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A Systems Biology Approach for Studying Heterotopic Ossification： Proteomic Analysis of Clinical Serum and Tissue Samples

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Genomics, Proteomics & Bioinformatics 2018年第3期16卷 212-220页

作者： Erin L. Crowgey Jennifer T. Wyffels Patrick M. Osborn Thomas T. Wood Laura E. Edsberg Nemours Biomedical Research Nemours Alfred I. duPont Hospital for Children Wilmington DE 19803 USA Natural and Health Sciences Researeh Center Center for Wound Healing Research Daemen College Amherst NY 14226 USA department of Computer and Information Sciences Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711 USA san Antonio Military Medical Center San Antonio TX 78219 USA

Heterotopic ossification （HO） refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation （iTRAQ） and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with （HO ＋） and without （HO-） heterotopic ossification. The resulting data were then analyzed using a systems biology approach. We found that serum samples from subjects experiencing traumatic injuries with resulting HO have a different proteomic expression controls. Subsequent quantitative ELISA identified profile compared to those from the matched five blood serum proteins that were differentially regulated between the HO-- and HO- groups. Compared to HO- samples, the amount of insulin-like growth factor I （IGF1） was up-regulated in HO＋ samples, whereas a lower amount of osteopontin （OPN）, myeloperoxidase （MPO）, runt-related transcription factor 2 （RUNX2）,and growth differentiation factor 2 or bone morphogenetic protein 9 （BMP-9） was found in HO ＋ samples （Welch two sample t-test; P 〈 0.05）. These proteins, in combination with potential serum biomarkers previously reported, are key candidates for a serum diagnostic panel that may enable early detection of HO prior to radiographic and clinical manifestations.

关键词： Heterotopic ossification Proteomics Runt-related transcriptionfactor 2 Extracellular matrixorganization Keratinization

Boundary Plasma Turbulence Simulations for Tokamaks

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Communications in Computational Physics 2008年第10期4卷 949-979页

作者： X.Q.Xu M.V.Umansky B.Dudson P.B.Snyder Lawrence Livermore national Laboratory L-630P.O.Box 8087000 East Ave.LivermoreCA 94550USA Institute of Fusion Theory and Simulation ZhejiangUniversityHangzhou 310027China department of Physics University of YorkHeslingtonYorkYO105DDUK general Atomics 13-303P.O.Box 85608San DiegoCA 92186-5608USA.

The boundary plasma turbulence code BOUT models tokamak boundaryplasma turbulence in a realistic divertor geometry usingmodified Braginskii equations for plasma vorticity,density(ni),electron and ion temperature(Te,Ti)and *** BOUT code solves for the plasma fluid equations in a three dimensional(3D)toroidal segment(or a toroidal wedge),including the region somewhat inside the separatrix and extending into the scrape-off layer;the private flux region is also *** this paper,a description is given of the sophisticated physical models,innovative numerical algorithms,and modern software design used to simulate edgeplasmas in magnetic fusion energy *** BOUT code’s unique capabilities and functionality are exemplified via simulations of the impact of plasma density on tokamak edge turbulence and blob dynamics.

关键词： Plasma turbulence simulation plasma two-fluids equation field-aligned coordinates plasma blobs

Altered regional homogeneity in post-traumatic stress disorder: a resting-state functional magnetic resonance imaging study

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Neuroscience Bulletin 2012年第5期28卷 541-549页

作者： Yan Yin Changfeng Jin Lisa T. Eyler Hua Jin Xiaolei Hu Lian Duan Huirong Zheng Bo Feng Xuanyin Huang Baoci Shan Qiyong Gong Lingjiang Li Mental Health Institute The Second Xiangya Hospital of Central South University Changsha 410011 China Shenyang Gongan Hospital Shenyang 110003 China Chinese University of Hong Kong Hong Kong China department of Psychiatry University of California-San Diego School of Medicine San Diego California USA VA san Diego Mental Illness Research Education and Clinical Center San Diego California USA VA san Diego Healthcare System San Diego California USA China University of Mining and Technology Xuzhou 221116 China Guangdong Mental Health Institute Guangdong General Hospital Guangdong Academy of Medical Sciences Guangzhou 510120 China Mianzhu Psychiatric Hospital Deyang 618200 China Mental Health Center of Sichuan Province Mianyang 621000 China Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China Huaxi MR Research Center Department of Radiology West China Hospital of Sichuan University Chengdu 610041 China

Objective Little is known about the brain systems that contribute to vulnerability to post-traumatic stress disorder （PTSD）. Comparison of the resting-state patterns of intrinsic functional synchronization, as measured by functional magnetic resonance imaging （fMRI）, between groups with and without PTSD following a traumatic event can help identify the neural mechanisms of the disorder and targets for intervention. Methods Fifty-four PTSD patients and 72 matched traumatized subjects who experienced the 2008 Sichuan earthquake were imaged with blood oxygen level-dependent （BOLD） fMRI and analyzed using the measure of regional homogeneity （ReHo） during the resting state. Results PTSD patients presented enhanced ReHo in the left inferior parietal lobule and right superior frontal gyrus, and reduced ReHo in the right middle temporal gyrus and lingual gyrus, relative to traumatized individuals without PTSD. Conclusion Our findings showed that abnormal brain activity exists under resting conditions in PTSD patients who had been exposed to a major earthquake. Alterations in the local functional connectivity of cortical regions are likely to contribute to the neural mechanisms underlying PTSD.

关键词： functional magnetic resonance imaging post-traumatic stress disorder regional homogeneity resting-state

Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis

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Journal of Genetics and Genomics 2018年第1期45卷 41-45页

作者： Sebastia Franch-Exposito Clara Esteban-Jurado Pilar Garre Isabel Quintanilla Saray Duran-sanchon Marcos Diaz-Gay Laia Bonjoch Miriam Cuatrecasas Esther Samper Jenifer Munoz Teresa Ocana Sabela Carballal Maria Lopez-Ceron Antoni Castells Maria Vila-Casadesus Sophia derdak Steven Laurie Sergi Beltran Jaime carvajal Luis Bujanda Clara Ruiz-Ponte Jordi Camps Meritxell Gironella Juan Jose Lozano Francesc Balaguer Joaquin Cubiella Trinidad Caldes Sergi Castellvi-Bel Gastroenterology department Hospital Clinic de Barcelona August Pi i Sunyer Biomedical Research Institute CIBER of Hepatic and Digestive Diseases University of Barcelona Barcelona 08036 Spain Molecular Oncology Laboratory Hospital Clinico San Carlos Health Research Institute of the Hospital Clinico San Carlos Madrid 28040 Spain department of Pathology Hospital Clinic de Barcelona Barcelona 08036 Spain EPICOLON consortium Bioinformatics Platform CIBER of Hepatic and Digestive Diseases Barcelona 08036 Spain national Center of Genomic Analysis Science Park of Barcelona Barcelona 08028 Spain Andalusian developmental Biology Institute CSIC-Pablo de Olavide University-Andalusian Regional Government SeviUa 41013 Spain Gastroenterology department Hospital Donostia-Biodonostia Institute CIBER of Hepatic and Digestive Diseases University of the Basque Country (UPV/EHU) San Sebastian 20080 Spain Galician Public Foundation of Genomic Medicine (FPGMX) CIBER of Rare Diseases Genomics Medicine Group Hospital Clinico Universitario University of Santiago de Compostela Santiago de Cornpostela 15706 Spain Castroenterology department Complexo Hospitalario Universitario de Ourense Ourense Biomedical Research Institute Ourense 32005 Spain

Colorectal cancer （CRC） is one of the most common neoplasms and an important cause of mortality worldwide （http：//globocan. ***]）. Approximately 35% of the variation in CRC susceptibility is likely due to heritable factors （Lichtenstein et al., 2000}. Genetic variations in the human genome include single nucleotide variants （SNVs）, short insertions and deletions, and larger structural variants resulting in gain or loss of genomic DNA larger than 1 kb, such as copy number variants （CNVs）. Leaving aside the importance of CNVs in sporadic tumor development, these variants can also be present in the germline DNA of healthy individuals from the general population and be considered polymorphic.

关键词： WHOLE-EXOME GENE

Transcriptomic analyses of localized prostate cancers of East Asian and North American men reveal race-specific luminal-basal and microenvironmental differences

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Cancer Communications 2023年第10期43卷 1164-1168页

作者： Melvin L.K.Chua Alexander K.Hakansson Enya H.W.Ong Boon Hao Hong Jing Jing Miao Adelene Y.L.Sim Janice S.H.Tan Kah Min Tan Gabrielle C.J.Lee Kar Perng Low Jeffrey K.L.Tuan Terence W.K.Tan Michael L.C.Wang Joe P.S.Yeong Michael C.S.Tan Lui Shiong Lee Ravindran Kanesvaran Xin Zhao Julian Ho Daniel E.Spratt Edward M.Schaeffer Kae-Jack Tay Yang Liu Elai Davicioni Li Yan Khor Division of Radiation Oncology National Cancer Centre SingaporeSingaporeSingapore Duke-NUS Medical School SingaporeSingapore Division of Medical Sciences National Cancer Centre SingaporeSingaporeSingapore Veracyte IncSan DiegoCAUSA department of Nasopharyngeal Carcinoma State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapySun Yat-sen University Cancer CenterGuangzhouGuangdongP.R.China Faculty of Medicine Nursing and Health SciencesMonash UniversityVictoriaAustralia department of Anatomical Pathology Singapore General HospitalSingaporeSingapore department of Pathology Changi General HospitalSingaporeSingapore department of Urology Sengkang General HospitalSingaporeSingapore Division of Medical Oncology National Cancer Centre SingaporeSingaporeSingapore department of Radiation Oncology University Hospitals Seidman Cancer CenterCase Comprehensive Cancer CenterClevelandOHUSA department of Urology Northwestern University Feinberg School of MedicineChicagoILUSA department of Urology Singapore General HospitalSingaporeSingapore

dear editor,Prostate cancer(PCa)remains a major healthcare burden in men globally[1].Most patients present with localized disease,and treatment is recommended based on risk classification systems like the national Comprehensive Cancer Network(NCCN)[2].However,these methods are imprecise for estimating metastasis-free survival and prostate cancer-specific mortality and thus biomarkers that can predict tumor aggression are needed[3–5].Several studies have since characterized the molecular landscape of localized PCa in White[4,5]and Black/African-American men[6],but data is lacking in Asian *** Chinese Prostate Cancer Genome and Epigenome Atlas(CPGEA)reported on the genomic and epigenomic landscape of 208 PCa of men from China[7].Comparative analyses between the CPGEA cohort and data from The Cancer Genome Atlas(TCGA)revealed higher frequencies of Forkhead box A1(FOXA1)and chromodomain-helicase DNA-binding 1(CHD1)mutations,and lower frequencies of phosphatase and tensin homolog(PTEN)mutations and transmembrane protease serine 2-E26 transformationspecific related gene(TMPRSS2-ERG)fusion in Chinese compared with White men[7].These preliminary findings highlight the presence of race-specific differences in molecular phenotypes of PCa.

关键词： landscape Atlas editor

Enterococcal urinary tract infections: eight years experience at a regional hospital in Trinidad, West Indies

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Chinese Medical Journal 2001年第1期114卷 90-92页

作者： Fitzroy A.Orrett Ehlich Connors Faculty of Medical Sciences Department of ParaClinical SciencesThe University of the West IndiesSt.AugustineTrinidad and TobagoWest Indies san Fernando general Hospital San FernandoTrinidad and TobagoWest Indies

OBJECTIVE: To investigate the prevalence of significant enterococcal isolates from urine and determine what factors are associated with the increased prevalence, with particular reference to antibiotic susceptibilities. METHODS: Retrospective analysis over an 8-year period of hospital laboratory records of urinary isolates of enterococci was done. Species were identified via colony morphology, growth in 6.5% sodium chloride and their ability to hydrolyze esculin in the presence of 40% bile salts. Susceptibility testing via the disc diffusion technique with 9 commonly used antibiotics was also done as defined by the national Committee for Clinical Laboratory Standards. RESULTS: From 39,881 urine specimens, 9116 (22.9%) were culture positive. Of this 9116, 1001 (11.0%) were enterococci, the 4th most common urinary isolate. E. coli was the most common (36.2%). Most enterococci were from pediatric patients (28.4%) and the urology unit (24.5%). All enterococci were fully sensitive to ampicillin and augmentin (amoxicillin-clavulanic acid). Sensitivity to gentamicin decreased significantly from 79% in 1990 to 58% in 1997 (P

关键词： Drug Resistance, Multiple Enterococcus Gram-Positive Bacterial Infections Humans Microbial Sensitivity Tests Prevalence Retrospective Studies Urinary Tract Infections West Indies

Photodynamic therapy as salvage therapy for residual microscopic cancer after ultra-low anterior resection: A case report

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World Journal of Clinical Cases 2019年第6期7卷 798-804页

作者： Si-Qi Zhang Kui-Jie Liu Hong-Liang Yao san-Lin Lei Zhen-Dong Lei Wen-Jun Yi Li Xiong Hua Zhao department of general Surgery the Second Xiangya HospitalCentral South University

BACKGROUND The rate of positive resection margins(R1) in patients with low rectal cancer is substantial. Recommended remedies such as extended resection or chemoradiotherapy have their own serious drawbacks. It has been reported that photodynamic therapy(PDT) as a remedial treatment for esophageal *** cancer and esophageal cancer has many similarities,however,PDT as a salvage therapy for rectal cancer is *** SUMMARY Here,we describe a 56-year-old man who was admitted to the hospital due to a 6-mo history of hemafecia,which had been aggravated for 1 mo. Colonoscopy revealed a 3 × 4 cm ulcerated mass in the rectum 4 cm from the *** pathological examination showed villous adenoma,moderate-tohigh-grade dysplasia,good differentiation,and invasion of the mucosal *** patient had R1 after ultra-low anterior resection,but he refused extended resection and experienced severe liver function impairment after 3 cycles of chemotherapy. Ultimately,the patient underwent PDT to remove R1. After five years of follow-up,there was no liver function impairment,recurrence,metastasis,sexual dysfunction,or abnormal defecation *** This is the first case worldwide in which R1 of rectal cancer were successfully treated by PDT.

关键词： Low rectal cancer Photodynamic therapy Positive microscopic distal margin Salvage therapy Removal Residual microscopic cancer Case report

Anabolic steroid abuse causing recurrent hepatic adenomas and hemorrhage

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World Journal of Gastroenterology 2008年第28期14卷 4573-4575页

作者： Nicole M martin Barham K Abu Dayyeh Raymond T Chung Gastrointestinal Unit Massachusetts General HospitalBostonMassachusetts 02114United States

Anabolic steroid abuse is common among athletes and is associated with a number of medical complications. We describe a case of a 27-year-old male bodybuilder with multiple hepatic adenomas induced by anabolic steroids. He initially presented with tumor hemorrhage and was treated with left lateral hepatic segmentectomy. Regression of the remaining tumors was observed with cessation of steroid use. However, 3 years and a half after his initial hepatic segmentectomy, he presented with recurrent tumor enlargement and intraperitoneal hemorrhage in the setting of steroid abuse relapse. Given his limited hepatic reserve, he was conservatively managed with embolization of the right accessory hepatic artery. This is the first reported case of hepatic adenoma re- growth with recidivistic steroid abuse, complicated by life-threatening hemorrhage. While athletes and bodybuilders are often aware of the legal and social ramifications of steroid abuse, they should continue to be counseled about its serious medical risks.

关键词： Anabolic steroids Adenoma Liver Hemorrhage

Systematic review of the outcomes of surgical resection for intermediate and advanced Barcelona Clinic Liver Cancer stage hepatocellular carcinoma:A critical appraisal of the evidence

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World Journal of Hepatology 2018年第6期10卷 433-447页

作者： Ye Xin Koh Hwee Leong Tan Weng Kit Lye Juinn Huar Kam Adrian Kah Heng Chiow Siong san Tan Su Pin Choo Alexander Yaw Fui Chung Brian Kim Poh Goh department of Hepatopancreatobiliary and Transplant Surgery Singapore General HospitalSingapore 169608Singapore Center for Quantitative Medicine Duke-NUS Graduate Medical SchoolSingapore 169857Singapore department of general Surgery Hepatopancreatobiliary ServiceChangi General HospitalSingapore 529889Singapore department of Medical Oncology National Cancer Centre SingaporeSingapore 169610Singapore Duke-NUS Graduate Medical School Singapore 169857Singapore

AIM To perform a systematic review to determine the survival outcomes after curative resection of intermediate and advanced hepatocellular carcinomas(HCC).METHODS A systematic review of the published literature was performed using the PubM ed database from 1 st January 1999 to 31 st dec 2014 to identify studies that reported outcomes of liver resection as the primary curative treatment for Barcelona Clinic Liver Cancer(BCLC) stage B or C HCC. The primary end point was to determine the overall survival(OS) and disease free survival(DFS) of liver resection of HCC in BCLC stage B or C in patients with adequate liver reserve(i.e., Child's A or B status). The secondary end points were to assess the morbidity and mortality of liver resection in large HCC(defined as lesions larger than 10 cm in diameter) and to compare the OS and DFS after surgical resection of solitary vs multifocal *** We identified 74 articles which met the inclusion criteria and were analyzed in this systematic review. Analysis of the resection outcomes of the included studies were grouped according to(1) BCLC stage B or C HCC,(2) Size of HCC and(3) multifocal tumors. The median 5-year OS of BCLC stage B was 38.7%(range 10.0-57.0); while the median 5-year OS of BCLC stage C was 20.0%(range 0.0-42.0). The collective median 5-year OS of both stages was 27.9%(0.0-57.0). In examining the morbidity and mortality following liver resection in large HCC, the pooled RR for morbidity [RR(95%CI) = 1.00(0.76-1.31)] and mortality [RR(95%CI) = 1.15(0.73-1.80)] were not significant. Within the spectrum of BCLC B and C lesions, tumors greater than 10 cm were reported to have median 5-year OS of 33.0% and multifocal lesions 54.0%.CONCLUSION Indication for surgical resection should be extended to BCLC stage B lesions in selected patients. Further studies are needed to stratify stage C lesions for resection.

关键词： Barcelona Clinic Liver Cancer Hepatocellular carcinoma Hepatectomy Milan criteria