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JAX-CNV:A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level

Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1197-1206页

作者： Wan-Ping Lee Qihui Zhu Xiaofei Yang silvia liu Eliza Cerveira Mallory Ryan Adam Mil-Homens Lauren Bellfy Kai Ye Charles Lee Chengsheng Zhang Precision Medicine Center The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA School of Cyber Science and Engineering Xi’an Jiaotong UniversityXi’an 710049China Department of Pathology and Laboratory Medicine Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Department of Life Sciences Ewha Womans UniversitySeoul 03760South Korea

We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical ***-CNV is thus developed for CNV detection from WGS *** performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 *** result showed that JAX-CNV recalled 100%of these ***,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated *** validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×*** CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to ***-CNV is available at https://***/TheJacksonLaboratory/JAX-CNV.

关键词： Copy number variant Chromosomal microarray assay Whole-genome sequencing JAX-CNV Genetic testing

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Engineering osteoarthritic cartilage model through differentiating senescent human mesenchymal stem cells for testing disease-modifying drugs

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Science China(Life Sciences) 2022年第2期65卷 309-327页

作者： Ning Wang Yuchen He silvia liu Meagan J.Makarcyzk Guanghua Lei Alexander Chang Peter G Alexander Tingjun Hao Anne-Marie Padget Nuria de Pedro Tsapekos Menelaos Hang Lin Department of Orthopaedic Surgery University of Pittsburgh School of MedicinePittsburgh PA 15219USA Department of Orthopedic Surgery Xiangya HospitalCentral South UniversityChangsha 410008China Department of Pathology University of Pittsburgh School of MedicinePittsburgh PA 15219USA Department of Bioengineering University of Pittsburgh Swanson School of EngineeringPittsburgh PA 15219USA Department of Bioinformatics University of Pittsburgh School of MedicinePittsburgh PA 15219USA McGowan Institute for Regenerative Medicine University of Pittsburgh School of MedicinePittsburgh PA 15219USA Department of Biology University of Pittsburgh Dietrich School of Arts and SciencePittsburgh PA 15219USA Department of Research B2B Life Length SLMadrid 28010Spain Xiangya Third Hospital Central South UniversityChangsha 410013China

Significant cellular senescence has been observed in cartilage harvested from patients with osteoarthritis(OA).In this study,we aim to develop a senescence-relevant OA-like cartilage model for developing disease-modifying OA drugs(DMOADs).Spe-cifically,human bone marrow-derived mesenchymal stromal cells(MSCs)were expanded in vitro up to passage 10(P10-MSCs).Following their senescent phenotype formation,P10-MSCs were subjected to pellet culture in chondrogenic *** from qRT-PCR,histology,and immunostaining indicated that cartilage generated from P10-MSCs displayed both senescent and OA-like phenotypes without using other OA-inducing agents,when compared to that from normal passage 4(P4)-***,the same gene expression differences observed between P4-MSCs and P10-MSC-derived cartilage tissues were also observed between the preserved and damaged OA cartilage regions taken from human samples,as demonstrated by RNA sequencing data and other analysis ***,the utility of this senescence-initiated OA-like cartilage model in drug development was assessed by testing several potential DMOADs and *** results suggest that pre-existing cellular senescence can induce the generation of OA-like changes in *** P4-and P10-MSCs derived cartilage models also represent a novel platform for predicting the efficacy and toxicity of potential DMOADs on both preserved and damaged cartilage in humans.

关键词： osteoarthritis MSC senescence cartilage tissue engineering disease-modifying OA drug senolytic

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Altered birefringence of peripapillary retinal nerve fiber layer in multiple sclerosis measured by polarization sensitive optical coherence tomography

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Eye and Vision 2018年第1期5卷 137-143页

作者： Hong Jiang Wan Chen silvia Delgado Yi liu Ying Lin Jianhua Wang Bascom Palmer Eye Institute University of Miami Miller School of Medicine1638 NW 10th AvenueMcKnight Vision Research Building-Room 202AMiamiFL 33136USA Department of Neurology University of Miami Miller School of MedicineMiamiFLUSA State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangzhouChina Department of Ophthalmology Third Affiliated Hospital of Nanjing University of Chinese MedicineNanjingChina

Background:The retina has been used to study the pathophysiology of multiple sclerosis(MS).Peripapillary retinal nerve fiber layer(pRNFL)thinning has been suggested as an ocular biomarker of neurodegeneration in *** goal of this project was to determine the birefringence of the pRNFL by measuring the fiber birefringence using polarization sensitive optical coherence tomography(PS-OCT).Methods:Sixty-six MS patients without history of optic neuritis(age:39.9±11.0 ***,53 females and 13 males)and 66 age-and gender-matched normal controls(age:40.7±11.4 ***)were *** built PS-OCT was used to measure phase retardation per unit depth(PR/UD,proportional to the birefringence)and pRNFL thickness in each quadrant of the *** addition,clinical manifestation was used to correlate with the pRNFL ***:The pRNFL was thinner in the temporal and inferior quadrants in MS patients compared with normal controls(P0.05).In MS patients,the PR/UD was not related to the expanded disability status scale(EDSS)nor disease duration(r ranged from−0.17 to 0.02,P>0.05).Conclusion:This is the first study using PS-OCT to study the pRNFL birefringence in MS *** birefringence of the pRNFL may indicate microtubule abnormality,and could be a potential biomarker for detecting early neurodegeneration in MS.

关键词： Remitting relapsing multiple sclerosis(RRMS) Peripapillary retinal nerve Fiber layer(pRNFL) Microtubule dysfunction Polarization sensitive optical coherence tomography(PS-OCT)

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Dynamic Recrystallization Behavior of Q370qE Bridge Steel

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Chinese Journal of Mechanical Engineering 2023年第5期36卷 330-340页

作者： Caiyi liu Shicheng Liang Yan Peng Jianliang Sun Carlo Mapelli silvia Barella Andrea Gruttadauria Marco Belf Ludovica Rovatti National Engineering Research Center for Equipment and Technology of Cold Roll Strip Rolling Yanshan UniversityQinhuangdao 066004China Department of Mechanical Engineering Politecnico di Milano20156 MilanItaly

Bridge steel has been widely used in recent years for its excellent performance. Understanding the high-temperature Dynamic Recrystallization (DRX) behavior of high-performance bridge steel plays an important role in guiding the thermomechanical processing process. In the present study, the hot deformation behavior of Q370qE bridge steel was investigated by hot compression tests conducted on a Gleeble 3800-GTC thermal-mechanical physical simulation system at temperatures ranging from 900 ℃ to 1100 ℃ and strain rates ranging from 0.01 s^(−1) to 10 s^(−1). The obtained results were used to plot the true stress-strain and work-hardening rate curves of the experimental steel, with the latter curves used to determine the critical strains for the initiation of DRX. The Zener-Hollomon equation was subsequently applied to establish the correspondence between temperature and strain rate during the high-temperature plastic deformation of bridge steel. In terms of the DRX volume fraction solution, a new method for establishing DRX volume fraction was proposed based on two theoretical models. The good weathering and corrosion resistance of bridge steel lead to difculties in microstructure etching. To solve this, the MTEX technology was used to further develop EBSD data to characterize the original microstructure of Q370qE bridge steel. This paper lays the theoretical foundation for studying the DRX behavior of Q370qE bridge steel.

关键词： Dynamic recrystallization Materials characterization Hot deformation DRX volume fraction model

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Delivery of dsRNA for RNAi in insects： an overview and future directions

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Insect Science 2013年第1期20卷 4-14页

作者： Na yu Olivier Christiaens Jisheng liu Jinzhi Niu Kaat Cappelle silvia Caccia Hanneke Huvenne Guy Smagghe Department of Crop Protection Faculty of Bioscience Engineering Ghent University Coupure links 653 B-9000 Ghent Belgium

RNA interference （RNAi） refers to the process of exogenous double-stranded RNA （dsRNA） silencing the complementary endogenous messenger RNA. RNAi has been widely used in entomological research for functional genomics in a variety of insects and its potential for RNAi-based pest control has been increasingly emphasized mainly because of its high specificity. This review focuses on the approaches of introducing dsRNA into insect cells or insect bodies to induce effective RNAi. The three most common delivery methods, namely, microinjection, ingestion, and soaking, are illustrated in details and their advantages and limitations are summarized for purpose of feasible RNAi research. In this review, we also briefly introduce the two possible dsRNA uptake machineries, other dsRNA delivery methods and the history of RNAi in entomology. Factors that influence the specificity and efficiency of RNAi such as transfection reagents, selection of dsRNA region, length, and stability of dsRNA in RNAi research are discussed for further studies.

关键词： dsRNA uptake ingestion microinjection pest control RNA interference soaking

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Bile acid signaling and bariatric surgery

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Liver Research 2017年第4期1卷 208-213页

作者： Jingyan Tian silvia Huang Siming Sun Lili Ding Eryun Zhang Yanjun liu Wendong Huang National Clinical Research Center for Endocrine and Metabolic Diseases Shanghai Institute of Endocrine and Metabolic DiseasesDepartment of Endocrinology and MetabolismRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina Department of Diabetes Complications and Metabolism Beckman Research Institute of City of HopeDuarteCAUSA Eugene Robert Summer Program City of HopeDuarteCAUSA Shanghai Key Laboratory of Compound Chinese Medicines and the Ministry of Education(MOE)Key Laboratory of Standardization of Chinese Medicines Institute of Chinese Materia MedicaShanghai University of Traditional Chinese MedicineShanghaiChina

The rapid worldwide rise in obesity rates over the past few decades imposes an urgent need to develop effective strategies for treating obesity and associated metabolic *** surgical procedures,such as Roux-en-Y gastric bypass(RYGB)and vertical sleeve gastrectomy(VSG),currently provide the most effective treatment for obesity and type 2 diabetes(T2D),as well as for non-alcoholic steatohepatitis(NASH).However,the underlying mechanisms of the beneficial effects of bariatric surgery remain *** studies have identified bile acids as potential signaling molecules involved in the beneficial effects of bariatric *** review focuses on the most recent studies on the roles of bile acids and bile acid receptors Farnesoid X receptor(FXR)and G protein-coupled bile acid receptor 5(TGR5)in bariatric *** also discuss the possibility of modulating bile acid signaling as a pharmacological therapeutic approach to treating obesity and its associated metabolic complications.

关键词： Bile acid(BA) Bariatric surgery Farnesoid X receptor(FXR) G protein-coupled bile acid receptor 5 (TGR5) Microbiota

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Transcriptome analysis of Sinorhizobium meliloti nodule bacteria in nifA mutant background

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Chinese Science Bulletin 2006年第17期51卷 2079-2086页

作者： TIAN Zhexian ZOU Huasong LI Jian ZHANG Yuantao liu Ying YU Guanqiao ZHU Jiabi RUBERG silvia BECKER Anke WANG Yiping National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences Peking University Beijing 10087 lChina National Laboratory of Plant Molecular Genetics Shanghai Institute of Plant Physiology & Ecology Shanghai Institute of Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Lehrstuhl fur Genetik Universitait Bielefeld Postfach 100131 33501 Bielefeld Germany

Gene expression profiles of a Si- norhizobium meliloti 1021 nifA mutant and wild type nodule bacteria were compared using whole genome microarrays. The results revealed a large scale al- teration of gene expression (601 genes) in the nifA minus background. The loss of NifA altered the ex- pression of many functional groups of genes (mac- romolecular metabolism, TCA cycle and respiration, nodulation and nitrogen fixation) and may lead to quite different life stages of the nodule bacteria. Upregulation of fixK and its associated genes was observed in the nifA mutant nodule bacteria. Addi- tional quantitative real-time PCR experiments re- vealed that the transcript levels of fixLJ were signifi- cantly upshifted in the nifA mutant nodule bacteria. Putative NifA binding sites were predicted by a statis- tical method in the upstream sequences of 13 differ- entially regulated genes from the nifA- transcriptome.

关键词：根瘤菌基因突变基因表达染色体组 nifA

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The Forgotten Nutrient——The Role of Nitrogen in Permafrost Soils of Northern China

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Advances in Atmospheric Sciences 2020年第8期37卷 793-799页

作者： Elisabeth RAMM Chunyan liu Xianwei WANG Hongyu YUE Wei ZHANG Yuepeng PAN Michael SCHLOTER silvia GSCHWENDTNER Carsten W.MUELLER Bin HU Heinz RENNENBERG Michael DANNENMANN Institute of Meteorology and Climate Research Atmospheric Environmental Research(IMK-IFU)Karlsruhe Institute of Technology(KIT)Garmisch-Partenkirchen 82467Germany State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry(LAPC) Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Key Laboratory of Wetland Ecology and Environment Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchun 130102China Chair of Soil Science Science Center WeihenstephanDepartment of Ecology and Ecosystem ManagementTechnical University MunichFreising 85354Germany Research Unit for Comparative Microbiome Analyses Helmholtz Zentrum MünchenOberschleissheim 85764Germany Center of Molecular Ecophysiology(CMEP) College of Resources and EnvironmentSouthwest UniversityChongqing 400715China Department of Geosciences and Natural Resource Management University of CopenhagenCopenhagen DK-1350Denmark

***:permafrost carbon and nitrogen feedback to climate change Permafrost refers to any ground,including soils,sediments and rocks,with a temperature at or below the freezing point of water(0℃)for two or more consecut... 详细信息

关键词： ground climate freezing

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A Comparison of Value Elicitation Question Formats in Multiple-Good Contingent Valuation

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Frontiers of Economics in China-Selected Publications from Chinese Universities 2014年第1期9卷 85-108页

作者： Chih-Chen liu Joseph A. Herriges C. L. Kling silvia Secchi Joan I. Nassauer Daniel J. Phaneuf Department of Applied Economics National University of Kaohsiung Kaohsiung 81148Taiwan China Department of Economics Iowa State University Ames IA 50011 USA Department of Agribusiness Economics Southern Illinois University Carbondale IL 62901USA School of Natural Resources and Environment University of Michigan Ann Arbor M148103USA Department of Agricultural and Applied Economics University of Wisconsin Madison WI53706 USA

This paper provides a convergent validity test of two types of multinomial choice questions vis-a-vis a dichotomous choice question by formally testing whether these stated preference elicitation question formats provide comparable welfare estimates. In particular, a dichotomous choice question, a traditional multinomial choice question, and a modified multinomial choice question suggested by Carson and Groves （2007） were applied in split samples to assess the influence of the informational and incentive properties on the respondents＇ annual willingness to accept compensation for adopting costly conservation practices in agriculture that benefit the environment. Our findings suggest that the two multinomial choice question formats elicit a similar mean willingness to accept distributions, but they are both different from a standarddichotomous choice question. Further, the willingness to accept distributions derived from the multinomial choice question formats are more dispersed than those from the dichotomous choice question.

关键词： stated preference choice experiment dichotomous choice,incentive compatibility multinomial choice

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SYNTHESIS AND CHARACTERIZATION OF PHENOTHIAZINE-BASED PPV-TYPE COPOLYMERS CONTAINING FLUORENE AND THIOPHENE MOIETIES

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Chinese Journal of Reactive Polymers 2005年第1期14卷 28-34页

作者： WANG Chen LU Yan liu Song YANG Liying YIN Shougen silvia Janietz Hartmut Krueger Armin Wedel HUA Yulin Institute of Material Physics Tianjin University of Technology Tianjin 300191 China Fraunhofer Institute of Applied Polymer Research Geiselbergstrasse 69 D-14476 Golm Germany

Copolymers of fluorene-co-phenothiazine （ P1） and th iophene-co-phenothiazine （ P2 ） were prepared respectively by Wittig reaction. The synthesis, photo-physical and electroluminescent properties of the resulting polymers were analyzed by FT-IR, GPC, IH-NMR, UV-Vis, Photoluminescence （PL）, Electroluminescence （EL） and Cyclic Voltammetry （CV）. Their single layer devices with configuration of lTO/polymers/Ca/Al were studied. GPC results revealed the weight-average molecular weight （Mw） was 3.0×10^3 and 5.4×10^3, respectively. The device with a single layer structure of ITO/P1/Ca/Al emits green light with the maximum peak at 552nm. However, the device with a single layer structure of ITO/P2/Ca/Al emit red light with the maximum peak at 616nm.

关键词： Phenothiazine Fluorene Thiophene Wittig-reaction Electroluminescence.

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