reference panels,sequencing depth,and feature selection *** results demonstrate that expanding the references is critical for improving annotation *** to many existing state-of-the-art annotation tools,deCS significantly reduced computation time and increased *** can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type ***,we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits,providing deep insights into the cellular mechanisms underlying disease pathogenesis.

关键词： Cell type-specific enrichment analysis scRNA-seq Cell type annotation Trait-cell type association Cell typemarkergene

Epidemiology and mutational Analysis of Global Strains of Crimean-Congo Haemorrhagic Fever Virus

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Virologica Sinica 2011年第4期26卷 229-244页

作者： simon Rayner Bioinformatics Group State Key Laboratory for VirologyWuhan Institute of VirologyChinese Academy of Sciences

Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high *** are reported in several countries in Africa,Europe,the middle East,and *** analyses based on the virus S (nucleocapsid),m (glycoprotein),and L (polymerase) genome segments sequences indicate distinct geographic lineages exist but their specific genetic characteristics require *** this work we collected all full length S segment sequences and generated a phylogenetic tree based on the alignment of these 62 *** then analyzed the alignment using entries from AAIndex,the Amino Acid Index database,to identify amino acid mutations that performed significant changes in charge,pka,hydropathy and side chain ***,we mapped these changes back to the tree and alignment to identify correlated mutations or sites that characterized a specific *** on this analysis we are able to propose a number of sites that appear to be important for virus function and which would be good candidates for experimental mutational analysis studies.

关键词： Crimean-Congo hemorrhagic fever virus (CCHFV) Epidemiology mutational Analysis

Axisymmetric alternating direction explicit scheme for efficient coupled simulation of hydro-mechanical interaction in geotechnical engineering-Application to circular footing and deep tunnel in saturated ground

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Journal of Rock mechanics and Geotechnical Engineering 2018年第2期10卷 259-279页

作者： simon Heru Prassetyo marte Gutierrez Department of Civil and Environmental Engineering Colorado School of MinesGoldenUSA mining Engineering Program Institut Teknologi BandungBandungIndonesia

Explicit solution techniques have been widely used in geotechnical engineering for simulating the coupled hydro-mechanical(H-m) interaction of fluid flow and deformation induced by structures built above and under saturated ground, i.e. circular footing and deep tunnel. However, the technique is only conditionally stable and requires small time steps, portending its inefficiency for simulating large-scale H-m problems. To improve its efficiency, the unconditionally stable alternating direction explicit(ADE)scheme could be used to solve the flow problem. The standard ADE scheme, however, is only moderately accurate and is restricted to uniform grids and plane strain flow conditions. This paper aims to remove these drawbacks by developing a novel high-order ADE scheme capable of solving flow problems in nonuniform grids and under axisymmetric conditions. The new scheme is derived by performing a fourthorder finite difference(FD) approximation to the spatial derivatives of the axisymmetric fluid-diffusion equation in a non-uniform grid configuration. The implicit Crank-Nicolson technique is then applied to the resulting approximation, and the subsequent equation is split into two alternating direction sweeps,giving rise to a new axisymmetric ADE scheme. The pore pressure solutions from the new scheme are then sequentially coupled with an existing geomechanical simulator in the computer code fast Lagrangian analysis of continua(FLAC). This coupling procedure is called the sequentially-explicit coupling technique based on the fourth-order axisymmetric ADE scheme or SEA-4-AXI. Application of SEA-4-AXI for solving axisymmetric consolidation of a circular footing and of advancing tunnel in deep saturated ground shows that SEA-4-AXI reduces computer runtime up to 42%-50% that of FLAC’s basic scheme without numerical instability. In addition, it produces high numerical accuracy of the H-m solutions with average percentage difference of only 0.5%-1.8%.

关键词： Hydro-mechanical(H-m) interaction Explicit coupling technique Alternating direction explicit(ADE) scheme High-order finite difference(FD) Non-uniform grid Axisymmetric consolidation Circular footing Deep tunnel in saturated ground

Effect of surface loading on the hydro-mechanical response of a tunnel in saturated ground

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Underground Space 2016年第1期1卷 1-19页

作者： simon Heru Prassetyo marte Gutierrez Department of Civil and Environmental Engineering Colorado School of MinesGoldenCO 80401USA

The design of underground spaces in urban areas must account not only for the current overburden load but also for future surface loads,such as from construction of high-rise buildings above underground *** saturated ground,the surface load will generate an additional mechanical response through stress changes and ground displacement,as well as a hydraulic response through pore pressure *** hydro-mechanical(H-m)changes can severely influence tunnel *** paper examines the effect of surface loading on the H-m response of a typical horseshoe-shaped tunnel in saturated *** tunnel models were created in the computer code Fast Lagrangian Analysis of Continua(FLAC).One model represented weak and low permeability ground(stiff clay),and the other represented strong and high permeability ground(weathered granite).Each of the models was run under two liner permeabilities:permeable and *** main cases were *** Case 1,the surface load was applied 10 years after tunnel *** Case 2,the surface load was applied after the steady state pore pressure condition was *** simulation results show that tunnels with impermeable liners experienced the most severe influence from the surface loading,with high pore pressures,large inward displacement around the tunnels,and high bending moments in the *** addition,the severity of the response increased toward steady *** induced H-m response was worse for tunnels in clay than for those in ***,the long-term liner stabilities in Case 1 and Case 2 were similar,indicating that the influence of the length of time between when the tunnel was completed and when the surface load was applied was *** findings suggest that under surface loading,in addition to the ground strength,tunnel stability in saturated ground is largely influenced by liner permeability and the long-term H-m response of the ground.

关键词： Surface loading Hydro-mechanical response Urban tunnels Saturated ground

Elevated free cholesterol in a p62 overexpression model of non-alcoholic steatohepatitis

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World Journal of Gastroenterology 2014年第47期20卷 17839-17850页

作者： Yvette simon Sonja m Kessler Katja Gemperlein Rainer m Bohle Rolf müller Johannes Haybaeck Alexandra K Kiemer Department of Pharmacy Pharmaceutical BiologySaarland University66123 SaarbrückenGermany medical University of Graz Institute of PathologyGraz 8036Austria Department of Pharmacy Pharmaceutical BiotechnologySaarland University and Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)66123 SaarbrückenGermany Saarland University Department of Pathology66421 HomburgGermany

AIm: To characterize how insulin-like growth factor 2 (IGF2) mRNA binding protein p62/ImP2-2 promotes steatohepatitis in the absence of dietary cholesterol.

关键词： Insulin-like growth factor 2 mRNA binding protein 2-2 methionine/choline deficient Non-alcoholic fatty liver disease Filipin Iron

Treatment of eosinophlic esophagitis with swallowed topical corticosteroids

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World Journal of Gastroenterology 2020年第36期26卷 5395-5407页

作者： simon Nennstiel Christoph Schlag Klinikum rechts der Isar der Technischen Universität münchen Klinik und Poliklinik für Innere Medizin IIMunich 81675Germany

Eosinophilic esophagitis(EoE)is an emerging chronic local immune-mediated disease of the *** proton pump inhibitors and food-restrictiondiets swallowed topical corticosteroids(STC)can be offered as a first line therapy according to current *** review describes the background and practical management of STCs in *** far,mainly asthma inhalers containing either budesonide or fluticasone have been administered to the esophagus by swallowing these medications“off label”.Recently esophagus-targeted formulations of topical steroids have been developed showing clinicopathological response rates up to 85%-an orodispersible tablet of budesonide has been approved as the first“in label”medication for EoE in Europe in June *** it was shown that disease remission induction of EoE by STCs is highly effective,there is still a lack of data regarding long-term and maintenance ***,current studies on STC maintenance therapy add some movement into the game.

关键词： Eosinophilic esophagitis Swallowed topical corticosteroids Esophagustargeted formulations of topical steroids Fluticasone Budesonide Budesonide orodispersible tablet Budesonide oral suspension

Combined garnet,scheelite and apatite U-Pb dating of mineralizing events in the Qiaomaishan Cu-W skarn deposit,eastern China

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Geoscience Frontiers 2023年第1期14卷 17-32页

作者： Yue Li Feng Yuan simon m.Jowitt Xiangling Li Taofa Zhou Fangyue Wang Yufeng Deng Ore Deposit and Exploration Centre(ODEC) Hefei University of TechnologyHefei 23009China Anhui Province Engineering Research Center for mineral Resources and mine Environments Hefei 23009China Department of Geoscience University of Nevada Las Vegas4505 S.Maryland Pkwy.NV 89154-4010USA

Determining the precise timing of mineralization and mineralizing events is crucial to understanding regional mineralizing and other geological events and ***,there are a number of mineralogical and analytical limitations to the approaches developed for the absolute dating of mineralizing systems,such as molybdenite Re-Os and zircon and garnet U-Pb,among *** means that the precise and accurate dating of mineralizing systems that may not contain minerals suitable for dating using existing approaches requires the development of new(and ideally in situ)approaches to absolute *** study outlines a new in situ analytical approach that has the potential to rapidly and accurately evaluate the timing of ore *** study employs a novel application of in situ scheelite U-Pb dating analysis using laser ablation-inductively coupled plasma-mass spectrometry(LA-ICP-mS)and samples from the Qiaomaishan deposit,a representative example of skarn mineralization within the Xuancheng ore district of eastern *** approach to scheelite dating of the deposit is verified by cross-comparison to dating of cogenetic garnet and apatite,proving the effectiveness of this *** new approach to dating of scheelite-bearing geological systems is rapid,cheap,requires little sample preparation,and is undertaken in situ,allowing crucial geological and mineralogical context to be retained during *** approaches outlined here not only allow the determination of the absolute timing of formation of the Qiaomaishan deposit through the U-Pb dating of scheelite[138.6±3.2 ma,N=39,mean square weighted deviation(mSWD)=1.17],garnet(138.4±1.0 ma,N=40,mSWD=1.3),and apatite(139.6+3.3 ma,N=35,mSWD=0.72),but also further supports the theoretical genetic links between this mineralization and the emplacement of a proximal porphyritic granodiorite intrusion(zircon U-Pb age:139.5±1.2 ma,N=23,mSWD=0.3).moreover,our research indicates that the higher the concentrations

关键词： In-situ scheelite U-Pb dating In-situ garnet U-Pb dating In-situ apatite U-Pb dating Qiaomaishan skarn deposit

Cholesterol crystal embolism leading to perforation of the gallbladder

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Hepatobiliary & Pancreatic Diseases International 2007年第6期6卷 653-655页

作者： Janine Tappenden simon K. Suvarna Roger Ackroyd Badri m. Shrestha Northern General Hospital Herries Road Sheffield S5 7AU UK

BACKGROUND: Cholesterol crystal embolism (CCE) from atherosclerotic arterial disease leading to perforation of the gallbladder is rare. We describe our experience of managing a patient with perforation of gallbladder caused by CCE. mETHODS: A 64-year-old man was admitted to this hospital because of acute abdominal pain with clinical features suggestive of peritonitis. He was known to suffer from atherosclerotic peripheral arterial disease and had undergone aortobifemoral bypass 17 years ago. A CT scan showed a collection of peri-hepatic fluid. The gallbladder was normal in appearance but contained multiple calculi. At laparotomy, free bile was observed in the peritoneal cavity, leaking from a pin-hole size peroration of the fundus of the gallbladder. Hence cholecystectomy was performed. RESULTS: The patient made an uneventful recovery. Histological study of the gallbladder showed chronic cholecystitis and obliteration of the lumen of the mural arteries with cholesterol crystals within, indicating CCE. CONCLUSIONS: Although perforation of the gallbladder following CCE of its mural arteries is rare, the diagnosis should be considered in patients with abdominal pain and known atherosclerotic arterial disease. management should include an early recognition of this condition, prompt institution of treatment, prevention of further insults by discontinuing or avoiding predisposing factors, and modification of cardiovascular risk factors.

关键词： cholesterol crystal embolism perforation gallbladder peritonitis

Spatial distribution of water and wind erosion and their influence on the soil quality at the agropastoral ecotone of North China

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International Soil and Water Conservation Research 2020年第3期8卷 253-265页

作者： Yanzai Wang Yifan Dong Zhengan Su simon m.mudd Qiuhong Zheng Gang Hu Dong Yan Institute of International Rivers and Eco-Security Yunnan UniversityKunming650091PR China Key Laboratory of mountain Hazards&Surface Process Institute of Mountain Hazards and EnvironmentChinese Academy of SciencesChengdu610041PR China College of Geography and Tourism Chongqing Normal UniversityChongqing401331PR China School of GeoSciences University of EdinburghEdinburghEH89XPUK China meteorological Administration Training Center CMABeijing100081PR China School of Tourism and Geography Sciences Qingdao266071ShandongPR China National Institute for Radiological Protection Chinese Center for Disease Control and PreventionBeijing100088PR China

In semiarid regions,wind and water erosion are serious environmental and ecological problems around *** have different impacts on soil quality over a range of spatial *** the spatial distribution of soil erosion and understanding the impacts of wind and water erosion on soil quality at the regional scale is vital for mitigating soil erosion *** this study we explore the spatial distributions of water and wind erosion around Zhangjiakou city which suffers both water and wind erosion contemporaneously,and detect the influence of soil erosion on soil *** find that annual wind erosion intensities range 4.99-10.05 t ha-1 yr-1,and annual water erosion intensities range 2.92-4.14 t ha-1 *** with higher potential wind and total erosion risk occur mainly in northwest and southeast Zhangjiakou city,whereas potential water erosion risk is highest in the southwest and central *** highest erosion rates are concentrated in gentle parts of the landscape,where agriculture has led to low vegetation *** portions of the landscape,which remain forested,have lower erosion *** spatial patterns are dominated by higher wind erosion,which correlates with sur-face soil coarsening and higher water infiltration,whereas the soil water holding capacity decreases with increasing wind erosion *** regions with high water infiltration rates,we find the intensity of water erosion *** mitigate risks of soil degradation,suitable erosion measures should be imple-mented according to the dominant erosion type,which varies in space.

关键词： Soil erosion Soil quality Spatial distribution Agropastoral ecotone