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  1. Reporting of Human Genome Epidemiology (HuGE association studies: An empirical assessment

    Directory of Open Access Journals (Sweden)

    Gwinn Marta

    2008-05-01

    Full Text Available Abstract Background Several thousand human genome epidemiology association studies are published every year investigating the relationship between common genetic variants and diverse phenotypes. Transparent reporting of study methods and results allows readers to better assess the validity of study findings. Here, we document reporting practices of human genome epidemiology studies. Methods Articles were randomly selected from a continuously updated database of human genome epidemiology association studies to be representative of genetic epidemiology literature. The main analysis evaluated 315 articles published in 2001–2003. For a comparative update, we evaluated 28 more recent articles published in 2006, focusing on issues that were poorly reported in 2001–2003. Results During both time periods, most studies comprised relatively small study populations and examined one or more genetic variants within a single gene. Articles were inconsistent in reporting the data needed to assess selection bias and the methods used to minimize misclassification (of the genotype, outcome, and environmental exposure or to identify population stratification. Statistical power, the use of unrelated study participants, and the use of replicate samples were reported more often in articles published during 2006 when compared with the earlier sample. Conclusion We conclude that many items needed to assess error and bias in human genome epidemiology association studies are not consistently reported. Although some improvements were seen over time, reporting guidelines and online supplemental material may help enhance the transparency of this literature.

  2. HuGE Watch: tracking trends and patterns of published studies of genetic association and human genome epidemiology in near-real time.

    Science.gov (United States)

    Yu, Wei; Wulf, Anja; Yesupriya, Ajay; Clyne, Melinda; Khoury, Muin Joseph; Gwinn, Marta

    2008-09-01

    HuGE Watch is a web-based application for tracking the evolution of published studies on genetic association and human genome epidemiology in near-real time. The application allows users to display temporal trends and spatial distributions as line charts and google maps, providing a quick overview of progress in the field. http://www.hugenavigator.net/HuGENavigator/startPageWatch.do

  3. Epidemiology & Genomics Research Program

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    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  4. A probabilistic algorithm for interactive huge genome comparison.

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    Courtois, P R; Moncany, M L

    1995-12-01

    We designed a new probabilistic algorithm, named PAGEC (probabilistic algorithm for genome comparison), which allowed a highly interactive study of long genomic strings. The comparison between two nucleic acid sequences is based on the creation of multiple index tables, which drastically reduces processing time for huge genomes, e.g. 13 min for a 4 Mb/4 Mb comparison. PAGEC lowered the need for memory when compared with other types of algorithm and took into account the low resolution of the final representation (paper or computer screen). Considering that standard printers permit a 300 d.p.i. resolution, the loss of computed information due to the probabilistic conception of the algorithm was not usually noticeable in the present study, mainly due to increased genomic sizes. Refinement was possible through an interactive zooming system, which enabled the visualization of the lexical base sequences of a considered part of both of the studied genomes. Biological examples of computation based on yeast and animal nucleic acid sequences presented in this paper reveal the flexibility of the PAGEC program, which is a valuable tool for genetic studies as it offers a solution to an important problem that will become even more important as time passes.

  5. Genomic Resources for Cancer Epidemiology

    Science.gov (United States)

    This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.

  6. A systematic appraisal of field synopses in genetic epidemiology: a HuGE review.

    Science.gov (United States)

    Belbasis, Lazaros; Panagiotou, Orestis A; Dosis, Vasilios; Evangelou, Evangelos

    2015-01-01

    Evidence from genetic association studies is accumulating rapidly. Field synopses have recently arisen as an unbiased way of systematically synthesizing this evidence. We performed a systematic review and appraisal of published field synopses in genetic epidemiology and assessed their main findings and methodological characteristics. We identified 61 eligible field synopses, published between January 1, 2007, and October 31, 2013, on 52 outcomes reporting 734 significant associations at the P < 0.05 level. The median odds ratio for these associations was 1.25 (interquartile range, 1.15-1.43). Egger's test was the most common method (n = 30 synopses) of assessing publication bias. Only 12 synopses (20%) used the Venice criteria to evaluate the epidemiologic credibility of their findings (n = 449 variants). Eleven synopses (18%) were accompanied by an online database that has been regularly updated. These synopses received more citations (P = 0.01) and needed a larger research team (P = 0.02) than synopses without an online database. Overall, field synopses are becoming a valuable tool for the identification of common genetic variants, especially when researchers follow relevant methodological guidelines. Our work provides a summary of the current status of the field synopses published to date and may help interested readers efficiently identify the online resources containing the relevant genetic evidence. © The Author 2014. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Whole Genome Epidemiological Typing of Salmonella

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas

    . Technological advances and effective price in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Typing of Salmonella, especially sub-typing within the same serotype or even the same clone, the genetic variation of the target genes being...... used for typing is crucial for successful discrimination. The core genes or the genes that are conserved in all members of a genus or species are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. A total of 2,882 core genes have been observed among 73...... evolution and remain useful as candidate genes for bacterial genome typing-even if they cannot be expected to differentiate highly clonal isolates e.g. outbreak cases of Salmonella [I]. To achieve successful ‘real-time’ monitoring and identification of outbreaks, rapid and reliable sub-typing is essential...

  8. Human Genome Epidemiology : A scientific foundation for using genetic information to improve health and prevent disease

    Directory of Open Access Journals (Sweden)

    Stefania Boccia

    2005-03-01

    Full Text Available

    Human health is determined by the interplay of genetic factors and the environment. In this context the recent advances in human genomics are expected to play a central role in medicine and public health by providing genetic information for disease prediction and prevention.

    After the completion of the human genome sequencing, a fundamental step will be represented by the translation of these discoveries into meaningful actions to improve health and prevent diseases, and the field of epidemiology plays a central role in this effort. These are some of the issues addressed by Human Genome Epidemiology –A scientific foundation for using genetic information to improve health and prevent disease, a volume edited by Prof. M. Khoury, Prof. J. Little, Prof.W. Burke and published by Oxford university Press 2004.

    This book describes the important role that epidemiological methods play in the continuum from gene discovery to the development and application of genetic tests. The Authors calls this continuum human genome epidemiology (HuGE to denote an evolving field of inquiry that uses systematic applications of epidemiological methods to assess the impact of human genetic variation on health and disease.

    The book is divided into four sections and it is structured to allow readers to proceed systematically from the fundamentals of genome technology and discovery, to the epidemiological approaches, to gene characterisation, to the evaluation of genetic tests and their use in health services and public health.

  9. Online genetic databases informing human genome epidemiology

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    Higgins Julian PT

    2007-07-01

    Full Text Available Abstract Background With the advent of high throughput genotyping technology and the information available via projects such as the human genome sequencing and the HapMap project, more and more data relevant to the study of genetics and disease risk will be produced. Systematic reviews and meta-analyses of human genome epidemiology studies rely on the ability to identify relevant studies and to obtain suitable data from these studies. A first port of call for most such reviews is a search of MEDLINE. We examined whether this could be usefully supplemented by identifying databases on the World Wide Web that contain genetic epidemiological information. Methods We conducted a systematic search for online databases containing genetic epidemiological information on gene prevalence or gene-disease association. In those containing information on genetic association studies, we examined what additional information could be obtained to supplement a MEDLINE literature search. Results We identified 111 databases containing prevalence data, 67 databases specific to a single gene and only 13 that contained information on gene-disease associations. Most of the latter 13 databases were linked to MEDLINE, although five contained information that may not be available from other sources. Conclusion There is no single resource of structured data from genetic association studies covering multiple diseases, and in relation to the number of studies being conducted there is very little information specific to gene-disease association studies currently available on the World Wide Web. Until comprehensive data repositories are created and utilized regularly, new data will remain largely inaccessible to many systematic review authors and meta-analysts.

  10. Genome network medicine: innovation to overcome huge challenges in cancer therapy.

    Science.gov (United States)

    Roukos, Dimitrios H

    2014-01-01

    The post-ENCODE era shapes now a new biomedical research direction for understanding transcriptional and signaling networks driving gene expression and core cellular processes such as cell fate, survival, and apoptosis. Over the past half century, the Francis Crick 'central dogma' of single n gene/protein-phenotype (trait/disease) has defined biology, human physiology, disease, diagnostics, and drugs discovery. However, the ENCODE project and several other genomic studies using high-throughput sequencing technologies, computational strategies, and imaging techniques to visualize regulatory networks, provide evidence that transcriptional process and gene expression are regulated by highly complex dynamic molecular and signaling networks. This Focus article describes the linear experimentation-based limitations of diagnostics and therapeutics to cure advanced cancer and the need to move on from reductionist to network-based approaches. With evident a wide genomic heterogeneity, the power and challenges of next-generation sequencing (NGS) technologies to identify a patient's personal mutational landscape for tailoring the best target drugs in the individual patient are discussed. However, the available drugs are not capable of targeting aberrant signaling networks and research on functional transcriptional heterogeneity and functional genome organization is poorly understood. Therefore, the future clinical genome network medicine aiming at overcoming multiple problems in the new fields of regulatory DNA mapping, noncoding RNA, enhancer RNAs, and dynamic complexity of transcriptional circuitry are also discussed expecting in new innovation technology and strong appreciation of clinical data and evidence-based medicine. The problematic and potential solutions in the discovery of next-generation, molecular, and signaling circuitry-based biomarkers and drugs are explored.

  11. Whole Genome Epidemiological Typing of Escherichia coli

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer

    is in general expensive and to some extent unreliable. Next generation sequencing has quickly become a tool widely available and has enabled even smaller laboratories to do whole genome sequencing (WGS). Having the entire genome available provides the opportunity to create the ultimate typing method. This Ph...... validating each position analyzed and ignoring the positions that cannot be validated thereby creating a distance matrix that is used as input to an UPGMA method that creates the final phylogeny. The ND method was also implemented as a web server and published. If whole genome sequencing is to be used...... compared to the background strains, but only the SNP method was able to set one common threshold for outbreak isolates versus non-outbreak isolates for the entire dataset. Whole genome sequencing is a powerful but also a rather new tool. This PhD thesis has hopefully shed some light on how we can continue...

  12. Genomic variation in Salmonella enterica core genes for epidemiological typing

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    Leekitcharoenphon Pimlapas

    2012-03-01

    Full Text Available Abstract Background Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology. Results We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes. Conclusions Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.

  13. Arenaviruses and hantaviruses: from epidemiology and genomics to antivirals.

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    Charrel, R N; Coutard, B; Baronti, C; Canard, B; Nougairede, A; Frangeul, A; Morin, B; Jamal, S; Schmidt, C L; Hilgenfeld, R; Klempa, B; de Lamballerie, X

    2011-05-01

    The arenaviruses and hantaviruses are segmented genome RNA viruses that are hosted by rodents. Due to their association with rodents, they are globally widespread and can infect humans via direct or indirect routes of transmission, causing considerable human morbidity and mortality. Nevertheless, despite their obvious and emerging importance as pathogens, there are currently no effective antiviral drugs (except ribavirin which proved effective against Lassa virus) with which to treat humans infected by any of these viruses. The EU-funded VIZIER project (Comparative Structural Genomics of Viral Enzymes Involved in Replication) was instigated with an ultimate view of contributing to the development of antiviral therapies for RNA viruses, including the arenaviruses and bunyaviruses. This review highlights some of the major features of the arenaviruses and hantaviruses that have been investigated during recent years. After describing their classification and epidemiology, we review progress in understanding the genomics as well as the structure and function of replicative enzymes achieved under the VIZIER program and the development of new disease control strategies.

  14. The GLOBE 3D Genome Platform : Towards a novel System-Biological Paper-Tool to integrate the Huge Complexity of Genome Organization and Function - Presentation

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); F.G. Grosveld (Frank)

    2009-01-01

    textabstractThe combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various forms

  15. The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

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    Kuller, Lewis H; Bracken, Michael B; Ogino, Shuji; Prentice, Ross L; Tracy, Russell P

    2013-11-01

    On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?" The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.

  16. Epidemiological studies of esophageal cancer in the era of genome-wide association studies

    Institute of Scientific and Technical Information of China (English)

    An-Hui; Wang; Yuan; Liu; Bo; Wang; Yi-Xuan; He; Ye-Xian; Fang; Yong-Ping; Yan

    2014-01-01

    Esophageal cancer(EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma(ESCC) is the predominant histologic type(90%-95%), while the incidence of esophageal adenocarcinoma(EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved inthe process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies(GWAS). Here we review the epidemiological studies of EC(especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants(genes, SNPs, miRNAs, proteins) involved in the process of ESCC.

  17. Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.

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    Kingry, Luke C; Rowe, Lori A; Respicio-Kingry, Laurel B; Beard, Charles B; Schriefer, Martin E; Petersen, Jeannine M

    2016-04-01

    Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST) is a recently developed methodology that simplifies genomic analyses by transforming millions of base pairs of sequence into character data for each gene. We sequenced 13 US Y. pestis isolates with known epidemiologic relationships. Sequences were assembled de novo, and multilocus sequence typing alleles were assigned by comparison against 3979 open reading frames from the reference strain CO92. Allele-based cluster analysis accurately grouped the 13 isolates, as well as 9 publicly available Y. pestis isolates, by their epidemiologic relationships. Our findings indicate wgMLST is a simplified, sensitive, and scalable tool for epidemiologic analysis of Y. pestis strains.

  18. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis.

    Science.gov (United States)

    Guthrie, Jennifer L; Gardy, Jennifer L

    2017-01-01

    Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission. © 2016 New York Academy of Sciences.

  19. Genomic variation in Salmonella enterica core genes for epidemiological typing

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Rundsten, Carsten Friis

    2012-01-01

    Background: Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over...... genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher...... that there is a positive selection towards mutations leading to amino acid changes. Conclusions: Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important...

  20. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.

    Directory of Open Access Journals (Sweden)

    Guillaume Méric

    Full Text Available The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation--focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb. The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥ 70% identity over ≥ 50% of the locus length--aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.

  1. Whole Genome Analysis of Epidemiologically Closely Related Staphylococcus aureus Isolates

    NARCIS (Netherlands)

    M. Schijffelen (Maarten); S.R. Konstantinov (Sergey); G. Lina (Gérard); I. Spiliopoulou (Iris); E. van Duijkeren (Engeline); E.C. Brouwer (Ellen); A.C. Fluit (Ad)

    2013-01-01

    textabstractThe change of the bacteria from colonizers to pathogens is accompanied by a drastic change in expression profiles. These changes may be due to environmental signals or to mutational changes. We therefore compared the whole genome sequences of four sets of S. aureus isolates. Three sets

  2. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread.

    Science.gov (United States)

    Coscolla, Mireia; Barry, Pennan M; Oeltmann, John E; Koshinsky, Heather; Shaw, Tambi; Cilnis, Martin; Posey, Jamie; Rose, Jordan; Weber, Terry; Fofanov, Viacheslav Y; Gagneux, Sebastien; Kato-Maeda, Midori; Metcalfe, John Z

    2015-07-15

    The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains.

  3. Frontiers in cancer epidemiology: a challenge to the research community from the Epidemiology and Genomics Research Program at the National Cancer Institute.

    Science.gov (United States)

    Khoury, Muin J; Freedman, Andrew N; Gillanders, Elizabeth M; Harvey, Chinonye E; Kaefer, Christie; Reid, Britt C; Rogers, Scott; Schully, Sheri D; Seminara, Daniela; Verma, Mukesh

    2012-07-01

    The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is developing scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop in December 2012 to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies.

  4. Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis

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    Mustapha M. Mustapha

    2015-10-01

    Full Text Available Neisseria meningitidis is a leading bacterial cause of sepsis and meningitis globally with dynamic strain distribution over time. Beginning with an epidemic among Hajj pilgrims in 2000, serogroup W (W sequence type (ST 11 emerged as a leading cause of epidemic meningitis in the African ‘meningitis belt’ and endemic cases in South America, Europe, Middle East and China. Previous genotyping studies were unable to reliably discriminate sporadic W ST-11 strains in circulation since 1970 from the Hajj outbreak strain (Hajj clone. It is also unclear what proportion of more recent W ST-11 disease clusters are caused by direct descendants of the Hajj clone. Whole genome sequences of 270 meningococcal strains isolated from patients with invasive meningococcal disease globally from 1970 to 2013 were compared using whole genome phylogenetic and major antigen-encoding gene sequence analyses. We found that all W ST-11 strains were descendants of an ancestral strain that had undergone unique capsular switching events. The Hajj clone and its descendants were distinct from other W ST-11 strains in that they shared a common antigen gene profile and had undergone recombination involving virulence genes encoding factor H binding protein, nitric oxide reductase, and nitrite reductase. These data demonstrate that recent acquisition of a distinct antigen-encoding gene profile and variations in meningococcal virulence genes was associated with the emergence of the Hajj clone. Importantly, W ST-11 strains unrelated to the Hajj outbreak contribute a significant proportion of W ST-11 cases globally. This study helps illuminate genomic factors associated with meningococcal strain emergence and evolution.

  5. MANAGEMENT OF HUGE ENCEPHALOCELE

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    Rajeev

    2015-11-01

    Full Text Available Among all neural tube defects, encephalocele incidents are 1 in 5000 live births. (1 Newborn with encephalocele may be associated with other congenital malformations. Encephalocele patient’s management pose many challenge to neurosurgeon due to other associated anomalies that may present like ventriculocele, Dandy Walker and Arnold-Chiari malformation, and difficult positioning airway management to anaesthesiologist. We discuss a case of huge encephalocele and its management

  6. Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

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    Scholz, Matthias; Ward, Doyle V; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian; Morrow, Ardythe L; Segata, Nicola

    2016-05-01

    Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.

  7. Population stratification in the context of diverse epidemiologic surveys sans genome-wide data

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    Matthew T. Oetjens

    2016-05-01

    Full Text Available Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES, population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n=14,998 were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2 and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n=6,634, non-Hispanic blacks (n=3,458, and Mexican Americans (n=3,950. We as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology (PAGE I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants

  8. Whole genome analysis of epidemiologically closely related Staphylococcus aureus isolates.

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    Maarten Schijffelen

    Full Text Available The change of the bacteria from colonizers to pathogens is accompanied by a drastic change in expression profiles. These changes may be due to environmental signals or to mutational changes. We therefore compared the whole genome sequences of four sets of S. aureus isolates. Three sets were from the same patients. The isolates of each pair (S1800/S1805, S2396/S2395, S2398/S2397, an isolate from colonization and an isolate from infection, respectively were obtained within <30 days of each other and the isolate from infection caused skin infections. The isolates were then compared for differences in gene content and SNPs. In addition, a set of isolates from a colonized pig and a farmer from the same farm at the same time (S0462 and S0460 were analyzed. The isolates pair S1800/S1805 showed a difference in a prophage, but these are easily lost or acquired. However, S1805 contained an integrative conjugative element not present in S1800. In addition, 92 SNPs were present in a variety of genes and the isolates S1800 and S1805 were not considered a pair. Between S2395/S2396 two SNPs were present: one was in an intergenic region and one was a synonymous mutation in a putative membrane protein. Between S2397/S2398 only one synonymous mutation in a putative lipoprotein was found. The two farm isolates were very similar and showed 12 SNPs in genes that belong to a number of different functional categories. However, we cannot pinpoint any gene that explains the change from carrier status to infection. The data indicate that differences between the isolate from infection and the colonizing isolate for S2395/S2396 and S2397/S2398 exist as well as between isolates from different hosts, but S1800/S1805 are not clonal.

  9. Comparative genomic fingerprinting of Campylobacter: application in routine public health surveillance and epidemiological investigations.

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    Schleihauf, E; Mutschall, S; Billard, B; Taboada, E N; Haldane, D

    2017-01-01

    A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.

  10. MRSA transmission on a neonatal intensive care unit: epidemiological and genome-based phylogenetic analyses.

    Directory of Open Access Journals (Sweden)

    Ulrich Nübel

    Full Text Available BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA may cause prolonged outbreaks of infections in neonatal intensive care units (NICUs. While the specific factors favouring MRSA spread on neonatal wards are not well understood, colonized infants, their relatives, or health-care workers may all be sources for MRSA transmission. Whole-genome sequencing may provide a new tool for elucidating transmission pathways of MRSA at a local scale. METHODS AND FINDINGS: We applied whole-genome sequencing to trace MRSA spread in a NICU and performed a case-control study to identify risk factors for MRSA transmission. MRSA genomes had accumulated sequence variation sufficiently fast to reflect epidemiological linkage among individual patients, between infants and their mothers, and between infants and staff members, such that the relevance of individual nurses' nasal MRSA colonization for prolonged transmission could be evaluated. In addition to confirming previously reported risk factors, we identified an increased risk of transmission from infants with as yet unknown MRSA colonisation, in contrast to known MRSA-positive infants. CONCLUSIONS: The integration of epidemiological (temporal, spatial and genomic data enabled the phylogenetic testing of several hypotheses on specific MRSA transmission routes within a neonatal intensive-care unit. The pronounced risk of transmission emanating from undetected MRSA carriers suggested that increasing the frequency or speed of microbiological diagnostics could help to reduce transmission of MRSA.

  11. Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

    KAUST Repository

    Perdigão, João

    2015-03-01

    Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20. years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS). Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon.It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB) isolates, mostly recovered in Lisbon, were genotyped by 24-. loci Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeats (MIRU-VNTR) and the genomes sequenced using a next generation sequencing platform - Illumina HiSeq 2000.The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1), two of which are associated with XDR-TB (Lisboa3-B and Q1), whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region: Lisboa3 and Q

  12. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.

    Science.gov (United States)

    Breurec, Sebastien; Criscuolo, Alexis; Diancourt, Laure; Rendueles, Olaya; Vandenbogaert, Mathias; Passet, Virginie; Caro, Valérie; Rocha, Eduardo P C; Touchon, Marie; Brisse, Sylvain

    2016-07-27

    Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.

  13. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition.

    Science.gov (United States)

    Houldcroft, Charlotte J; Underdown, Simon J

    2016-07-01

    High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.

  14. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).

    Science.gov (United States)

    Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A

    2015-07-01

    The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are

  15. A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

    Science.gov (United States)

    Katz, Lee S.; Griswold, Taylor; Williams-Newkirk, Amanda J.; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A.

    2017-01-01

    Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni, and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized

  16. Acinetobacter seifertii Isolated from China: Genomic Sequence and Molecular Epidemiology Analyses.

    Science.gov (United States)

    Yang, Yunxing; Wang, Jianfeng; Fu, Ying; Ruan, Zhi; Yu, Yunsong

    2016-03-01

    Clinical infections caused by Acinetobacter spp. have increasing public health concerns because of their global occurrence and ability to acquire multidrug resistance. Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex encompasses A. calcoaceticus, A. baumannii, A. pittii (formerly genomic species 3), and A nosocomial (formerly genomic species 13TU), which are predominantly responsible for clinical pathogenesis in the Acinetobacter genus. In our previous study, a putative novel species isolated from 385 non-A. baumannii spp. strains based on the rpoB gene phylogenetic tree was reported. Here, the putative novel species was identified as A. seifertii based on the whole-genome phylogenetic tree. A. seifertii was recognized as a novel member of the ACB complex and close to A. baumannii and A. nosocomials. Furthermore, we studied the characteristics of 10 A. seifertii isolates, which were distributed widely in 6 provinces in China and mainly caused infections in the elderly or children. To define the taxonomic status and characteristics, the biochemical reactions, antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome sequence analysis were performed. The phenotypic characteristics failed to distinguish A. serfertii from other species in the ACB complex. Most of the A. seifertii isolates were susceptible to antibiotics commonly used for nosocomial Acinetobacter spp. infections, but one isolate (strain A362) was resistant to ampicillin/sulbactam, ceftazidime and amikacin. The different patterns of MLST and PFGE suggested that the 10 isolates were not identical and lacked clonal relatedness. Our study reported for the first time the molecular epidemiological and genomic features of widely disseminated A. seifertii in China. These observations could enrich the knowledge of infections caused by non-A. baumannii and may provide a scientific basis for future clinical treatment.

  17. A Review of Study Designs and Statistical Methods for Genomic Epidemiology Studies using Next Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Qian eWang

    2015-04-01

    Full Text Available Results from numerous linkage and association studies have greatly deepened scientists’ understanding of the genetic basis of many human diseases, yet some important questions remain unanswered. For example, although a large number of disease-associated loci have been identified from genome-wide association studies (GWAS in the past 10 years, it is challenging to interpret these results as most disease-associated markers have no clear functional roles in disease etiology, and all the identified genomic factors only explain a small portion of disease heritability. With the help of next-generation sequencing (NGS, diverse types of genomic and epigenetic variations can be detected with high accuracy. More importantly, instead of using linkage disequilibrium to detect association signals based on a set of pre-set probes, NGS allows researchers to directly study all the variants in each individual, therefore promises opportunities for identifying functional variants and a more comprehensive dissection of disease heritability. Although the current scale of NGS studies is still limited due to the high cost, the success of several recent studies suggests the great potential for applying NGS in genomic epidemiology, especially as the cost of sequencing continues to drop. In this review, we discuss several pioneer applications of NGS, summarize scientific discoveries for rare and complex diseases, and compare various study designs including targeted sequencing and whole-genome sequencing using population-based and family-based cohorts. Finally, we highlight recent advancements in statistical methods proposed for sequencing analysis, including group-based association tests, meta-analysis techniques, and annotation tools for variant prioritization.

  18. Epidemiological Investigation and Genome Analysis of Duck Circovirus in Southern China

    Institute of Scientific and Technical Information of China (English)

    Chun-he Wan; Guang-hua Fu; Shao-hua Shi; Long-fei Cheng; Hong-mei Chen; Chun-xiang Peng; Su Lin; Yu Huang

    2011-01-01

    Duck circovirus(DuCV),a potential immunosuppressive virus,was investigated in Southern China from March 2006 to December 2009 by using a polymerase chain reaction(PCR)based method. In this study,a total of 138 sick or dead duck samples from 18 different farms were examined with an average DuCV infection rate of~35%. It was found that ducks between the ages of 40~60 days were more susceptible to DuCV. There was no evidence showing that the DuCV virus was capable of vertical transmission. Farms with positive PCR results exhibited no regularly apparent clinical abnormalities such as feathering disorders,growth retardation or lower-than-average weight. The complete genomes of 9. strains from Fujian Province and 1 from Zhejiang Province were sequenced and analyzed. The 10 DuCV genomes,compared with others genomes downloaded from GenBank,ranged in size from 1988 to 1996 base pairs,with sequence identities ranging from 83.2% to 99.8%. Phylogenetic analysis based on genome sequences demonstrated that DuCVs can be divided into two distinct genetic genotypes,Group I(the Euro-USA lineage)and Group II(the Taiwan lineage),with approximately 10.0% genetic difference between the two types. Molecular epidemiological data suggest there is no obvious difference among DuCV strains isolated from different geographic locations or different species,including Duck,Muscovy duck,Mule duck,Cheery duck,Mulard duck and Pekin duck.

  19. Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli.

    Science.gov (United States)

    Tyson, Gregory H; Li, Cong; Ayers, Sherry; McDermott, Patrick F; Zhao, Shaohua

    2016-02-01

    For Enterobacteriaceae such as Salmonella spp. and Escherichia coli, no unified interpretive resistance criteria exist for streptomycin, an epidemiologically important antibiotic. As part of the National Antimicrobial Resistance Monitoring System, we had previously used a minimum inhibitory concentration of ≥ 64 μg mL(-1) as an epidemiological cutoff value (ECV) to define non-wild-type isolates. To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes. From this analysis, we found that using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type. Therefore, to improve the concordance between genotypic and phenotypic data, we propose reducing the phenotypic cutoff values to ≥ 32 μg mL(-1) for both Salmonella and E. coli, to be used widely as ECVs to categorize non-wild-type isolates.

  20. The GLOBE 3D Genome Platform Live Movie of the Presentation : Towards a novel System-Biological Paper-Tool to integrate the Huge Complexity of Genome Organization and Function. Live Movie of the Lecture

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); F.G. Grosveld (Frank)

    2009-01-01

    textabstractThe combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various forms

  1. Epidemiological and Genomic Landscape of Azole Resistance Mechanisms in Aspergillus Fungi

    Science.gov (United States)

    Hagiwara, Daisuke; Watanabe, Akira; Kamei, Katsuhiko; Goldman, Gustavo H.

    2016-01-01

    Invasive aspergillosis is a life-threatening mycosis caused by the pathogenic fungus Aspergillus. The predominant causal species is Aspergillus fumigatus, and azole drugs are the treatment of choice. Azole drugs approved for clinical use include itraconazole, voriconazole, posaconazole, and the recently added isavuconazole. However, epidemiological research has indicated that the prevalence of azole-resistant A. fumigatus isolates has increased significantly over the last decade. What is worse is that azole-resistant strains are likely to have emerged not only in response to long-term drug treatment but also because of exposure to azole fungicides in the environment. Resistance mechanisms include amino acid substitutions in the target Cyp51A protein, tandem repeat sequence insertions at the cyp51A promoter, and overexpression of the ABC transporter Cdr1B. Environmental azole-resistant strains harboring the association of a tandem repeat sequence and punctual mutation of the Cyp51A gene (TR34/L98H and TR46/Y121F/T289A) have become widely disseminated across the world within a short time period. The epidemiological data also suggests that the number of Aspergillus spp. other than A. fumigatus isolated has risen. Some non-fumigatus species intrinsically show low susceptibility to azole drugs, imposing the need for accurate identification, and drug susceptibility testing in most clinical cases. Currently, our knowledge of azole resistance mechanisms in non-fumigatus Aspergillus species such as A. flavus, A. niger, A. tubingensis, A. terreus, A. fischeri, A. lentulus, A. udagawae, and A. calidoustus is limited. In this review, we present recent advances in our understanding of azole resistance mechanisms particularly in A. fumigatus. We then provide an overview of the genome sequences of non-fumigatus species, focusing on the proteins related to azole resistance mechanisms. PMID:27708619

  2. Epidemiology.

    Science.gov (United States)

    Walsh, Kyle M; Ohgaki, Hiroko; Wrensch, Margaret R

    2016-01-01

    More than 250,000 new cases of primary malignant brain tumors are diagnosed annually worldwide, 77% of which are gliomas. A small proportion of gliomas are caused by the inheritance of rare high-penetrance genetic variants or high-dose radiation. Since 2009, inherited genetic variants in 10 regions near eight different genes have been consistently associated with glioma risk via genome-wide association studies. Most of these variants increase glioma risk by 20-40%, but two have higher relative risks. One on chromosome 8 increases risk of IDH-mutated gliomas sixfold and another that affects TP53 function confers a 2.5-fold increased risk of glioma. Functions of some of the other risk variants are known or suspected, but future research will determine functions of other risk loci. Recent progress also has been made in defining subgroups of glioma based on acquired alterations within tumors. Allergy history has been consistently associated with reduced glioma risk, though the mechanisms have not yet been clarified. Future studies will need to be large enough so that environmental and constitutive genetic risk factors can be examined within molecularly defined, etiologically homogeneous subgroups.

  3. Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks.

    Science.gov (United States)

    Fitzpatrick, Margaret A; Ozer, Egon A; Hauser, Alan R

    2016-03-01

    Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.

  4. Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data.

    Directory of Open Access Journals (Sweden)

    Thibaut Jombart

    2014-01-01

    Full Text Available Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees ("who infected whom" from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic approaches having been explored to date. We introduce a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks. Our approach identifies likely transmission events and infers dates of infections, unobserved cases and separate introductions of the disease. It also proves useful for inferring numbers of secondary infections and identifying heterogeneous infectivity and super-spreaders. After testing our approach using simulations, we illustrate the method with the analysis of the beginning of the 2003 Singaporean outbreak of Severe Acute Respiratory Syndrome (SARS, providing new insights into the early stage of this epidemic. Our approach is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker. It is applicable to various densely sampled epidemics, and improves previous approaches by detecting unobserved and imported cases, as well as allowing multiple introductions of the pathogen. Because of its generality, we believe this method will become a tool of choice for the analysis of densely sampled disease outbreaks, and will form a rigorous framework for subsequent methodological developments.

  5. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies

    Science.gov (United States)

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids. PMID:26425340

  6. Gene set analyses of genome-wide association studies on 49 quantitative traits measured in a single genetic epidemiology dataset.

    Science.gov (United States)

    Kim, Jihye; Kwon, Ji-Sun; Kim, Sangsoo

    2013-09-01

    Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr neuronal or nerve systems.

  7. Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash.

    Science.gov (United States)

    García-Closas, M; Egan, K M; Abruzzo, J; Newcomb, P A; Titus-Ernstoff, L; Franklin, T; Bender, P K; Beck, J C; Le Marchand, L; Lum, A; Alavanja, M; Hayes, R B; Rutter, J; Buetow, K; Brinton, L A; Rothman, N

    2001-06-01

    Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 microg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 microg/mouthwash sample for phases 1 and 2, respectively. Most (94-100%) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61% of the brush extracts. PCR success rates for amplification of beta-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100%). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although

  8. Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic

    DEFF Research Database (Denmark)

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S. K.

    2014-01-01

    of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain...... collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data......In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree...

  9. Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC-Producing K. pneumoniae.

    Directory of Open Access Journals (Sweden)

    Jane W Marsh

    Full Text Available Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC-producing Klebsiella pneumoniae (KPC-Kp was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel electrophoresis (PFGE and multi-locus sequence typing (MLST. Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS. Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak.

  10. Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae.

    Science.gov (United States)

    Marsh, Jane W; Krauland, Mary G; Nelson, Jemma S; Schlackman, Jessica L; Brooks, Anthony M; Pasculle, A William; Shutt, Kathleen A; Doi, Yohei; Querry, Ashley M; Muto, Carlene A; Harrison, Lee H

    2015-01-01

    Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL)-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak.

  11. Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium

    NARCIS (Netherlands)

    J.C. Bis (Joshua); A.L. DeStefano (Anita); X. Liu (Xiaoming); J. Brody (Jennifer); S.-H. Choi (Seung-Hoan); B.F.J. Verhaaren (Benjamin); S. Debette (Stéphanie); M.A. Ikram (Arfan); E. Shahar (Eyal); K.R. Butler Jr. (Kenneth); R.F. Gottesman (Rebecca); D. Muzny (Donna); C.L. Kovar (Christie); B.M. Psaty (Bruce); A. Hofman (Albert); T. Lumley (Thomas); M. Gupta (Mayetri); P.A. Wolf (Philip); C.M. van Duijn (Cock); R.A. Gibbs (Richard); T.H. Mosley (Thomas); W.T. Longstreth Jr. (W.); E.A. Boerwinkle (Eric); S. Seshadri (Sudha); M. Fornage (Myriam)

    2014-01-01

    textabstractBackground: Stroke, the leading neurologic cause of death and disability, has a substantial genetic component. We previously conducted a genome-wide association study (GWAS) in four prospective studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consort

  12. Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.

    Directory of Open Access Journals (Sweden)

    Andreas Roetzer

    Full Text Available BACKGROUND: Understanding Mycobacterium tuberculosis (Mtb transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. METHODS AND FINDINGS: During long-term (1997 to 2010 prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs, subdividing the outbreak into seven genome clusters (two to 24 isolates each, plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed "Hamburg clone" started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year. Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological

  13. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

    Science.gov (United States)

    Orlek, Alex; Stoesser, Nicole; Anjum, Muna F.; Doumith, Michel; Ellington, Matthew J.; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A. Sarah; Phan, Hang; Sheppard, Anna E.

    2017-01-01

    Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of ‘accessory genes,’ such as antibiotic resistance genes, as well as ‘backbone’ loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made. PMID:28232822

  14. Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations.

    Science.gov (United States)

    Mohandas, Namitha; Pozio, Edoardo; La Rosa, Giuseppe; Korhonen, Pasi K; Young, Neil D; Koehler, Anson V; Hall, Ross S; Sternberg, Paul W; Boag, Peter R; Jex, Aaron R; Chang, Bill C H; Gasser, Robin B

    2014-12-01

    In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.

  15. Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study.

    Science.gov (United States)

    Fesinmeyer, Megan D; North, Kari E; Lim, Unhee; Bůžková, Petra; Crawford, Dana C; Haessler, Jeffrey; Gross, Myron D; Fowke, Jay H; Goodloe, Robert; Love, Shelley-Ann; Graff, Misa; Carlson, Christopher S; Kuller, Lewis H; Matise, Tara C; Hong, Ching-Ping; Henderson, Brian E; Allen, Melissa; Rohde, Rebecca R; Mayo, Ping; Schnetz-Boutaud, Nathalie; Monroe, Kristine R; Ritchie, Marylyn D; Prentice, Ross L; Kolonel, Lawrence N; Manson, JoAnn E; Pankow, James; Hindorff, Lucia A; Franceschini, Nora; Wilkens, Lynne R; Haiman, Christopher A; Le Marchand, Loic; Peters, Ulrike

    2013-01-11

    Although smoking behavior is known to affect body mass index (BMI), the potential for smoking to influence genetic associations with BMI is largely unexplored. As part of the 'Population Architecture using Genomics and Epidemiology (PAGE)' Consortium, we investigated interaction between genetic risk factors associated with BMI and smoking for 10 single nucleotide polymorphisms (SNPs) previously identified in genome-wide association studies. We included 6 studies with a total of 56,466 subjects (16,750 African Americans (AA) and 39,716 European Americans (EA)). We assessed effect modification by testing an interaction term for each SNP and smoking (current vs. former/never) in the linear regression and by stratified analyses. We did not observe strong evidence for interactions and only observed two interactions with p-values smoking status may modify genetic effects of previously identified genetic risk factors for BMI. Larger studies are needed to follow up our results. NCT00000611.

  16. Epidemiological studies in the information and genomics era: experience of the Clinical Genome of Cancer Project in São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Wünsch-Filho V.

    2006-01-01

    Full Text Available Genomics is expanding the horizons of epidemiology, providing a new dimension for classical epidemiological studies and inspiring the development of large-scale multicenter studies with the statistical power necessary for the assessment of gene-gene and gene-environment interactions in cancer etiology and prognosis. This paper describes the methodology of the Clinical Genome of Cancer Project in São Paulo, Brazil (CGCP, which includes patients with nine types of tumors and controls. Three major epidemiological designs were used to reach specific objectives: cross-sectional studies to examine gene expression, case-control studies to evaluate etiological factors, and follow-up studies to analyze genetic profiles in prognosis. The clinical groups included patients' data in the electronic database through the Internet. Two approaches were used for data quality control: continuous data evaluation and data entry consistency. A total of 1749 cases and 1509 controls were entered into the CGCP database from the first trimester of 2002 to the end of 2004. Continuous evaluation showed that, for all tumors taken together, only 0.5% of the general form fields still included potential inconsistencies by the end of 2004. Regarding data entry consistency, the highest percentage of errors (11.8% was observed for the follow-up form, followed by 6.7% for the clinical form, 4.0% for the general form, and only 1.1% for the pathology form. Good data quality is required for their transformation into useful information for clinical application and for preventive measures. The use of the Internet for communication among researchers and for data entry is perhaps the most innovative feature of the CGCP. The monitoring of patients' data guaranteed their quality.

  17. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

    Science.gov (United States)

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S K; Pearson, Ofori; Hicks, Nathan; Agrawal, Sonia; Sanjar, Fatemeh; Galens, Kevin; Daugherty, Sean; Crabtree, Jonathan; Hendriksen, Rene S; Price, Lance B; Upadhyay, Bishnu P; Shakya, Geeta; Fraser, Claire M; Ravel, Jacques; Keim, Paul S

    2014-11-04

    For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and

  18. Comparative genomic hybridization analysis shows different epidemiology of chromosomal and plasmid-borne cpe-carrying Clostridium perfringens type A.

    Directory of Open Access Journals (Sweden)

    Päivi Lahti

    Full Text Available Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmental samples. Different tolerance to food processing conditions by the plasmid-borne and chromosomal cpe-carrying strains has been reported, but the reservoirs and contamination routes of enterotoxin-producing C. perfringens remain unknown. A comparative genomic hybridization (CGH analysis with a DNA microarray based on three C. perfringens type A genomes was conducted to shed light on the epidemiology of C. perfringens food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains by comparing chromosomal and plasmid-borne cpe-positive and cpe-negative C. perfringens isolates from human, animal, environmental, and food samples. The chromosomal and plasmid-borne cpe-positive C. perfringens genotypes formed two distinct clusters. Variable genes were involved with myo-inositol, ethanolamine and cellobiose metabolism, suggesting a new epidemiological model for C. perfringens food poisonings. The CGH results were complemented with growth studies, which demonstrated different myo-inositol, ethanolamine, and cellobiose metabolism between the chromosomal and plasmid-borne cpe-carrying strains. These findings support a ubiquitous occurrence of the plasmid-borne cpe-positive strains and their adaptation to the mammalian intestine, whereas the chromosomal cpe-positive strains appear to have a narrow niche in environments containing degrading plant material. Thus the epidemiology of the food poisonings caused by two populations appears different, the plasmid-borne cpe-positive strains probably contaminating foods via humans and the chromosomal strains being connected to plant material.

  19. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

    DEFF Research Database (Denmark)

    Grad, Yonatan H; Lipsitch, Marc; Feldgarden, Michael

    2012-01-01

    The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the ...

  20. Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium

    Science.gov (United States)

    Debette, Stéphanie; Ibrahim Verbaas, Carla A.; Bressler, Jan; Schuur, Maaike; Smith, Albert; Bis, Joshua C.; Davies, Gail; Wolf, Christiane; Gudnason, Vilmundur; Chibnik, Lori B.; Yang, Qiong; deStefano, Anita L.; de Quervain, Dominique J.F.; Srikanth, Velandai; Lahti, Jari; Grabe, Hans J.; Smith, Jennifer A.; Priebe, Lutz; Yu, Lei; Karbalai, Nazanin; Hayward, Caroline; Wilson, James F.; Campbell, Harry; Petrovic, Katja; Fornage, Myriam; Chauhan, Ganesh; Yeo, Robin; Boxall, Ruth; Becker, James; Stegle, Oliver; Mather, Karen A.; Chouraki, Vincent; Sun, Qi; Rose, Lynda M.; Resnick, Susan; Oldmeadow, Christopher; Kirin, Mirna; Wright, Alan F.; Jonsdottir, Maria K.; Au, Rhoda; Becker, Albert; Amin, Najaf; Nalls, Mike A.; Turner, Stephen T.; Kardia, Sharon L.R.; Oostra, Ben; Windham, Gwen; Coker, Laura H.; Zhao, Wei; Knopman, David S.; Heiss, Gerardo; Griswold, Michael E.; Gottesman, Rebecca F.; Vitart, Veronique; Hastie, Nicholas D.; Zgaga, Lina; Rudan, Igor; Polasek, Ozren; Holliday, Elizabeth G.; Schofield, Peter; Choi, Seung Hoan; Tanaka, Toshiko; An, Yang; Perry, Rodney T.; Kennedy, Richard E.; Sale, Michèle M.; Wang, Jing; Wadley, Virginia G.; Liewald, David C.; Ridker, Paul M.; Gow, Alan J.; Pattie, Alison; Starr, John M.; Porteous, David; Liu, Xuan; Thomson, Russell; Armstrong, Nicola J.; Eiriksdottir, Gudny; Assareh, Arezoo A.; Kochan, Nicole A.; Widen, Elisabeth; Palotie, Aarno; Hsieh, Yi-Chen; Eriksson, Johan G.; Vogler, Christian; van Swieten, John C.; Shulman, Joshua M.; Beiser, Alexa; Rotter, Jerome; Schmidt, Carsten O.; Hoffmann, Wolfgang; Nöthen, Markus M.; Ferrucci, Luigi; Attia, John; Uitterlinden, Andre G.; Amouyel, Philippe; Dartigues, Jean-François; Amieva, Hélène; Räikkönen, Katri; Garcia, Melissa; Wolf, Philip A.; Hofman, Albert; Longstreth, W.T.; Psaty, Bruce M.; Boerwinkle, Eric; DeJager, Philip L.; Sachdev, Perminder S.; Schmidt, Reinhold; Breteler, Monique M.B.; Teumer, Alexander; Lopez, Oscar L.; Cichon, Sven; Chasman, Daniel I.; Grodstein, Francine; Müller-Myhsok, Bertram; Tzourio, Christophe; Papassotiropoulos, Andreas; Bennett, David A.; Ikram, Arfan M.; Deary, Ian J.; van Duijn, Cornelia M.; Launer, Lenore; Fitzpatrick, Annette L.; Seshadri, Sudha; Mosley, Thomas H.

    2015-01-01

    BACKGROUND Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting. METHODS We conducted genome-wide association studies for paragraph or word list delayed recall in 19 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, comprising 29,076 dementia-and stroke-free individuals of European descent, aged ≥45 years. Replication of suggestive associations (p < 5 × 10−6) was sought in 10,617 participants of European descent, 3811 African-Americans, and 1561 young adults. RESULTS rs4420638, near APOE, was associated with poorer delayed recall performance in discovery (p = 5.57 × 10−10) and replication cohorts (p = 5.65 × 10−8). This association was stronger for paragraph than word list delayed recall and in the oldest persons. Two associations with specific tests, in subsets of the total sample, reached genome-wide significance in combined analyses of discovery and replication (rs11074779 [HS3ST4], p = 3.11 × 10−8, and rs6813517 [SPOCK3], p = 2.58 × 10−8) near genes involved in immune response. A genetic score combining 58 independent suggestive memory risk variants was associated with increasing Alzheimer disease pathology in 725 autopsy samples. Association of memory risk loci with gene expression in 138 human hippocampus samples showed cis-associations with WDR48 and CLDN5, both related to ubiquitin metabolism. CONCLUSIONS This largest study to date exploring the genetics of memory function in ~ 40,000 older individuals revealed genome-wide associations and suggested an involvement of immune and ubiquitin pathways. PMID:25648963

  1. A genome-wide association study for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.

    Science.gov (United States)

    Tang, Weihong; Teichert, Martina; Chasman, Daniel I; Heit, John A; Morange, Pierre-Emmanuel; Li, Guo; Pankratz, Nathan; Leebeek, Frank W; Paré, Guillaume; de Andrade, Mariza; Tzourio, Christophe; Psaty, Bruce M; Basu, Saonli; Ruiter, Rikje; Rose, Lynda; Armasu, Sebastian M; Lumley, Thomas; Heckbert, Susan R; Uitterlinden, André G; Lathrop, Mark; Rice, Kenneth M; Cushman, Mary; Hofman, Albert; Lambert, Jean-Charles; Glazer, Nicole L; Pankow, James S; Witteman, Jacqueline C; Amouyel, Philippe; Bis, Joshua C; Bovill, Edwin G; Kong, Xiaoxiao; Tracy, Russell P; Boerwinkle, Eric; Rotter, Jerome I; Trégouët, David-Alexandre; Loth, Daan W; Stricker, Bruno H Ch; Ridker, Paul M; Folsom, Aaron R; Smith, Nicholas L

    2013-07-01

    Venous thromboembolism (VTE) is a common, heritable disease resulting in high rates of hospitalization and mortality. Yet few associations between VTE and genetic variants, all in the coagulation pathway, have been established. To identify additional genetic determinants of VTE, we conducted a two-stage genome-wide association study (GWAS) among individuals of European ancestry in the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) VTE consortium. The discovery GWAS comprised 1,618 incident VTE cases out of 44,499 participants from six community-based studies. Genotypes for genome-wide single-nucleotide polymorphisms (SNPs) were imputed to approximately 2.5 million SNPs in HapMap and association with VTE assessed using study-design appropriate regression methods. Meta-analysis of these results identified two known loci, in F5 and ABO. Top 1,047 tag SNPs (P ≤ 0.0016) from the discovery GWAS were tested for association in an additional 3,231 cases and 3,536 controls from three case-control studies. In the combined data from these two stages, additional genome-wide significant associations were observed on 4q35 at F11 (top SNP rs4253399, intronic to F11) and on 4q28 at FGG (rs6536024, 9.7 kb from FGG; P FGG locus were not completely explained by previously reported variants. Loci at or near SUSD1 and OTUD7A showed borderline yet novel associations (P FGG loci for VTE. Future studies are warranted to better characterize the associations with F11 and FGG and to replicate the new candidate associations.

  2. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

    Science.gov (United States)

    Brown, Tyler S; Narechania, Apurva; Walker, John R; Planet, Paul J; Bifani, Pablo J; Kolokotronis, Sergios-Orestis; Kreiswirth, Barry N; Mathema, Barun

    2016-11-21

    Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods. M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City. Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with

  3. Cancer Epidemiology Matters Blog

    Science.gov (United States)

    The Cancer Epidemiology Matters blog helps foster a dialogue between the National Cancer Institute's (NCI) Epidemiology and Genomics Research Program (EGRP), extramural researchers, and other individuals, such as clinicians, community partners, and advocates, who are interested in cancer epidemiology and genomics.

  4. Intelligent Classification in Huge Heterogeneous Data Sets

    Science.gov (United States)

    2015-06-01

    INTELLIGENT CLASSIFICATION IN HUGE HETEROGENEOUS DATA SETS JUNE 2015 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED...To) JUL 2013 – APR 2015 4. TITLE AND SUBTITLE INTELLIGENT CLASSIFICATION IN HUGE HETEROGENEOUS DATA SETS 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT...signals and through data dimension reduction, and to develop and tailor algorithms for the extraction of intelligence from several huge heterogeneous

  5. Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

    Science.gov (United States)

    van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made. PMID:11432813

  6. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

    Full Text Available We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs, bisphenols (BPs, and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors.

  7. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    Science.gov (United States)

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-01-01

    We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs), bisphenols (BPs), and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA) and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK) signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors. PMID:26512648

  8. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India.

    Directory of Open Access Journals (Sweden)

    Sushila Maan

    Full Text Available Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV. Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp. and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV 'topotype'. However, genome-segment 5 (Seg-5 encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03 are closely related (>99% identity to a South African BTV-2 vaccine-strain (western topotype. Similarly BTV-10 isolates (IND2003/06; IND2005/04 show >99% identity in all genome segments, to the prototype BTV-10 (CA-8 strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of 'live' South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies.

  9. Molecular epidemiology of bovine rotaviruses. Characterization of rotaviruses isolated from diarrhoeic calves by genome profile analysis.

    Science.gov (United States)

    Legrottaglie, R; Rizzi, V; Agrimi, P

    1995-04-01

    Fifteen bovine rotavirus group A strains were isolated in several Italian regions over the period 1981-1989 from calves in ten neonatal diarrhoea outbreaks. The electrophoretical analysis of the genoma showed genomic variations and five different profiles were observed, including one with thirteen dsRNA segments. The finding of extra RNA fragments, with respect to the regular eleven genome segments, suggests the possibility of simultaneous or sequential infection by more than one electropherotype or a modification in the length of RNA segments during infection.

  10. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages

    Science.gov (United States)

    Salmonella enterica serotype Enteritidis (SE) is one of the most commonly reported causes of human salmonellosis. The low genetic diversity of SE measured by fingerprinting methods has made subtyping a challenge. In this study, we used whole genome sequencing to characterize a total of 125 SE and Sa...

  11. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon

    2016-01-01

    It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally struc...

  12. Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

    DEFF Research Database (Denmark)

    Deng, Xiangyu; Desai, Prerak T.; den Bakker, Henk C.

    2014-01-01

    Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica...

  13. Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia.

    Science.gov (United States)

    McCallum, Nadine; Gray, Timothy J; Wang, Qinning; Ng, Jimmy; Hicks, Leanne; Nguyen, Trang; Yuen, Marion; Hill-Cawthorne, Grant A; Sintchenko, Vitali

    2015-09-01

    Infant botulism is a potentially life-threatening paralytic disease that can be associated with prolonged morbidity if not rapidly diagnosed and treated. Four infants were diagnosed and treated for infant botulism in NSW, Australia, between May 2011 and August 2013. Despite the temporal relationship between the cases, there was no close geographical clustering or other epidemiological links. Clostridium botulinum isolates, three of which produced botulism neurotoxin serotype A (BoNT/A) and one BoNT serotype B (BoNT/B), were characterized using whole-genome sequencing (WGS). In silico multilocus sequence typing (MLST) found that two of the BoNT/A-producing isolates shared an identical novel sequence type, ST84. The other two isolates were single-locus variants of this sequence type (ST85 and ST86). All BoNT/A-producing isolates contained the same chromosomally integrated BoNT/A2 neurotoxin gene cluster. The BoNT/B-producing isolate carried a single plasmid-borne bont/B gene cluster, encoding BoNT subtype B6. Single nucleotide polymorphism (SNP)-based typing results corresponded well with MLST; however, the extra resolution provided by the whole-genome SNP comparisons showed that the isolates differed from each other by >3,500 SNPs. WGS analyses indicated that the four infant botulism cases were caused by genomically distinct strains of C. botulinum that were unlikely to have originated from a common environmental source. The isolates did, however, cluster together, compared with international isolates, suggesting that C. botulinum from environmental reservoirs throughout NSW have descended from a common ancestor. Analyses showed that the high resolution of WGS provided important phylogenetic information that would not be captured by standard seven-loci MLST.

  14. Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

    Science.gov (United States)

    Jackson, Robert; Rosa, Bruce A; Lameiras, Sonia; Cuninghame, Sean; Bernard, Josee; Floriano, Wely B; Lambert, Paul F; Nicolas, Alain; Zehbe, Ingeborg

    2016-11-02

    Human papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host. To investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various "omics" and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells. We show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral

  15. Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

    Science.gov (United States)

    Shah, Muhammad Ali; Mutreja, Ankur; Thomson, Nicholas; Baker, Stephen; Parkhill, Julian; Dougan, Gordon; Bokhari, Habib; Wren, Brendan W

    2014-01-01

    In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks.

  16. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology.

    Science.gov (United States)

    Baltrus, David A; McCann, Honour C; Guttman, David S

    2017-01-01

    A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens. © 2016 BSPP and John Wiley & Sons Ltd.

  17. Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines.

    Science.gov (United States)

    David, Sophia; Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R; Afshar, Baharak; Underwood, Anthony; Fry, Norman K; Parkhill, Julian; Harrison, Timothy G

    2016-08-01

    Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current "gold standard" typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard "typing panel," previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila.

  18. Feral swine brucellosis in the United States and prospective genomic techniques for disease epidemiology.

    Science.gov (United States)

    Leiser, Owen P; Corn, Joseph L; Schmit, Brandon S; Keim, Paul S; Foster, Jeffrey T

    2013-09-27

    Brucellosis is a common infection of feral swine throughout the United States. With the recent expansion of feral swine populations across the country, this disease poses an increasing threat to agriculture and hunters. The standard approach to Brucella surveillance in feral swine has been serological testing, which gives an indication of past exposure and is a rapid method of determining populations where Brucella is present. More in-depth analyses require bacterial isolation to determine the Brucella species and biovar involved. Ultimately, for a comprehensive understanding of Brucella epizootiology in feral swine, incorporation of genotyping assays has become essential. Fortunately, the past decade has given rise to an array of genetic tools for assessing Brucella transmission and dispersal. This review aims to synthesize what is known about brucellosis in feral swine and will cover prospective genomic techniques that may be utilized to develop more complete understanding of the disease and its transmission history. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates

    Directory of Open Access Journals (Sweden)

    Taya L. Forde

    2016-11-01

    Full Text Available Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host

  20. Molecular epidemiology and complete genome characterization of H1N1pdm virus from India.

    Directory of Open Access Journals (Sweden)

    Shashi Sharma

    Full Text Available BACKGROUND: Influenza A virus is one of world's major uncontrolled pathogen, causing seasonal epidemic as well as global pandemic. This was evidenced by recent emergence and continued prevalent 2009 swine origin pandemic H1N1 Influenza A virus, provoking first true pandemic in the past 40 years. In the course of its evolution, the virus acquired many mutations and multiple unidentified molecular determinants are likely responsible for the ability of the 2009 H1N1 virus to cause increased disease severity in humans. Availability of limited data on complete genome hampers the continuous monitoring of this type of events. Outbreaks with considerable morbidity and mortality have been reported from all parts of the country. METHODS/RESULTS: Considering a large number of clinical cases of infection complete genome based sequence characterization of Indian H1N1pdm virus and their phylogenetic analysis with respect to circulating global viruses was undertaken, to reveal the phylodynamic pattern of H1N1pdm virus in India from 2009-2011. The Clade VII was observed as a major circulating clade in phylogenetic analysis. Selection pressure analysis revealed 18 positively selected sites in major surface proteins of H1N1pdm virus. CONCLUSIONS: This study clearly revealed that clade VII has been identified as recent circulating clade in India as well globally. Few clade VII specific well identified markers undergone positive selection during virus evolution. Continuous monitoring of the H1N1pdm virus is warranted to track of the virus evolution and further transmission. This study will serve as a baseline data for future surveillance and also for development of suitable therapeutics.

  1. Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates.

    Science.gov (United States)

    Forde, Taya L; Orsel, Karin; Zadoks, Ruth N; Biek, Roman; Adams, Layne G; Checkley, Sylvia L; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T; Finnegan, Laura; Macbeth, Bryan J; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M; van der Meer, Frank; Kutz, Susan J

    2016-01-01

    Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

  2. Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study

    Directory of Open Access Journals (Sweden)

    Fesinmeyer Megan D

    2013-01-01

    Full Text Available Abstract Background Although smoking behavior is known to affect body mass index (BMI, the potential for smoking to influence genetic associations with BMI is largely unexplored. Methods As part of the ‘Population Architecture using Genomics and Epidemiology (PAGE’ Consortium, we investigated interaction between genetic risk factors associated with BMI and smoking for 10 single nucleotide polymorphisms (SNPs previously identified in genome-wide association studies. We included 6 studies with a total of 56,466 subjects (16,750 African Americans (AA and 39,716 European Americans (EA. We assessed effect modification by testing an interaction term for each SNP and smoking (current vs. former/never in the linear regression and by stratified analyses. Results We did not observe strong evidence for interactions and only observed two interactions with p-values TMEM18, the risk allele (C was associated with BMI only among AA females who were former/never smokers (β = 0.018, p = 0.002, vs. current smokers (β = 0.001, p = 0.95, pinteraction = 0.10. For rs9939609/FTO, the A allele was more strongly associated with BMI among current smoker EA females (β = 0.017, p = 3.5x10-5, vs. former/never smokers (β = 0.006, p = 0.05, pinteraction = 0.08. Conclusions These analyses provide limited evidence that smoking status may modify genetic effects of previously identified genetic risk factors for BMI. Larger studies are needed to follow up our results. Clinical Trial Registration NCT00000611

  3. Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE study.

    Directory of Open Access Journals (Sweden)

    Logan Dumitrescu

    2011-06-01

    Full Text Available For the past five years, genome-wide association studies (GWAS have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C, low-density lipoprotein cholesterol (LDL-C, and triglyceride (TG levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG levels in self-identified European American (~20,000, African American (~9,000, American Indian (~6,000, Mexican American/Hispanic (~2,500, Japanese/East Asian (~690, and Pacific Islander/Native Hawaiian (~175 adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92% SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05 and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG in European Americans generalized to African Americans (48%, 61%, and 57%, American Indians (45%, 64%, and 77%, and Mexican Americans/Hispanics (57%, 56%, and 86%. Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.

  4. Outcome of Hepatectomy for Huge Hepatocellular Carcinoma.

    Science.gov (United States)

    Jo, Sungho

    2011-05-01

    In spite of the recent improved results of hepatectomy for huge hepatocellular carcinomas (HCC), the prognosis of patients with huge HCCs is still poor compared to that of patients with small HCCs. This study was performed to compare the results of hepatectomy between patients with huge HCCs and those with small HCCs, to identify the prognostic factors in patients with huge HCCs, and to determine the preoperative selection criteria. We retrospectively analyzed 51 patients who underwent hepatectomy, between July 1994 and February 2009 at Dankook University Hospital. Patients with HCC≥10 cm were classified in large (L) group and others were classified in small (S) group. The clinicopathological features, operative procedures, and postoperative outcome were compared between both groups and various prognostic factors were investigated in group L. Eleven patients were classified in group L. Tumor size, vascular invasion, and tumor stage were higher in group L. Postoperative morbidity was higher in group L, but mortality was not different between the groups. Disease-free survivals were significantly lower in group L than in group S (36.4%, and 24.2% vs. 72.0%, and 44.0% for 1- and 3-year), but overall survival rates were similar in both groups (45.5%, and 15.2% in group L vs. 60.3%, and 41.3% in group S for 3- and 5-year). Presence of satellite nodules was the only prognostic factor in multivariate analysis after surgery for huge HCC. Regardless of tumor size, huge HCCs deserve consideration for surgery in patients with preserved liver function. Furthermore, the effect of surgery could be maximized with appropriate selection criteria, such as huge HCC without satellite nodules.

  5. Neck Circumference and Incidence of Diabetes Mellitus over 10 Years in the Korean Genome and Epidemiology Study (KoGES).

    Science.gov (United States)

    Cho, Nam H; Oh, Tae Jung; Kim, Kyoung Min; Choi, Sung Hee; Lee, Jae Ho; Park, Kyong Soo; Jang, Hak Chul; Kim, Jong Yeol; Lee, Hong Kyu; Lim, Soo

    2015-12-18

    Neck circumference, a proxy for upper-body fat, may be a unique fat depot that indicates metabolic risk beyond whole body fat. We investigated whether neck circumference is associated with development of diabetes mellitus (DM) in a subset of data with Korean Genome and Epidemiology Study (n = 3521, age range = 42-71 years). Nondiabetic subjects at the baseline were categorized into 4 groups (Q1-Q4) according to their neck circumference. Parameters related with β-cell function and insulin resistance including Epworth sleepiness scale and snoring habit were examined. The development of DM was confirmed biannually based on a 75-g oral glucose tolerance test. Over the 10 years, 2623 (74.5%) among 3521 subjects were followed-up. Among them, 632 (24.1%) developed DM. The incidence of DM increased from 17.6% in Q1 to 18.2% in Q2, to 25.4% in Q3, and to 36.0% in Q4 (P neck circumference in the development of DM.

  6. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

    Science.gov (United States)

    Grubaugh, Nathan D.; Ladner, Jason T.; Kraemer, Moritz U. G.; Dudas, Gytis; Tan, Amanda L.; Gangavarapu, Karthik; Wiley, Michael R.; White, Stephen; Thézé, Julien; Magnani, Diogo M.; Prieto, Karla; Reyes, Daniel; Bingham, Andrea M.; Paul, Lauren M.; Robles-Sikisaka, Refugio; Oliveira, Glenn; Pronty, Darryl; Barcellona, Carolyn M.; Metsky, Hayden C.; Baniecki, Mary Lynn; Barnes, Kayla G.; Chak, Bridget; Freije, Catherine A.; Gladden-Young, Adrianne; Gnirke, Andreas; Luo, Cynthia; Macinnis, Bronwyn; Matranga, Christian B.; Park, Daniel J.; Qu, James; Schaffner, Stephen F.; Tomkins-Tinch, Christopher; West, Kendra L.; Winnicki, Sarah M.; Wohl, Shirlee; Yozwiak, Nathan L.; Quick, Joshua; Fauver, Joseph R.; Khan, Kamran; Brent, Shannon E.; Reiner, Robert C.; Lichtenberger, Paola N.; Ricciardi, Michael J.; Bailey, Varian K.; Watkins, David I.; Cone, Marshall R.; Kopp, Edgar W.; Hogan, Kelly N.; Cannons, Andrew C.; Jean, Reynald; Monaghan, Andrew J.; Garry, Robert F.; Loman, Nicholas J.; Faria, Nuno R.; Porcelli, Mario C.; Vasquez, Chalmers; Nagle, Elyse R.; Cummings, Derek A. T.; Stanek, Danielle; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Sabeti, Pardis C.; Gillis, Leah D.; Michael, Scott F.; Bedford, Trevor; Pybus, Oliver G.; Isern, Sharon; Palacios, Gustavo; Andersen, Kristian G.

    2017-06-01

    Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016—several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

  7. Connecting slow earthquakes to huge earthquakes.

    Science.gov (United States)

    Obara, Kazushige; Kato, Aitaro

    2016-07-15

    Slow earthquakes are characterized by a wide spectrum of fault slip behaviors and seismic radiation patterns that differ from those of traditional earthquakes. However, slow earthquakes and huge megathrust earthquakes can have common slip mechanisms and are located in neighboring regions of the seismogenic zone. The frequent occurrence of slow earthquakes may help to reveal the physics underlying megathrust events as useful analogs. Slow earthquakes may function as stress meters because of their high sensitivity to stress changes in the seismogenic zone. Episodic stress transfer to megathrust source faults leads to an increased probability of triggering huge earthquakes if the adjacent locked region is critically loaded. Careful and precise monitoring of slow earthquakes may provide new information on the likelihood of impending huge earthquakes.

  8. Connecting slow earthquakes to huge earthquakes

    Science.gov (United States)

    Obara, Kazushige; Kato, Aitaro

    2016-07-01

    Slow earthquakes are characterized by a wide spectrum of fault slip behaviors and seismic radiation patterns that differ from those of traditional earthquakes. However, slow earthquakes and huge megathrust earthquakes can have common slip mechanisms and are located in neighboring regions of the seismogenic zone. The frequent occurrence of slow earthquakes may help to reveal the physics underlying megathrust events as useful analogs. Slow earthquakes may function as stress meters because of their high sensitivity to stress changes in the seismogenic zone. Episodic stress transfer to megathrust source faults leads to an increased probability of triggering huge earthquakes if the adjacent locked region is critically loaded. Careful and precise monitoring of slow earthquakes may provide new information on the likelihood of impending huge earthquakes.

  9. Treatment strategies for huge central neurocytomas.

    Science.gov (United States)

    Xiong, Zhong-wei; Zhang, Jian-jian; Zhang, Ting-bao; Sun, Shou-jia; Wu, Xiao-lin; Wang, Hao; You, Chao; Wang, Yu; Zhang, Hua-qiu; Chen, Jin-cao

    2015-02-01

    Central neurocytomas (CNs), initially asymptomatic, sometimes become huge before detection. We described and analyzed the clinical, radiological, operational and outcome data of 13 cases of huge intraventricular CNs, and discussed the treatment strategies in this study. All huge CNs (n=13) in our study were located in bilateral lateral ventricle with diameter ≥5.0 cm and had a broad-based attachment to at least one side of the ventricle wall. All patients received craniotomy to remove the tumor through transcallosal or transcortical approach and CNs were of typical histologic and immunohistochemical features. Adjuvant therapies including conventional radiation therapy (RT) or gamma knife radiosurgery (GKRS) were also performed postoperatively. Transcallosal and transcortical approaches were used in 8 and 5 patients, respectively. Two patients died within one month after operation and 3 patients with gross total resection (GTR) were additionally given a decompressive craniectomy (DC) and/or ventriculoperitoneal shunt (VPS) as the salvage therapy. Six patients received GTR(+RT) and 7 patients received subtotal resection (STR)(+GKRS). Eight patients suffered serious complications such as hydrocephalus, paralysis and seizure after operation, and patients who underwent GTR showed worse functional outcome [less Karnofsky performance scale (KPS) scores] than those having STR(+GKRS) during the follow-up period. The clinical outcome of huge CNs seemed not to be favorable as that described in previous reports. Surgical resection for huge CNs should be meticulously considered to guarantee the maximum safety. Better results were achieved in STR(+GKRS) compared with GTR(+RT) for huge CNs, suggesting that STR(+GKRS) may be a better treatment choice. The recurrent or residual tumor can be treated with GKRS effectively.

  10. A Huge Ancient Schwannoma of the Epiglottis.

    Science.gov (United States)

    Lee, Dong Hoon; Kim, Jo Heon; Yoon, Tae Mi; Lee, Joon Kyoo; Lim, Sang Chul

    2016-03-01

    Ancient schwannoma of the epiglottis is extremely rare. The authors report the first case of a patient with a huge ancient schwannoma of the epiglottis. Clinicians should consider the possibility that ancient schwannoma may originate in the epiglottis mimicking the other more frequently observed lesions.

  11. Genetic variation and reproductive timing: African American women from the Population Architecture using Genomics and Epidemiology (PAGE Study.

    Directory of Open Access Journals (Sweden)

    Kylee L Spencer

    Full Text Available Age at menarche (AM and age at natural menopause (ANM define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs in 4,159 and 1,860 African American women, respectively, in the Women's Health Initiative (WHI and Atherosclerosis Risk in Communities (ARIC studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10⁻⁰⁸; KCNQ1 rs79972789, p = 1.9×10⁻⁰⁷; COL4A3BP rs181686584, p = 2.9×10⁻⁰⁷. Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10⁻⁰⁶. While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations.

  12. Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

    Science.gov (United States)

    Dumitrescu, Logan; Carty, Cara L.; Taylor, Kira; Schumacher, Fredrick R.; Hindorff, Lucia A.; Ambite, José L.; Anderson, Garnet; Best, Lyle G.; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S.; Cochran, Barbara; Cole, Shelley A.; Devereux, Richard B.; Duggan, Dave; Eaton, Charles B.; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V.; Johnson, Karen C.; Laston, Sandra; Kolonel, Laurence N.; Lee, Elisa T.; MacCluer, Jean W.; Manolio, Teri A.; Pendergrass, Sarah A.; Quibrera, Miguel; Shohet, Ralph V.; Wilkens, Lynne R.; Haiman, Christopher A.; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E.; Crawford, Dana C.

    2011-01-01

    For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS–identified variants in diverse population-based studies. We genotyped 49 GWAS–identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (∼20,000), African American (∼9,000), American Indian (∼6,000), Mexican American/Hispanic (∼2,500), Japanese/East Asian (∼690), and Pacific Islander/Native Hawaiian (∼175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits. PMID:21738485

  13. Relationship between prehypertension and chronic kidney disease in middle-aged people in Korea: the Korean genome and epidemiology study

    Directory of Open Access Journals (Sweden)

    Kim Min-Ju

    2012-11-01

    Full Text Available Abstract Background Elevated blood pressure (BP is a major risk factor for the progression of chronic kidney disease (CKD. However, little is known about the influence of prehypertension on CKD. In this study, we investigated the relationship between prehypertension and CKD in a middle-aged Korean population. Furthermore, we prospectively evaluated the effect of active BP control on deterioration of kidney function during the two-year follow-up. Methods The Korean Genome and Epidemiology Study is a community-based prospective cohort study started in 2001, with a follow-up survey conducted every two years. A total of 9509 participants aged 40–69 years were included in a baseline study. BP was classified according to the Seventh Report of the Joint National Committee on High BP (JNC-7 categories and CKD was defined as the presence of proteinuria or eGFR2. A multivariable logistic regression model was used to identify associations between BP and CKD. Results The overall prevalence of CKD was 13.2%, and significantly increased with BP level. The multivariable-adjusted odds ratio of CKD was 1.59 for prehypertension and 2.27 for hypertension, compared with a normal BP. At the two-year follow-up, among the participants with prehypertension, subjects whose BP was poorly controlled had a significantly higher risk of eGFR drop (OR, 1.37; 95% CI, 1.13-1.67, as compared to controls. The prevalence of eGFR drop was 57.8% in the controlled BP group and 66.0% in the poorly-controlled BP group. Conclusions Prehypertension, as well as hypertension, is significantly associated with CKD among middle-aged Koreans. Our results indicate that active control of the blood-pressure of prehypertensive individuals is needed to prevent deterioration of kidney function.

  14. A huge presacral Tarlov cyst. Case report.

    Science.gov (United States)

    Ishii, Kazuhiko; Yuzurihara, Masahito; Asamoto, Shunji; Doi, Hiroshi; Kubota, Motoo

    2007-08-01

    Perineural cysts have become a common incidental finding during lumbosacral magnetic resonance (MR) imaging. Only some of the symptomatic cysts warrant treatment. The authors describe the successful operative treatment of a patient with, to the best of their knowledge, the largest perineural cyst reported to date. A 29-year-old woman had been suffering from long-standing constipation and low-back pain. During an obstetric investigation for infertility, the clinician discovered a huge presacral cystic mass. Computed tomography myelography showed the lesion to be a huge Tarlov cyst arising from the left S-3 nerve root and compressing the ipsilateral S-2 nerve. The cyst was successfully treated by ligation of the cyst neck together with sectioning of the S-3 nerve root. Postoperative improvement in her symptoms and MR imaging findings were noted. Identification of the nerve root involved by the cyst wall, operative indication, operative procedure, and treatment of multiple cysts are important preoperative considerations.

  15. From tiny microalgae to huge biorefineries

    OpenAIRE

    Gouveia, L.

    2014-01-01

    Microalgae are an emerging research field due to their high potential as a source of several biofuels in addition to the fact that they have a high-nutritional value and contain compounds that have health benefits. They are also highly used for water stream bioremediation and carbon dioxide mitigation. Therefore, the tiny microalgae could lead to a huge source of compounds and products, giving a good example of a real biorefinery approach. This work shows and presents examples of experimental...

  16. A rare clinic entity: Huge trichobezoar

    Directory of Open Access Journals (Sweden)

    Hidayatullah Hamidi, Dr, MD

    2016-01-01

    Conclusion: Trichobezoars should be suspected in young females with long standing upper abdominal masses; as the possibility of malignancy is not very common in this age group. While USG is inconclusive, trichobezoar can be accurately diagnosed with CT. In patient with huge trichobezoar, laparotomy can be performed firstly because of big size and location of mass, and psychiatric recommendation should be made to prevent relapse of this entity.

  17. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    Science.gov (United States)

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.

  18. Laparoscopic Management of Huge Cervical Myoma.

    Science.gov (United States)

    Peker, Nuri; Gündoğan, Savaş; Şendağ, Fatih

    To demonstrate the feasibility of laparoscopic management of a huge cervical myoma. Step-by-step video demonstration of the surgical procedure (Canadian Task Force classification III-C). Uterine myoma is the most common benign neoplasm of the female reproductive tract, with an estimated incidence of 25% to 30% at reproductive age [1,2]. Patients generally have no symptoms; however, those with such symptoms as severe pelvic pain, heavy uterine bleeding, or infertility may be candidates for surgery. The traditional management is surgery; however, uterine artery embolization or hormonal therapy using a gonadotropin-releasing hormone agonist or a selective estrogen receptor modulator should be preferred as the medical approach. Surgical management should be performed via laparoscopy or laparotomy; however, the use of laparoscopic myomectomy is being debated for patients with huge myomas. Difficulties in the excision, removal, and repair of myometrial defects, increased operative time, and blood loss are factors keeping physicians away from laparoscopic myomectomy [1,2]. A 40-year-old gravida 0, para 0 woman was admitted to our clinic with complaints of chronic pelvic pain, dyspareunia, and infertility. Her health history was unremarkable. Ultrasonographic examination revealed a 14 × 10-cm myoma in the cervical region. On bimanual examination, an immobile solid mass originating from the uterine cervix and filling the pouch of Douglas was palpated. The patient was informed of the findings, and laparoscopic myomectomy was recommended because of her desire to preserve her fertility. Abdominopelvic examination revealed a huge myoma filling and enlarging the cervix. Myomectomy was performed using standard technique as described elsewhere. A transverse incision was made using a harmonic scalpel. The myoma was fixed with a corkscrew manipulator and enucleated. Once bleeding was controlled, the myoma bed was filled with Spongostan to prevent possible bleeding from leakage

  19. Huge music archives on mobile devices

    DEFF Research Database (Denmark)

    Blume, H.; Bischl, B.; Botteck, M.

    2011-01-01

    The availability of huge nonvolatile storage capacities such as flash memory allows large music archives to be maintained even in mobile devices. With the increase in size, manual organization of these archives and manual search for specific music becomes very inconvenient. Automated dynamic...... and difficult to tackle on mobile platforms. Against this background, we provided an overview of algorithms for music classification as well as their computation times and other hardware-related aspects, such as power consumption on various hardware architectures. For mobile platforms such as smartphones...

  20. Hepatitis B and hepatitis C viruses: a review of viral genomes, viral induced host immune responses, genotypic distributions and worldwide epidemiology

    Directory of Open Access Journals (Sweden)

    Umar Saeed

    2014-04-01

    Full Text Available Hepatitis B and hepatitis C viruses (HCV are frequently propagating blood borne pathogens in global community. Viral hepatitis is primarily associated with severe health complications, such as liver cirrhosis, hepatocellular carcinoma, hepatic fibrosis and steatosis. A literature review was conducted on hepatitis B virus (HBV, HBV genome, genotypic distribution and global epidemiology of HBV, HCV, HCV genome, HCV and host immune responses, HCV genotypic distribution and global epidemiology. The valued information was subjected for review. HBV has strict tissue tropism to liver. The virus infecting hepatocytes produces large amount of hepatitis B surface antigen particles which lack the DNA. It has capability to integrate into host genome. It has been found that genotype C is most emerging genotype associated with more severe liver diseases (cirrhosis. The approximate prevalence rate of genotype C is 27.7% which represents a major threat to future generations. Approximately 8% of population is chronic carrier of HBV in developing countries. The chronic carrier rate of HBV is 2%-7% in Middle East, Eastern and Southern Europe, South America and Japan. Among HCV infected individuals, 15% usually have natural tendency to overcome acute viral infection, where as 85% of individuals were unable to control HCV infection. The internal ribosomal entry site contains highly conserved structures important for binding and appropriate positioning of viral genome inside the host cell. HCV infects only in 1%-10% of hepatocytes, but production of tumor necrosis factor alpha (from CD8+ cells and interferon-gamma cause destruction of both infected cells and non-infected surrounding cells. Almost 11 genotypes and above 100 subtypes of HCV exists worldwide with different geographical distribution. Many efforts are still needed to minimize global burden of these infections. For the complete eradication of HBV (just like small pox and polio via vaccination strategies

  1. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

    Science.gov (United States)

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

    2015-06-19

    The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

  2. Laparoscopic Management of Huge Myoma Nascendi.

    Science.gov (United States)

    Peker, Nuri; Gündoğan, Savas; Şendağ, Fatih

    To demonstrate the feasibility of laparoscopic management of a huge myoma nascendi. Step-by-step video demonstration of the surgical procedure (Canadian Task Force classification III-C). Uterine myoma is the most common benign neoplasm of the female reproductive tract, with an estimated incidence of 25% to 30% at reproductive age [1,2]. Patients generally have no symptoms; however, those with such symptoms as severe pelvic pain, heavy uterine bleeding, or infertility may be candidates for surgery. The traditional management is surgery; however, uterine artery embolization or hormonal therapy using a gonadotropin-releasing hormone agonist or a selective estrogen receptor modulator should be preferred as the medical approach. Surgical management should be performed via laparoscopy or laparotomy; however, the use of laparoscopic myomectomy is being debated for patients with huge myomas. Difficulties in the excision, removal, and repair of myometrial defects, increased operative time, and blood loss are factors keeping physicians away from laparoscopic myomectomy [1,2]. A 35-year-old woman was admitted to our clinic with complaints of chronic pelvic pain and heavy menstrual bleeding. Her medical history included multiple hospitalizations for blood transfusions, along with a recently measured hemoglobin level of 9.5 g/dL and a hematocrit value of 29%. She had never been married and had no children. Pelvic ultrasonography revealed a 12 × 10-cm uterine myoma located on the posterior side of the corpus uteri and protruding through to the cervical channel. This was a huge intramural submucous myoma in close proximity to the endometrial cavity and spreading through the myometrium. On vaginal examination, the myoma was found to extend into the vagina through the cervical channel. Laparoscopic myomectomy was planned because of the patient's desire for fertility preservation. Abdominopelvic exploration revealed a huge myoma filling the posterior side of the corpus uteri and

  3. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

    Science.gov (United States)

    Park, Kyung-Hwa; Greenwood-Quaintance, Kerryl E; Uhl, James R; Cunningham, Scott A; Chia, Nicholas; Jeraldo, Patricio R; Sampathkumar, Priya; Nelson, Heidi; Patel, Robin

    2017-01-01

    Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin-resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.

  4. Huge Tongue Lipoma: A Case Report

    Directory of Open Access Journals (Sweden)

    Mohammad Ali Damghani

    2015-03-01

    Full Text Available Introduction: Lipomas are among the most common tumors of the human body. However, they are uncommon in the oral cavity and are observed as slow growing, painless, and asymptomatic yellowish submucosal masses. Surgical excision is the treatment of choice and recurrence is not expected.    Case Report: The case of a 30-year-old woman with a huge lipoma on the tip of her tongue since 3 years, is presented. She had difficulty with speech and mastication because the tongue tumor was filling the oral cavity. Clinical examination revealed a yellowish lesion, measuring 8 cm in maximum diameter, protruding from the lingual surface. The tumor was surgically excised with restoration of normal tongue function and histopathological examination of the tumor confirmed that it was a lipoma.   Conclusion:  Tongue lipoma is rarely seen and can be a cause of macroglossia. Surgical excision for lipoma is indicated for symptomatic relief and exclusion of associated malignancy.

  5. Galaxies Collide to Create Hot, Huge Galaxy

    Science.gov (United States)

    2009-01-01

    This image of a pair of colliding galaxies called NGC 6240 shows them in a rare, short-lived phase of their evolution just before they merge into a single, larger galaxy. The prolonged, violent collision has drastically altered the appearance of both galaxies and created huge amounts of heat turning NGC 6240 into an 'infrared luminous' active galaxy. A rich variety of active galaxies, with different shapes, luminosities and radiation profiles exist. These galaxies may be related astronomers have suspected that they may represent an evolutionary sequence. By catching different galaxies in different stages of merging, a story emerges as one type of active galaxy changes into another. NGC 6240 provides an important 'missing link' in this process. This image was created from combined data from the infrared array camera of NASA's Spitzer Space Telescope at 3.6 and 8.0 microns (red) and visible light from NASA's Hubble Space Telescope (green and blue).

  6. A rare clinic entity: Huge trichobezoar.

    Science.gov (United States)

    Hamidi, Hidayatullah; Muhammadi, Marzia; Saberi, Bismillah; Sarwari, Mohammad Arif

    2016-01-01

    Trichobezoar is a rare clinical entity in which a ball of hair amasses within the alimentary tract. It can either be found as isolated mass in the stomach or may extend into the intestine. Trichobezoars mostly occur in young females with psychiatric disorders such as trichophagia and trichotillomania. Authors present a giant trichobezoar in an 18year old female presented with complaints of upper abdominal mass, epigastric area pain, anorexia and weight loss. The patient underwent trans-abdominal ultrasonography (USG), Computed tomography (CT), upper gastrointestinal endoscopy and subsequently laparotomy. USG was inconclusive due to non-specific findings. It revealed a thick echogenic layer with posterior dirty shadowing extending from the left sub-diaphragmatic area to the right sub hepatic region obscuring the adjacent structures. Abdominal CT images revealed a huge, well defined, multi-layered, heterogeneous, solid appearing, non-enhancing mass lesion in the gastric lumen extending from the gastric fundus to the pyloric canal. An endoscopic attempt was performed for removal of this intraluminal mass, but due to its large size, and hard nature, the endoscopic removal was unsuccessful. Finally the large trichobezoar was removed with open laparotomy. Trichobezoars should be suspected in young females with long standing upper abdominal masses; as the possibility of malignancy is not very common in this age group. While USG is inconclusive, trichobezoar can be accurately diagnosed with CT. In patient with huge trichobezoar, laparotomy can be performed firstly because of big size and location of mass, and psychiatric recommendation should be made to prevent relapse of this entity. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. HUBBLE SPIES HUGE CLUSTERS OF STARS FORMED

    Science.gov (United States)

    2002-01-01

    BY ANCIENT ENCOUNTER This stunningly beautiful image [right] taken with the NASA Hubble Space Telescope shows the heart of the prototypical starburst galaxy M82. The ongoing violent star formation due to an ancient encounter with its large galactic neighbor, M81, gives this galaxy its disturbed appearance. The smaller picture at upper left shows the entire galaxy. The image was taken in December 1994 by the Kitt Peak National Observatory's 0.9-meter telescope. Hubble's view is represented by the white outline in the center. In the Hubble image, taken by the Wide Field and Planetary Camera 2, the huge lanes of dust that crisscross M82's disk are another telltale sign of the flurry of star formation. Below the center and to the right, a strong galactic wind is spewing knotty filaments of hydrogen and nitrogen gas. More than 100 super star clusters -- very bright, compact groupings of about 100,000 stars -- are seen in this detailed Hubble picture as white dots sprinkled throughout M82's central region. The dark region just above the center of the picture is a huge dust cloud. A collaboration of European and American scientists used these clusters to date the ancient interaction between M82 and M81. About 600 million years ago, a region called 'M82 B' (the bright area just below and to the left of the central dust cloud) exploded with new stars. Scientists have discovered that this ancient starburst was triggered by the violent encounter with M81. M82 is a bright (eighth magnitude), nearby (12 million light-years from Earth) galaxy in the constellation Ursa Major (the Great Bear). The Hubble picture was taken Sept. 15, 1997. The natural-color composite was constructed from three Wide Field and Planetary Camera 2 exposures, which were combined in chromatic order: 4,250 seconds through a blue filter (428 nm); 2,800 seconds through a green filter (520 nm); and 2,200 seconds through a red (820 nm) filter. Credits for Hubble image: NASA, ESA, R. de Grijs (Institute of

  8. Genome-wide studies of verbal declarative memory in nondemented older people: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium

    NARCIS (Netherlands)

    S. Debette (Stéphanie); C.A. Ibrahim-Verbaas (Carla); J. Bressler (Jan); M. Schuur (Maaike); G.D. Smith; J.C. Bis (Joshua); G. Davies (Gail); C. Wolf (Christiane); V. Gudnason (Vilmundur); L.B. Chibnik (Lori); Q. Yang (Qiong Fang); A.L. DeStefano (Anita); D.J.F. De Quervain (Dominique J.F.); V. Srikanth (Velandai); J. Lahti (Jari); H.J. Grabe (Hans Jörgen); J.A. Smith (Jennifer A); L. Priebe; L. Yu (Lei); N. Karbalai (Nazanin); C. Hayward (Caroline); J.F. Wilson (James F); H. Campbell (Harry); K. Petrovic (Katja); M. Fornage (Myriam); G. Chauhan (Ganesh); R. Yeo (Robin); R. Boxall (Ruth); J.T. Becker (James); O. Stegle (Oliver); R. Mather; V. Chouraki (Vincent); Q. Sun (Qi); L.M. Rose (Lynda); S. Resnick (Susan); C. Oldmeadow (Christopher); M. Kirin (Mirna); A. Wright (Alan); M.K. Jonsdottir (Maria K.); R. Au (Rhoda); A. Becker (Albert); N. Amin (Najaf); M.A. Nalls (Michael); S.T. Turner (Stephen); S.L.R. Kardia (Sharon); B.A. Oostra (Ben); G. Windham (Gwen); L.H. Coker (Laura); W. Zhao (Wei); D.S. Knopman (David); G. Heiss (Gerardo); M.D. Griswold (Michael); R.F. Gottesman (Rebecca); V. Vitart (Veronique); N. Hastie (Nick); L. Zgaga (Lina); I. Rudan (Igor); O. Polasek (Ozren); E.G. Holliday (Elizabeth); P. Schofield (Peter); S.-H. Choi (Seung-Hoan); T. Tanaka (Toshiko); Y. An (Yang); R.T. Perry (Rodney T.); R.E. Kennedy (Richard E.); M.M. Sale (Michèle M.); J. Wang (Jing); V.G. Wadley (Virginia G.); D.C. Liewald (David C.); P.M. Ridker (Paul); A.J. Gow (Alan J.); A. Pattie (Alison); J.M. Starr (John); D.J. Porteous (David J.); X. Liu (Xuan); R. Thomson (Russell); N.J. Armstrong (Nicola J.); G. Eiriksdottir (Gudny); A.A. Assareh (Arezoo A.); N.A. Kochan (Nicole A.); E. Widen (Elisabeth); A. Palotie (Aarno); Y.-C. Hsieh (Yi-Chen); J.G. Eriksson (Johan G.); C. Vogler (Christian); J.C. van Swieten (John); L. Shulman (Lee); A. Beiser (Alexa); J.I. Rotter (Jerome I.); C.O. Schmidt (Carsten O.); W. Hoffmann (Wolfgang); M.M. Nöthen (Markus M.); L. Ferrucci (Luigi); J. Attia (John); A.G. Uitterlinden (André); P. Amouyel (Philippe); J.-F. Dartigues (Jean-François); H. Amieva (Hélène); K. Räikkönen (Katri); M. Garcia (Melissa); P.A. Wolf (Philip); A. Hofman (Albert); W.T. Longstreth Jr; B.M. Psaty (Bruce); E.A. Boerwinkle (Eric); P.L. DeJager (Philip L.); P.S. Sachdev (Perminder); R. Schmidt (Reinhold); M.M.B. Breteler (Monique); A. Teumer (Alexander); O.L. Lopez (Oscar); S. Cichon (Sven); D.I. Chasman (Daniel); F. Grodstein (Francine); B. Müller-Myhsok (B.); C. Tzourio (Christophe); A. Papassotiropoulos (Andreas); D.A. Bennett (David); M.A. Ikram (Arfan); I.J. Deary (Ian J.); C.M. van Duijn (Cock); L.J. Launer (Lenore); A.L. Fitzpatrick (Annette); S. Seshadri (Sudha); T.H. Mosley (Thomas H.)

    2015-01-01

    textabstractBACKGROUND: Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting. METHODS: We conducted genome-wide association studies for

  9. Genome-wide studies of verbal declarative memory in nondemented older people: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium

    NARCIS (Netherlands)

    S. Debette (Stéphanie); C.A. Ibrahim-Verbaas (Carla); J. Bressler (Jan); M. Schuur (Maaike); G.D. Smith; J.C. Bis (Joshua); G. Davies (Gail); C. Wolf (Christiane); V. Gudnason (Vilmundur); L.B. Chibnik (Lori); Q. Yang (Qiong Fang); A.L. DeStefano (Anita); D.J.F. De Quervain (Dominique J.F.); V. Srikanth (Velandai); J. Lahti (Jari); H.J. Grabe (Hans Jörgen); J.A. Smith (Jennifer A); L. Priebe; L. Yu (Lei); N. Karbalai (Nazanin); C. Hayward (Caroline); J.F. Wilson (James F); H. Campbell (Harry); K. Petrovic (Katja); M. Fornage (Myriam); G. Chauhan (Ganesh); R. Yeo (Robin); R. Boxall (Ruth); J.T. Becker (James); O. Stegle (Oliver); R. Mather; V. Chouraki (Vincent); Q. Sun (Qi); L.M. Rose (Lynda); S. Resnick (Susan); C. Oldmeadow (Christopher); M. Kirin (Mirna); A. Wright (Alan); M.K. Jonsdottir (Maria K.); R. Au (Rhoda); A. Becker (Albert); N. Amin (Najaf); M.A. Nalls (Michael); S.T. Turner (Stephen); S.L.R. Kardia (Sharon); B.A. Oostra (Ben); G. Windham (Gwen); L.H. Coker (Laura); W. Zhao (Wei); D.S. Knopman (David); G. Heiss (Gerardo); M.D. Griswold (Michael); R.F. Gottesman (Rebecca); V. Vitart (Veronique); N. Hastie (Nick); L. Zgaga (Lina); I. Rudan (Igor); O. Polasek (Ozren); E.G. Holliday (Elizabeth); P. Schofield (Peter); S.-H. Choi (Seung-Hoan); T. Tanaka (Toshiko); Y. An (Yang); R.T. Perry (Rodney T.); R.E. Kennedy (Richard E.); M.M. Sale (Michèle M.); J. Wang (Jing); V.G. Wadley (Virginia G.); D.C. Liewald (David C.); P.M. Ridker (Paul); A.J. Gow (Alan J.); A. Pattie (Alison); J.M. Starr (John); D.J. Porteous (David J.); X. Liu (Xuan); R. Thomson (Russell); N.J. Armstrong (Nicola J.); G. Eiriksdottir (Gudny); A.A. Assareh (Arezoo A.); N.A. Kochan (Nicole A.); E. Widen (Elisabeth); A. Palotie (Aarno); Y.-C. Hsieh (Yi-Chen); J.G. Eriksson (Johan G.); C. Vogler (Christian); J.C. van Swieten (John); L. Shulman (Lee); A. Beiser (Alexa); J.I. Rotter (Jerome I.); C.O. Schmidt (Carsten O.); W. Hoffmann (Wolfgang); M.M. Nöthen (Markus M.); L. Ferrucci (Luigi); J. Attia (John); A.G. Uitterlinden (André); P. Amouyel (Philippe); J.-F. Dartigues (Jean-François); H. Amieva (Hélène); K. Räikkönen (Katri); M. Garcia (Melissa); P.A. Wolf (Philip); A. Hofman (Albert); W.T. Longstreth Jr; B.M. Psaty (Bruce); E.A. Boerwinkle (Eric); P.L. DeJager (Philip L.); P.S. Sachdev (Perminder); R. Schmidt (Reinhold); M.M.B. Breteler (Monique); A. Teumer (Alexander); O.L. Lopez (Oscar); S. Cichon (Sven); D.I. Chasman (Daniel); F. Grodstein (Francine); B. Müller-Myhsok (B.); C. Tzourio (Christophe); A. Papassotiropoulos (Andreas); D.A. Bennett (David); M.A. Ikram (Arfan); I.J. Deary (Ian J.); C.M. van Duijn (Cock); L.J. Launer (Lenore); A.L. Fitzpatrick (Annette); S. Seshadri (Sudha); T.H. Mosley (Thomas H.)

    2015-01-01

    textabstractBACKGROUND: Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting. METHODS: We conducted genome-wide association studies for paragrap

  10. Descriptive Epidemiology and Whole Genome Sequencing Analysis for an Outbreak of Bovine Tuberculosis in Beef Cattle and White-Tailed Deer in Northwestern Minnesota.

    Science.gov (United States)

    Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce

    2016-01-01

    Bovine tuberculosis (bTB) was discovered in a Minnesota cow through routine slaughter surveillance in 2005 and the resulting epidemiological investigation led to the discovery of infection in both cattle and white-tailed deer in the state. From 2005 through 2009, a total of 12 beef cattle herds and 27 free-ranging white-tailed deer (Odocoileus virginianus) were found infected in a small geographic region of northwestern Minnesota. Genotyping of isolates determined both cattle and deer shared the same strain of bTB, and it was similar to types found in cattle in the southwestern United States and Mexico. Whole genomic sequencing confirmed the introduction of this infection into Minnesota was recent, with little genetic divergence. Aggressive surveillance and management efforts in both cattle and deer continued from 2010-2012; no additional infections were discovered. Over 10,000 deer were tested and 705 whole herd cattle tests performed in the investigation of this outbreak.

  11. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

    Directory of Open Access Journals (Sweden)

    Sebastian Grossmann

    2015-06-01

    Full Text Available Introduction: HIV-1 near full-length genome (HIV-NFLG sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods: Plasma samples (n=30 were obtained from HIV-1B (n=10, HIV-1C (n=10, CRF01_AE (n=5 and CRF01_AG (n=5 infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeqTM HIV-1 Genotyping System. Results: After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92% samples with the lowest viral load being 3000 copies/ml. High (>99% concordance was observed between HIV-NFLG and ViroSeqTM when determining the drug resistance mutations (DRMs. The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions: Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

  12. Molecular epidemiology of Crimean- Congo hemorrhagic fever virus genome isolated from ticks of Hamadan province of Iran

    DEFF Research Database (Denmark)

    Tahmasebi, F; Ghiasi, Seyed Mojtaba; Mostafavi, E

    2010-01-01

    .2% of the ticks collected from livestock of different regions of the Hamadan province in western Iran. The infected species belonged to Hyalomma detritum, H. anatolicum, Rhipicephalus sanguineus and Argas reflexus. With one exception, genetic analysis of the virus genome isolates showed high sequence identity......BACKGROUND & OBJECTIVES: Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne member of the genus Nairovirus, family Bunyaviridae. CCHFV has been isolated from at least 31 different tick species. The virus is transmitted through the bite of an infected tick, or by direct contact with CCHFV......-infected patients or the products of infected livestock. This study was undertaken to study the genetic relationship and distribution of CCHFV in the tick population of Hamadan province of Iran. METHOD: In this study, RT-PCR has been used for detection of the CCHFV genome. RESULTS: This genome was detected in 19...

  13. Umbilicoplasty in children with huge umbilical hernia

    Directory of Open Access Journals (Sweden)

    Akakpo-Numado Gamedzi Komlatsè

    2014-01-01

    Full Text Available Background: Huge umbilical hernias (HUH are voluminous umbilical hernia (UH that are frequent in black African children. Several surgical techniques are used in their treatment for umbilical reconstruction, but techniques using skin flaps provide better aesthetic results. In this study, we presented our technique of umbilicoplasty in HUH, and its results. Patients and Methods: It is a retrospective study on children treated for HUH, from January 2012 to December 2013. The UH was called HUH when its basis diameter (BD exceeds 3 cm. Every HUH was characterised by its height, BD and morphology. Our technique was a two lateral flaps technique; the flaps are symmetrical and drawn so as to reconstitute the different parts of the umbilicus. The results were appreciated with criteria, including the peripheral ring and the central depression of the neo-umbilicus. Results : Twelve children were concerned (7 boys and 5 girls. Their mean age was 5 years and 6 months. The mean BD was 5.6 cm (extremes 3 and 8 cm, and the mean height of the HUH was 7.45 cm (extremes 3 and 9 cm. All underwent umbilicoplasty. In early post-operative period, two children presented a transitory subcutaneous hematoma. Late complications were granulation tissue with two children, and cheloid scar with one. With a mean follow-up of 10 months, we had 10 excellent results and two fair results according to our criteria. Conclusion: Our two lateral flaps umbilicoplasty is well-adapted to HUH in children. It is simple and assures a satisfactory anatomical and cosmetic result.

  14. Hepatectomy for huge hepatocellular carcinoma: single institute's experience.

    Science.gov (United States)

    Yang, Lianyue; Xu, Jiangfeng; Ou, Dipeng; Wu, Wei; Zeng, Zhijun

    2013-09-01

    The surgical resection of huge hepatocellular carcinoma (HCC) is still controversial. This study was designed to introduce our experience of liver resection for huge HCC and evaluate the safety and outcomes of hepatectomy for huge HCC. A total of 258 hepatic resections for the patients with huge HCC were analysed retrospectively from December 2002 to December 2011. The operative outcomes were compared with 293 patients with HCC >5.0 cm but huge HCC group and HCC >5.0 cm but huge HCC group has significantly a more longer overall and disease-free survival time than nodular huge HCC (P = 0.026, P = 0.022). Univariate and multivariate analysis revealed that the types of tumour, vascular invasion, and UICC stage were independent prognostic factors for overall survival (P = 0.047, P = 0.037, P = 0.033). Hepatic resection can be performed safely for huge HCC with a low mortality and favorable survival outcomes. Solitary huge HCC has the better surgical outcomes than nodular huge HCC.

  15. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

    Science.gov (United States)

    Crotta, M.; Wall, B.; Good, L.; O'Brien, S. J.; Guitian, J.

    2017-01-01

    Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.

  16. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    Directory of Open Access Journals (Sweden)

    Laurel S Burall

    Full Text Available In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra analysis plots standardized (z-score tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2. This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as

  17. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    Science.gov (United States)

    Burall, Laurel S; Grim, Christopher J; Mammel, Mark K; Datta, Atin R

    2016-01-01

    In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as links between two

  18. Complete genome and molecular epidemiological data infer the maintenance of rabies among kudu (Tragelaphus strepsiceros in Namibia.

    Directory of Open Access Journals (Sweden)

    Terence P Scott

    Full Text Available Rabies in kudu is unique to Namibia and two major peaks in the epizootic have occurred since it was first noted in 1977. Due to the large numbers of kudu that were affected, it was suspected that horizontal transmission of rabies occurs among kudu and that rabies was being maintained independently within the Namibian kudu population - separate from canid cycles, despite geographic overlap. In this study, it was our aim to show, through phylogenetic analyses, that rabies was being maintained independently within the Namibian kudu population. We also tested, through complete genome sequencing of four rabies virus isolates from jackal and kudu, whether specific mutations occurred in the virus genome due to host adaptation. We found the separate grouping of all rabies isolates from kudu to those of any other canid species in Namibia, suggesting that rabies was being maintained independently in kudu. Additionally, we noted several mutations unique to isolates from kudu, suggesting that these mutations may be due to the adaptation of rabies to a new host. In conclusion, we show clear evidence that rabies is being maintained independently in the Namibian kudu population - a unique phenomenon with ecological and economic impacts.

  19. Unprocessed Meat Consumption and Incident Cardiovascular Diseases in Korean Adults: The Korean Genome and Epidemiology Study (KoGES

    Directory of Open Access Journals (Sweden)

    Kyong Park

    2017-05-01

    Full Text Available Meat consumption has been shown to be associated with cardiovascular disease (CVD risk in Western societies; however, epidemiological data are limited on the Korean population. Therefore, we examined the associations between unprocessed meat consumption and CVD incidence in Korea. Data were derived from the Ansung-Ansan cohort (2001–2012, including 9370 adults (40–69 years without CVD or cancer at baseline. Total unprocessed meat consumption was estimated as the sum of unprocessed red meat (beef, pork, and organ meat and poultry consumption. In the fully adjusted Cox regression model, the relative risks of CVD across increasing quintiles of total unprocessed meat intake were 1.0 (reference, 0.72 (95% confidence interval (CI: 0.55, 0.95, 0.57 (95% CI: 0.42, 0.78, 0.69 (95% CI: 0.51, 0.95, and 0.69 (95% CI: 0.48, 0.97, but no significant linear trend was detected (p for trend = 0.14. Frequent poultry consumption was significantly associated with a decreased CVD risk; this association showed a dose-response relationship (p for trend = 0.04. This study showed that a moderate intake of total unprocessed meat was inversely associated with CVD risk. A significant inverse association between poultry consumption and incident CVD was observed in Korean adults, requiring further confirmation in other populations.

  20. Optimization of Dynamically Generated SQL Queries for Tiny-Huge, Huge-Tiny Problem

    Directory of Open Access Journals (Sweden)

    Arjun K Sirohi

    2013-03-01

    Full Text Available In most new commercial business software applications like Customer Relationship Management, the datais stored in the database layer which is usually a Relational Database Management System (RDBMS likeOracle, DB2 UDB or SQL Server. To access data from these databases, Structured Query Language (SQLqueries are used that are generated dynamically at run time based on defined business models and businessrules. One such business rule is visibility- the capability of the application to restrict data access based onthe role and responsibility of the user logged in to the application. This is generally achieved by appendingsecurity predicates in the form of sub-queries to the main query based on the roles and responsibility of theuser. In some cases, the outer query may be more restrictive while in other cases, the security predicatesmay be more restrictive. This often results in a dilemma for the cost-based optimizer (CBO of the backenddatabase whether to drive from the outer query or drive from the security predicate sub-queries. Thisdilemma is sometimes called the “Tiny-Huge, Huge-Tiny” problem and results in serious performancedegradation by way of increased response times on the application User Interface (UI. This paperprovides a case study of a new approach to vastly reduce this CBO dilemma by a combination of denormalizedcolumns and re-writing of the security predicates’ sub-queries at run-time, thereby levelling theouter and security sub-queries. This approach results in more stable execution plans in the database andmuch better performance of such SQLs, effectively leading to higher performance and scalability of theapplication.

  1. Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study.

    Science.gov (United States)

    Carty, Cara L; Bhattacharjee, Samsiddhi; Haessler, Jeff; Cheng, Iona; Hindorff, Lucia A; Aroda, Vanita; Carlson, Christopher S; Hsu, Chun-Nan; Wilkens, Lynne; Liu, Simin; Selvin, Elizabeth; Jackson, Rebecca; North, Kari E; Peters, Ulrike; Pankow, James S; Chatterjee, Nilanjan; Kooperberg, Charles

    2014-08-01

    Metabolic syndrome (MetS) refers to the clustering of cardiometabolic risk factors, including dyslipidemia, central adiposity, hypertension, and hyperglycemia, in individuals. Identification of pleiotropic genetic factors associated with MetS traits may shed light on key pathways or mediators underlying MetS. Using the Metabochip array in 15 148 African Americans from the Population Architecture using Genomics and Epidemiology (PAGE) study, we identify susceptibility loci and investigate pleiotropy among genetic variants using a subset-based meta-analysis method, ASsociation-analysis-based-on-subSETs (ASSET). Unlike conventional models that lack power when associations for MetS components are null or have opposite effects, Association-analysis-based-on-subsets uses 1-sided tests to detect positive and negative associations for components separately and combines tests accounting for correlations among components. With Association-analysis-based-on-subsets, we identify 27 single nucleotide polymorphisms in 1 glucose and 4 lipids loci (TCF7L2, LPL, APOA5, CETP, and APOC1/APOE/TOMM40) significantly associated with MetS components overall, all PHispanic population, n=5172. A novel African American-specific variant, rs12721054/APOC1, and rs10096633/LPL are associated with ≥3 MetS components. We find additional evidence of pleiotropy for APOE, TOMM40, TCF7L2, and CETP variants, many with opposing effects (eg, the same rs7901695/TCF7L2 allele is associated with increased odds of high glucose and decreased odds of central adiposity). We highlight a method to increase power in large-scale genomic association analyses and report a novel variant associated with all MetS components in African Americans. We also identify pleiotropic associations that may be clinically useful in patient risk profiling and for informing translational research of potential gene targets and medications. © 2014 American Heart Association, Inc.

  2. Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE consortium.

    Directory of Open Access Journals (Sweden)

    Joshua C Bis

    Full Text Available Stroke, the leading neurologic cause of death and disability, has a substantial genetic component. We previously conducted a genome-wide association study (GWAS in four prospective studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE consortium and demonstrated that sequence variants near the NINJ2 gene are associated with incident ischemic stroke. Here, we sought to fine-map functional variants in the region and evaluate the contribution of rare variants to ischemic stroke risk.We sequenced 196 kb around NINJ2 on chromosome 12p13 among 3,986 European ancestry participants, including 475 ischemic stroke cases, from the Atherosclerosis Risk in Communities Study, Cardiovascular Health Study, and Framingham Heart Study. Meta-analyses of single-variant tests for 425 common variants (minor allele frequency [MAF] ≥ 1% confirmed the original GWAS results and identified an independent intronic variant, rs34166160 (MAF = 0.012, most significantly associated with incident ischemic stroke (HR = 1.80, p = 0.0003. Aggregating 278 putatively-functional variants with MAF≤ 1% using count statistics, we observed a nominally statistically significant association, with the burden of rare NINJ2 variants contributing to decreased ischemic stroke incidence (HR = 0.81; p = 0.026.Common and rare variants in the NINJ2 region were nominally associated with incident ischemic stroke among a subset of CHARGE participants. Allelic heterogeneity at this locus, caused by multiple rare, low frequency, and common variants with disparate effects on risk, may explain the difficulties in replicating the original GWAS results. Additional studies that take into account the complex allelic architecture at this locus are needed to confirm these findings.

  3. Genetic risk factors for BMI and obesity in an ethnically diverse population: results from the population architecture using genomics and epidemiology (PAGE) study.

    Science.gov (United States)

    Fesinmeyer, Megan D; North, Kari E; Ritchie, Marylyn D; Lim, Unhee; Franceschini, Nora; Wilkens, Lynne R; Gross, Myron D; Bůžková, Petra; Glenn, Kimberly; Quibrera, P Miguel; Fernández-Rhodes, Lindsay; Li, Qiong; Fowke, Jay H; Li, Rongling; Carlson, Christopher S; Prentice, Ross L; Kuller, Lewis H; Manson, Joann E; Matise, Tara C; Cole, Shelley A; Chen, Christina T L; Howard, Barbara V; Kolonel, Laurence N; Henderson, Brian E; Monroe, Kristine R; Crawford, Dana C; Hindorff, Lucia A; Buyske, Steven; Haiman, Christopher A; Le Marchand, Loic; Peters, Ulrike

    2013-04-01

    Several genome-wide association studies (GWAS) have demonstrated that common genetic variants contribute to obesity. However, studies of this complex trait have focused on ancestrally European populations, despite the high prevalence of obesity in some minority groups. As part of the "Population Architecture using Genomics and Epidemiology (PAGE)" Consortium, we investigated the association between 13 GWAS-identified single-nucleotide polymorphisms (SNPs) and BMI and obesity in 69,775 subjects, including 6,149 American Indians, 15,415 African-Americans, 2,438 East Asians, 7,346 Hispanics, 604 Pacific Islanders, and 37,823 European Americans. For the BMI-increasing allele of each SNP, we calculated β coefficients using linear regression (for BMI) and risk estimates using logistic regression (for obesity defined as BMI ≥ 30) followed by fixed-effects meta-analysis to combine results across PAGE sites. Analyses stratified by racial/ethnic group assumed an additive genetic model and were adjusted for age, sex, and current smoking. We defined "replicating SNPs" (in European Americans) and "generalizing SNPs" (in other racial/ethnic groups) as those associated with an allele frequency-specific increase in BMI. By this definition, we replicated 9/13 SNP associations (5 out of 8 loci) in European Americans. We also generalized 8/13 SNP associations (5/8 loci) in East Asians, 7/13 (5/8 loci) in African Americans, 6/13 (4/8 loci) in Hispanics, 5/8 in Pacific Islanders (5/8 loci), and 5/9 (4/8 loci) in American Indians. Linkage disequilibrium patterns suggest that tagSNPs selected for European Americans may not adequately tag causal variants in other ancestry groups. Accordingly, fine-mapping in large samples is needed to comprehensively explore these loci in diverse populations. Copyright © 2012 The Obesity Society.

  4. Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus hospital clone EMRSA-15.

    Science.gov (United States)

    Holmes, A; McAllister, G; McAdam, P R; Hsien Choi, S; Girvan, K; Robb, A; Edwards, G; Templeton, K; Fitzgerald, J R

    2014-02-01

    The EMRSA-15 clone is a major cause of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections in the UK and elsewhere but existing typing methodologies have limited capacity to discriminate closely related strains, and are often poorly reproducible between laboratories. Here, we report the design, development and validation of a genome-wide single nucleotide polymorphism (SNP) typing method and compare it to established methods for typing of EMRSA-15. In order to identify discriminatory SNPs, the genomes of 17 EMRSA-15 strains, selected to represent the breadth of genotypic and phenotypic diversity of EMRSA-15 isolates in Scotland, were determined and phylogenetic reconstruction was carried out. In addition to 17 phylogenetically informative SNPs, five binary markers were included to form the basis of an EMRSA-15 genotyping assay. The SNP-based typing assay was as discriminatory as pulsed-field gel electrophoresis, and significantly more discriminatory than staphylococcal protein A (spa) typing for typing of a representative panel of diverse EMRSA-15 strains, isolates from two EMRSA-15 hospital outbreak investigations, and a panel of bacteraemia isolates obtained in healthcare facilities in the east of Scotland during a 12-month period. The assay is a rapid, and reproducible approach for epidemiological analysis of EMRSA-15 clinical isolates in Scotland. Unlike established methods the DNA sequence-based method is ideally suited for inter-laboratory comparison of identified genotypes, and its flexibility lends itself to supplementation with additional SNPs or markers for the identification of novel S. aureus strains in other regions of the world.

  5. The future of epidemiology.

    Science.gov (United States)

    Ness, Roberta B; Andrews, Elizabeth B; Gaudino, James A; Newman, Anne B; Soskolne, Colin L; Stürmer, Til; Wartenberg, Daniel E; Weiss, Stanley H

    2009-11-01

    In this article, the authors discuss current challenges and opportunities in epidemiology that will affect the field's future. Epidemiology is commonly considered the methodologic backbone for the fields of public health and outcomes research because its practitioners describe patterns of disease occurrence, identify risk factors and etiologic determinants, and demonstrate the usefulness of interventions. Like most aspects of science, epidemiology is in rapid flux. Several factors that are influencing and will continue to influence epidemiology and the health of the public include factors fundamental to framing the discipline of epidemiology (i.e., its means of communication, its methodologies, its access to data, its values, its population perspective), factors relating to scientific advances (e.g., genomics, comparative effectiveness in therapeutics), and factors shaping human health (e.g., increasing globalism, the environment, disease and lifestyle, demographics, infectious disease).

  6. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation

    Directory of Open Access Journals (Sweden)

    Emily A. Pettengill

    2016-01-01

    Full Text Available As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing (WGS of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.

  7. Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation.

    Science.gov (United States)

    Pettengill, Emily A; Pettengill, James B; Binet, Rachel

    2015-01-01

    As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.

  8. Possible expressions of radiation-induced genomic instability, bystander effects or low-dose hypersensitivity in cancer epidemiology

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, Peter, E-mail: Jacob@helmholtz-muenchen.de [Helmholtz Zentrum Muenchen, Institute of Radiation Protection, 85764 Neuherberg (Germany); Meckbach, Reinhard; Kaiser, Jan Christian [Helmholtz Zentrum Muenchen, Institute of Radiation Protection, 85764 Neuherberg (Germany); Sokolnikov, Mikhail [Southern Urals Biophysics Institute, Ozyorsk 456780 (Russian Federation)

    2010-05-01

    Recent publications on the integration of radiobiological effects in the two-step clonal expansion (TSCE) model of carcinogenesis and applications to radioepidemiological data are reviewed and updated. First, a model version with radiation-induced genomic instability was shown to be a possible explanation for the age dependence of the radiation-induced cancer mortality in the Techa River Cohort. Second, it is demonstrated that inclusion of a bystander effect with a dose threshold allows an improved description of the lung cancer mortality risk for the Mayak workers cohort due to incorporation of plutonium. The threshold for the annual lung dose is estimated to 12 (90%CI: 4; 14) mGy/year. This threshold applies to the initiation of preneoplastic cells and to hyperplastic growth. There is, however, no evidence for a threshold for the effects of gamma radiation. Third, models with radiation-induced cell inactivation tend to predict lower cancer risks among the atomic bomb survivors with exposure at young age than conventionally used empirical models. Also, risks after exposures with doses in the order of 100 mGy are predicted to be higher in models with low-dose hypersensitivity than in models with conventional cell survival curves. In the reviewed literature, models of carcinogenesis tend to describe radioepidemiological data better than conventionally used empirical models.

  9. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

    Science.gov (United States)

    Downing, Tim

    2015-01-01

    High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols. PMID:27682088

  10. Sample Cancer Epidemiology Grant Applications

    Science.gov (United States)

    The National Cancer Institute frequently receives questions from investigators for examples of successfully funded grant applications. Several investigators agreed to let the Epidemiology and Genomics Research Program post excerpts of their grant applications online.

  11. ESR1 Gene Polymorphisms and Prostate Cancer Risk: A HuGE Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Yu-Mei Wang

    Full Text Available Many published data on the association between single nucleotide polymorphisms (SNPs in the ESR1 gene and prostate cancer susceptibility are inconclusive. The aim of this Human Genome Epidemiology (HuGE review and meta-analysis is to derive a more precise estimation of this relationship.A literature search of PubMed, Embase, Web of Science and Chinese Biomedical (CBM databases was conducted from their inception through July 1st, 2012. Crude odds ratios (ORs with 95% confidence intervals (CIs were calculated to assess the strength of association.Twelve case-control studies were included with a total 2,165 prostate cancer cases and 3,361 healthy controls. When all the eligible studies were pooled into the meta-analysis, ESR1 PvuII (C>T and XbaI (A>G polymorphisms showed no association with the risk of prostate cancer. However, in the stratified analyses based on ethnicity and country, the results indicated that ESR1 PvuII (C>T polymorphism was significantly associated with increased risk of prostate cancer among Asian populations, especially among Indian population; while ESR1 XbaI (A>G polymorphism may significantly increase the risk of prostate cancer among American population. Furthermore, we also performed a pooled analysis for all eligible case-control studies to explore the role of codon 10 (T>C, codon 325 (C>G, codon 594 (G>A and +261G>C polymorphisms in prostate cancer risk. Nevertheless, no significant associations between these polymorphisms and the risk of prostate cancer were observed.Results from the current meta-analysis indicate that ESR1 PvuII (C>T polymorphism may be a risk factor for prostate cancer among Asian populations, especially among Indian population; while ESR1 XbaI (A>G polymorphism may increase the risk of prostate cancer among American population.

  12. CYP3A4*1B polymorphism and cancer risk: a HuGE review and meta-analysis.

    Science.gov (United States)

    Zhou, Li-Ping; Yao, Fan; Luan, Hong; Wang, Yin-Ling; Dong, Xi-Hua; Zhou, Wen-Wen; Wang, Qi-Hui

    2013-04-01

    CYP450 3A4 (CYP3A4), encoded by the CYP3A4 gene, is a major enzyme catalyzing the metabolism of both endogenous and exogenous agents that may play a role in the etiology of carcinogenesis. Several potentially functional polymorphisms of the CYP3A4 gene have been implicated in cancer risk, but individually published studies have shown inconclusive results. The aim of this Human Genome Epidemiology (HuGE) review and meta-analysis was to investigate the association between CYP3A4*1B (rs2740574 A > G) polymorphism and cancer risk. Eleven studies were included with a total of 3,810 cancer patients and 3,173 healthy controls. We found that the G allele and GG genotype of CYP3A4*1B polymorphism were associated with increased risk of cancers using the fixed effects model (allele model: odds ratio (OR) = 1.24, 95 %CI: 1.09-1.42, P = 0.001; recessive model: OR = 1.77, 95 %CI: 1.30-2.41, P cancer type showed that the G allele and G carrier (AG + GG) of CYP3A4*1B polymorphism had significant associations with increased risk of prostate cancer, but not with breast cancer, leukemia, or other cancers. With further subgroup analysis based on different ethnicities, the results indicated that the GG genotype of CYP3A4*1B polymorphism might increase the risk of cancer among African populations. However, similar associations were not observed among Caucasian and Asian populations. Results from the current meta-analysis indicate that the G allele and GG genotype of CYP3A4*1B polymorphism might be associated with increased cancer risk, especially for prostate cancer among African populations.

  13. Scarless surgery for a huge liver cyst: A case report.

    Science.gov (United States)

    Kashiwagi, Hiroyuki; Kawachi, Jun; Isogai, Naoko; Ishii, Masanori; Miyake, Katsunori; Shimoyama, Rai; Fukai, Ryota; Ogino, Hidemitsu

    2017-09-01

    Symptomatic or complicated liver cysts sometimes require surgical intervention and laparoscopic fenestration is the definitive treatment for these cysts. We performed minimally invasive surgery, hybrid natural orifice transluminal endoscopic surgery (NOTES) without scarring, for a huge liver cyst. An 82-year-old female presented with a month-long history of right upper abdominal pain. We diagnosed her condition as a huge liver cyst by morphological studies. She denied any history of abdominal trauma. Her serum CEA and CA19-9 were normal and a serum echinococcus serologic test was negative. Laparoscopic fenestration, using a hybrid NOTES procedure via a transvaginal approach, was performed for a huge liver cyst because we anticipated difficulty with an umbilical approach, such as single incision laparoscopic surgery (SILS). Her post-operative course was uneventful and she was discharged from our hospital three days after surgery. Pain killers were not required during and after hospitalization. No recurrence of the liver cyst or bulging was detected by clinical examination two years later. A recent trend of laparoscopic procedure has been towards minimizing the number of incisions to achieve less invasiveness. This hybrid NOTES, with a small incision for abdominal access, along with vaginal access, enabled painless operation for a huge liver cyst. We report a huge liver cyst treated by hybrid NOTES. This approach is safe, less invasive, and may be the first choice for a huge liver cyst. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Cancer Epidemiology Data Repository (CEDR)

    Science.gov (United States)

    In an effort to broaden access and facilitate efficient data sharing, the Epidemiology and Genomics Research Program (EGRP) has created the Cancer Epidemiology Data Repository (CEDR), a centralized, controlled-access database, where Investigators can deposit individual-level de-identified observational cancer datasets.

  15. Phenome-wide association study (PheWAS for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE Network.

    Directory of Open Access Journals (Sweden)

    Sarah A Pendergrass

    Full Text Available Using a phenome-wide association study (PheWAS approach, we comprehensively tested genetic variants for association with phenotypes available for 70,061 study participants in the Population Architecture using Genomics and Epidemiology (PAGE network. Our aim was to better characterize the genetic architecture of complex traits and identify novel pleiotropic relationships. This PheWAS drew on five population-based studies representing four major racial/ethnic groups (European Americans (EA, African Americans (AA, Hispanics/Mexican-Americans, and Asian/Pacific Islanders in PAGE, each site with measurements for multiple traits, associated laboratory measures, and intermediate biomarkers. A total of 83 single nucleotide polymorphisms (SNPs identified by genome-wide association studies (GWAS were genotyped across two or more PAGE study sites. Comprehensive tests of association, stratified by race/ethnicity, were performed, encompassing 4,706 phenotypes mapped to 105 phenotype-classes, and association results were compared across study sites. A total of 111 PheWAS results had significant associations for two or more PAGE study sites with consistent direction of effect with a significance threshold of p<0.01 for the same racial/ethnic group, SNP, and phenotype-class. Among results identified for SNPs previously associated with phenotypes such as lipid traits, type 2 diabetes, and body mass index, 52 replicated previously published genotype-phenotype associations, 26 represented phenotypes closely related to previously known genotype-phenotype associations, and 33 represented potentially novel genotype-phenotype associations with pleiotropic effects. The majority of the potentially novel results were for single PheWAS phenotype-classes, for example, for CDKN2A/B rs1333049 (previously associated with type 2 diabetes in EA a PheWAS association was identified for hemoglobin levels in AA. Of note, however, GALNT2 rs2144300 (previously associated with high

  16. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

    Directory of Open Access Journals (Sweden)

    Abdulahi Alfonso-Morales

    Full Text Available Infectious bursal disease (IBD is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV strains worldwide.Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for

  17. Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes.

    Directory of Open Access Journals (Sweden)

    Maude Jacquot

    Full Text Available Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France, a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used

  18. Epidemiology: Then and Now.

    Science.gov (United States)

    Kuller, Lewis H

    2016-03-01

    Twenty-five years ago, on the 75th anniversary of the Johns Hopkins Bloomberg School of Public Health, I noted that epidemiologic research was moving away from the traditional approaches used to investigate "epidemics" and their close relationship with preventive medicine. Twenty-five years later, the role of epidemiology as an important contribution to human population research, preventive medicine, and public health is under substantial pressure because of the emphasis on "big data," phenomenology, and personalized medical therapies. Epidemiology is the study of epidemics. The primary role of epidemiology is to identify the epidemics and parameters of interest of host, agent, and environment and to generate and test hypotheses in search of causal pathways. Almost all diseases have a specific distribution in relation to time, place, and person and specific "causes" with high effect sizes. Epidemiology then uses such information to develop interventions and test (through clinical trials and natural experiments) their efficacy and effectiveness. Epidemiology is dependent on new technologies to evaluate improved measurements of host (genomics), epigenetics, identification of agents (metabolomics, proteomics), new technology to evaluate both physical and social environment, and modern methods of data collection. Epidemiology does poorly in studying anything other than epidemics and collections of numerators and denominators without specific hypotheses even with improved statistical methodologies.

  19. A case of a huge gastroepiploic arterial aneurysm.

    Science.gov (United States)

    Ikeda, Hirokuni; Takeo, Masahiko; Mikami, Ryuuichi; Yamamoto, Mistuo

    2015-08-05

    An 85-year-old man complaining of vague abdominal discomfort was admitted to our hospital. A pulsatile 8 × 7-cm mass in the right upper abdomen was noticed on clinical examination. Computed tomography of the abdomen showed a huge arterial aneurysm in the right gastroepiploic artery, and the left gastroepiploic artery was meandering and expanding. An image diagnosis of gastroepiploic arterial aneurysm (GEAA) was made. Because of the huge size of the aneurysm and the predicted high risk of perforation, surgical intervention was planned. The aneurysm was identified in the greater curve and was found to adhere firmly to the transverse colon. Partial resection of the stomach, aneurysmectomy and partial resection of the transverse colon were performed. Clinically, splanchnic arterial aneurysms are rare. Among them, GEAA is especially rare. We report a rare case of a huge GEAA that was treated successfully by surgery. Published by Oxford University Press and JSCR Publishing Ltd. All rights reserved. © The Author 2015.

  20. Anaesthetic management in a case of huge plunging ranula.

    Science.gov (United States)

    Sheet, Jagabandhu; Mandal, Anamitra; Sengupta, Swapnadeep; Jana, Debaleena; Mukherji, Sudakshina; Swaika, Sarbari

    2014-01-01

    Plunging ranula is a rare form of mucous retention cyst arising from submandibular and sublingual salivary glands, which may occasionally become huge occupying the whole of the floor of the mouth and extending into the neck, thus, restricting the neck movement as well as disfiguring the normal airway anatomy. Without fiberoptic assistance, blind or retrograde nasal intubation remains valuable choices in this type of situation. Here, we present a case of successful management of airway by blind nasal intubation in a patient posted for excision of a huge plunging ranula.

  1. Huge Gastric Teratoma in an 8-Year Old Boy.

    Science.gov (United States)

    Sisodiya, Rajpal S; Ratan, Simmi K; Man, Parveen K

    2016-01-01

    Gastric teratoma is very rare tumor and usually presents in early infancy. An 8-year-old boy presented with a huge mass in abdomen extending from epigastrium to the pelvis. Ultrasound and CT scan of abdomen revealed a huge mass with solid and cystic components and internal calcifications. The preoperative diagnosis was a teratoma but not specifically gastric one. At operation, it was found to be gastric teratoma. The mass was excised completely with part of the stomach wall. The histopathology confirmed it to be mature gastric teratoma. The rarity of the teratoma with delayed presentation prompted us to report the case.

  2. Anaesthetic challenges in a patient presenting with huge neck teratoma

    Directory of Open Access Journals (Sweden)

    Gaurav Jain

    2013-01-01

    Full Text Available Paediatric airway management is a great challenge even for an experienced anaesthesiologist. Difficult airway in huge cervical teratoma further exaggerates the complexity. This case report is intended at describing the intubation difficulties that were confronted during the airway management of a three year old girl presenting with huge neck teratoma and respiratory distress. This patient was successfully intubated with uncuffed endotracheal tubes in second attempt under inhalational anaesthesia with halothane and spontaneous ventilation. This case exemplifies the importance of careful preoperative workup of an anticipated difficult airway in paediatric patients with neck swelling to minimize any perioperative complications.

  3. Huge pelvic mass secondary to wear debris causing ureteral obstruction.

    Science.gov (United States)

    Hananouchi, Takehito; Saito, Masanobu; Nakamura, Nobuo; Yamamoto, Tetsuya; Yonenobu, Kazuo

    2005-10-01

    We report an unusual granulomatous reaction of wear debris that produced a huge pelvic mass causing ureteral obstruction. A 72-year-old woman, who received a cemented total hip arthroplasty 30 years ago, was referred to the department of gynecology for examination of a pelvic mass. A computed tomography scan revealed a huge homogenous mass, measuring approximately 20 x 16 x 12 cm, including extensive osteolysis of the left pelvis around the acetabular component. Intravenous pyelogram revealed complete obstruction of the left ureter resulting in hydronephrosis of the left kidney. Histological examination from the biopsy specimen detected polyethylene wear debris in the mass.

  4. Anaesthetic management in a case of huge plunging ranula

    Science.gov (United States)

    Sheet, Jagabandhu; Mandal, Anamitra; Sengupta, Swapnadeep; Jana, Debaleena; Mukherji, Sudakshina; Swaika, Sarbari

    2014-01-01

    Plunging ranula is a rare form of mucous retention cyst arising from submandibular and sublingual salivary glands, which may occasionally become huge occupying the whole of the floor of the mouth and extending into the neck, thus, restricting the neck movement as well as disfiguring the normal airway anatomy. Without fiberoptic assistance, blind or retrograde nasal intubation remains valuable choices in this type of situation. Here, we present a case of successful management of airway by blind nasal intubation in a patient posted for excision of a huge plunging ranula. PMID:25886120

  5. Q&A: Muin Khoury on cancer epidemiology.

    Science.gov (United States)

    Khoury, Muin J; Rose, Suzanne

    2014-02-01

    Muin J. Khoury, MD, PhD, director of the Centers for Disease Control and Prevention's Office of Public Health Genomics and head of the National Cancer Institute's Epidemiology and Genomics Research Program in the Division of Cancer Control and Population Sciences, talks about challenges and opportunities in cancer epidemiology research and efforts in the epidemiology community to transform the field.

  6. Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT.

    Directory of Open Access Journals (Sweden)

    Alexander P Reiner

    2011-06-01

    Full Text Available Total white blood cell (WBC and neutrophil counts are lower among individuals of African descent due to the common African-derived "null" variant of the Duffy Antigen Receptor for Chemokines (DARC gene. Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type levels in European and Japanese populations. No additional loci that account for WBC variability have been identified in African Americans. In order to address this, we performed a large genome-wide association study (GWAS of total WBC and cell subtype counts in 16,388 African-American participants from 7 population-based cohorts available in the Continental Origins and Genetic Epidemiology Network. In addition to the DARC locus on chromosome 1q23, we identified two other regions (chromosomes 4q13 and 16q22 associated with WBC in African Americans (P<2.5×10(-8. The lead SNP (rs9131 on chromosome 4q13 is located in the CXCL2 gene, which encodes a chemotactic cytokine for polymorphonuclear leukocytes. Independent evidence of the novel CXCL2 association with WBC was present in 3,551 Hispanic Americans, 14,767 Japanese, and 19,509 European Americans. The index SNP (rs12149261 on chromosome 16q22 associated with WBC count is located in a large inter-chromosomal segmental duplication encompassing part of the hydrocephalus inducing homolog (HYDIN gene. We demonstrate that the chromosome 16q22 association finding is most likely due to a genotyping artifact as a consequence of sequence similarity between duplicated regions on chromosomes 16q22 and 1q21. Among the WBC loci recently identified in European or Japanese populations, replication was observed in our African-American meta-analysis for rs445 of CDK6 on chromosome 7q21 and rs4065321 of PSMD3-CSF3 region on chromosome 17q21. In summary, the CXCL2, CDK6, and PSMD3-CSF3 regions are associated with WBC count in African American and other populations. We also demonstrate that large inter

  7. Imaging of huge lingual thyroid gland with goitre

    Energy Technology Data Exchange (ETDEWEB)

    Lee, C.C.; Chen, C.Y.; Chen, F.H.; Lee, G.W.; Hsiao, H.S. [Nat. Defense Medical Centre, Taipei (Taiwan, Province of China). Dept. of Diagnostic Radiol.; Zimmermann, R.A. [Department of Radiology, The Children`s Hospital of Philadelphia, 34th St. and Civic Blvd., Philadelphia, PA 19014 (United States)

    1998-05-01

    We present the CT and MRI findings in a 75-year-old woman with a huge pathologically proven lingual thyroid which underwent goitrous degeneration. CT and MRI showed a midline, tongue-based, exophytic mass with areas of necrosis and heterogeneous contrast enhancement, as seen in large goitres in the normal thyroid gland. (orig.) With 1 fig., 7 refs.

  8. Smart Cities as Support and Legacy of Huge Sport Events

    Directory of Open Access Journals (Sweden)

    TAURION, C.

    2012-12-01

    Full Text Available In this paper we discuss the concept of a smart city and the importance of huge Sport events as an incentive to the creation of the infrastructure necessary for the development of cities that provide quality of life for all its citizens using information technology.

  9. The big, large and huge case of state-building

    DEFF Research Database (Denmark)

    Harste, Gorm

      Using communication theory as point of departure, it is not evident how to study macro phenomena. Michel Foucault limited his studies to a non-Grand Theory when studying discursive events. At the same time, Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when trying...

  10. [Experience of surgical treatment of huge mediastinal tumors].

    Science.gov (United States)

    Li, Yuanbo; Zhang, Yi; Xu, Qingsheng; Su, Lei; Zhi, Xiuyi; Wang, Ruotian; Qian, Kun; Hu, Mu; Liu, Lei

    2014-09-23

    The diagnosis and surgical treatment of 36 huge mediastinal tumors were summarized in order to evaluate the effect and safety of the operation. Thirty-six huge mediastinal tumor patients treated in our department from June 2006 to June 2013 were retrospective analyzed, of whom clinical manifestations, diagnosis, surgical treatment and prognosis were carefully collected. Twenty-three cases were men and 13 were women. The average age was 39.2 years old. The pathology turned out to be benign in 23 cases and malignant in 13 cases. Complete resection was achieved in 34 cases while palliative resection in 2 cases with no perioperative death. Six cases had developed postoperative complications but all recovered after active treatment. Patients who had been diagnosed with benign tumors were all alive after follow-up periods of 6 months to 7 years. Nine malignat tumor patients developed recurrence or metastasis, including seven deaths. Surgery played a vital role in the diagnosis and treatment of huge mediastinal tumors. Preoperative diagnosis, accurate surgical approach and careful operation were the key to successful treatment. Benign huge mediastinal tumors had excellent prognosis with surgery.

  11. A Huge Ovarian Dermoid Cyst: Successful Laparoscopic Total Excision.

    Science.gov (United States)

    Uyanikoglu, Hacer; Dusak, Abdurrahim

    2017-08-01

    Giant ovarian cysts, ≥15 cm in diameter, are quite rare in women of reproductive age. Here, we present a case of ovarian cyst with unusual presentation treated by laparoscopic surgery. On histology, mass was found to be mature cystic teratoma. The diagnostic and management challenges posed by this huge ovarian cyst were discussed in the light of the literature.

  12. Huge mediastinal liposarcoma resected by clamshell thoracotomy: a case report.

    Science.gov (United States)

    Toda, Michihito; Izumi, Nobuhiro; Tsukioka, Takuma; Komatsu, Hiroaki; Okada, Satoshi; Hara, Kantaro; Ito, Ryuichi; Shibata, Toshihiko; Nishiyama, Noritoshi

    2017-12-01

    Liposarcoma is the single most common soft tissue sarcoma. Because mediastinal liposarcomas often grow rapidly and frequently recur locally despite adjuvant chemotherapy and radiotherapy, they require complete excision. Therefore, the feasibility of achieving complete surgical excision must be carefully considered. We here report a case of a huge mediastinal liposarcoma resected via clamshell thoracotomy. A 64-year-old man presented with dyspnea on effort. Cardiomegaly had been diagnosed 6 years previously, but had been left untreated. A computed tomography scan showed a huge (36 cm diameter) anterior mediastinal tumor expanding into the pleural cavities bilaterally. The tumor comprised mostly fatty tissue but contained two solid areas. Echo-guided needle biopsies were performed and a diagnosis of an atypical lipomatous tumor was established by pathological examination of the biopsy samples. Surgical resection was performed via a clamshell incision, enabling en bloc resection of this huge tumor. Although there was no invasion of surrounding organs, the left brachiocephalic vein was resected because it was circumferentially surrounded by tumor and could not be preserved. The tumor weighed 3500 g. Pathologic examination of the resected tumor resulted in a diagnosis of a biphasic tumor comprising dedifferentiated liposarcoma and non-adipocytic sarcoma with necrotic areas. The patient remains free of recurrent tumor 20 months postoperatively. Clamshell incision provides an excellent surgical field and can be performed safely in patients with huge mediastinal liposarcomas.

  13. Huge uterine-cervical diverticulum mimicking as a cyst

    Directory of Open Access Journals (Sweden)

    S Chufal

    2012-01-01

    Full Text Available Here we report an incidental huge uterine-cervical diverticulum from a total abdominal hysterectomy specimen in a perimenopausal woman who presented with acute abdominal pain. The diverticulum was mimicking with various cysts present in the lateral side of the female genital tract. Histopathological examination confirmed this to be a cervical diverticulum with communication to uterine cavity through two different openings. They can attain huge size if left ignored for long duration and present a diagnostic challenge to clinicians, radiologists, as well as pathologists because of its extreme rarity. Therefore, diverticula should also be included as a differential diagnosis. Its histopathological confirmation also highlights that diverticula can present as an acute abdomen, requiring early diagnosis with appropriate timely intervention. Immunohistochemistry CD 10 has also been used to differentiate it from a mesonephric cyst.

  14. Huge uterine-cervical diverticulum mimicking as a cyst.

    Science.gov (United States)

    Chufal, S; Thapliyal, Naveen; Gupta, Manoj; Pangtey, Nirmal

    2012-01-01

    Here we report an incidental huge uterine-cervical diverticulum from a total abdominal hysterectomy specimen in a perimenopausal woman who presented with acute abdominal pain. The diverticulum was mimicking with various cysts present in the lateral side of the female genital tract. Histopathological examination confirmed this to be a cervical diverticulum with communication to uterine cavity through two different openings. They can attain huge size if left ignored for long duration and present a diagnostic challenge to clinicians, radiologists, as well as pathologists because of its extreme rarity. Therefore, diverticula should also be included as a differential diagnosis. Its histopathological confirmation also highlights that diverticula can present as an acute abdomen, requiring early diagnosis with appropriate timely intervention. Immunohistochemistry CD 10 has also been used to differentiate it from a mesonephric cyst.

  15. A case of huge primary liposarcoma in the liver

    Institute of Scientific and Technical Information of China (English)

    Liang-Mou Kuo; Hong-Shiue Chou; Kun-Ming Chan; Ming-Chin Yu; Wei-Chen Lee

    2006-01-01

    Primary liver liposarcoma is a rare disease. Because of its rarity, the knowledge of the clinical course, management, and prognosis of primary liver liposarcoma are all limited for clinicians. A 61-year-old female patient who suffered from a huge primary liposarcoma in the central portion of the liver had the clinical presentations of fever, nausea, vomiting, jaundice, and body weight loss.The huge tumor was resected successfully. However,the tumor recurred repeatedly and she had repeated hepatectomies to remove the tumor. Thetumor became aggravating after repeated surgeries. Eventually, the patient had cervical spinal metastasis of liposarcoma and she survived for 26 months after liver liposarcoma was diagnosed. Although the tumor may become aggravating after repeated surgeries, repeated hepatectomies are still the best policy to achieve a long-term survival for the patients.

  16. Black Hole Firewalls Require Huge Energy of Measurement

    CERN Document Server

    Hotta, Masahiro; Funo, Ken

    2013-01-01

    The unitary moving mirror model is one of the best quantum systems for checking the reasoning of the firewall paradox in quantum black holes. The reasoning of Almheiri et al. inevitably raises a firewall paradox in the model. We resolve this paradox from the viewpoint of the energy cost of quantum measurements. No firewall with a deadly, huge energy flux appears, as long as the energy for the measurement is much smaller than the ultraviolet cutoff scale.

  17. Severe microphthalmos with cyst and unusually huge dermolipoma.

    Science.gov (United States)

    Li, Weidong; Zhang, Ping; Chen, Qiwen; Ye, Xuelian; Li, Jianqun; Yan, Jianhua

    2015-03-01

    The purpose of this study was to report an unusual case of severe microphthalmos, together with an orbital cyst and huge ocular surface dermolipoma. This is a clinical report relating clinical features as well as imaging and histopathologic findings, along with surgical management of the patient. A 5-month-old Chinese male infant was referred, with 2 large masses in the left eye that were present since birth. Ocular examination results revealed a complete absence of any eye structures in the left orbit. In its place were 2 large masses between the left upper and lower palpebral fissure. One was a 3 × 3 × 2.5-cm spherical red tumor with a smooth surface. The other was a large solid spherical tumor, 4 × 4 × 5 cm, covered with normal skin located in the temporal region and attached to the red mass by a pedicle. Orbital magnetic resonance imaging examination findings confirmed that no eye structures were present in the left orbit. However, a cystic lesion was found in the left orbit, with a low signal on T1-weighted imaging and high signal on T2-weighted imaging, and another huge spherical heterogeneous mass was located "outside" the left orbit. Anterior orbitotomy by conjunctival incision was performed under general anesthesia. A spherical cystic mass of 1.5 × 1.5 × 1.6 cm, a small eye of 0.7 × 0.7 × 0.6 cm, and a huge dermolipoma were removed completely. Pathologic examination results confirmed the diagnosis of severe microphthalmos, together with orbital dermoid cyst and dermolipoma. This rare case demonstrates that severe microphthalmos with a cyst may be completely covered by conjunctiva and associated with an unusually huge dermolipoma.

  18. Huge plastic bezoar: a rare cause of gastrointestinal obstruction.

    Science.gov (United States)

    Yaka, Mbarek; Ehirchiou, Abdelkader; Alkandry, Tariq Tajdin Sifeddine; Sair, Khalid

    2015-01-01

    Bezoars are rare causes of gastrointestinal obstruction. Basically, they are of four types: trichobezoars, phytobezoars, pharmacobezoars, and lactobezoars. Some rare types of bezoars are also known. In this article a unique case of plastic bezoars is presented. We describe a girl aged 14 years who ingested large amounts of plastic material used for knitting chairs and charpoys. The conglomerate of plastic threads, entrapped food material and other debris, formed a huge mass occupying the whole stomach and extended into small bowel.

  19. A Huge Cystic Retroperitoneal Lymphangioma Presenting with Back Pain

    Science.gov (United States)

    Kubachev, Kubach; Abdullaev, Elbrus; Babyshin, Valentin; Neronov, Dmitriy; Abdullaev, Abakar

    2016-01-01

    Retroperitoneal lymphangioma is a rare location and type of benign abdominal tumors. The clinical presentation of this rare disease is nonspecific, ranging from abdominal distention to sepsis. Here we present a 73-year-old female patient with 3-month history of back pain. USG and CT revealed a huge cystic mass which was surgically excised and appeared to be lymphangioma on histopathology. PMID:27843456

  20. Huge Left Atrium Accompanied by Normally Functioning Prosthetic Valve.

    Science.gov (United States)

    Sabzi, Feridoun

    2015-01-01

    Giant left atria are defined as those measuring larger than 8 cm and are typically found in patients who have rheumatic mitral valve disease with severe regurgitation. Enlargement of the left atrium may create compression of the surrounding structures such as the esophagus, pulmonary veins, respiratory tract, lung, inferior vena cava, recurrent laryngeal nerve, and thoracic vertebrae and lead to dysphagia, respiratory dysfunction, peripheral edema, hoarse voice, or back pain. However, a huge left atrium is usually associated with rheumatic mitral valve disease but is very rare in a normally functioning prosthetic mitral valve, as was the case in our patient. A 46-year-old woman with a past medical history of mitral valve replacement and chronic atrial fibrillation was admitted to our hospital with a chief complaint of cough and shortness of breath, worsened in the last month. Physical examination showed elevated jugular venous pressure, respiratory distress, cardiac cachexia, heart failure, hepatomegaly, and severe edema in the legs. Chest radiography revealed an inconceivably huge cardiac sell-out. Transthoracic echocardiography demonstrated a huge left atrium, associated with thrombosis, and normal function of the prosthetic mitral valve. Cardiac surgery with left atrial exploration for the extraction of the huge thrombosis and De Vega annuloplasty for tricuspid regurgitation were carried out. The postoperative course was eventful due to right ventricular failure and low cardiac output syndrome; and after two days, the patient expired with multiple organ failure. Thorough literature review showed that our case was the largest left atrium (20 × 22 cm) reported thus far in adults with a normal prosthetic mitral valve function.

  1. Huge Left Atrium Accompanied by Normally Function- ing Prosthetic Valve

    Directory of Open Access Journals (Sweden)

    Feridoun Sabzi

    2015-10-01

    Full Text Available Giant left atria are defined as those measuring larger than 8 cm and are typically found in patients who have rheumatic mitral valve disease with severe regurgitation. Enlargement of the left atrium may create compression of the surrounding structures such as the esophagus, pulmonary veins, respiratory tract, lung, inferior vena cava, recurrent laryngeal nerve, and thoracic vertebrae and lead to dysphagia, respiratory dysfunction, peripheral edema, hoarse voice, or back pain. However, a huge left atrium is usually associated with rheumatic mitral valve disease but is very rare in a normally functioning prosthetic mitral valve, as was the case in our patient. A 46-year-old woman with a past medical history of mitral valve replacement and chronic atrial fibrillation was admitted to our hospital with a chief complaint of cough and shortness of breath, worsened in the last month. Physical examination showed elevated jugular venous pressure, respiratory distress, cardiac cachexia, heart failure, hepatomegaly, and severe edema in the legs. Chest radiography revealed an inconceivably huge cardiac sell-out. Transthoracic echocardiography demonstrated a huge left atrium, associated with thrombosis, and normal function of the prosthetic mitral valve. Cardiac surgery with left atrial exploration for the extraction of the huge thrombosis and De Vega annuloplasty for tricuspid regurgitation were carried out. The postoperative course was eventful due to right ventricular failure and low cardiac output syndrome; and after two days, the patient expired with multiple organ failure. Thorough literature review showed that our case was the largest left atrium (20 × 22 cm reported thus far in adults with a normal prosthetic mitral valve function.

  2. Huge Nevus Lipomatosus Cutaneous Superficialis on Back: An Unusual Presentation.

    Science.gov (United States)

    Das, Dipti; Das, Anupam; Bandyopadhyay, Debabrata; Kumar, Dhiraj

    2015-01-01

    Nevus lipomatosus cutaneous superficialis (NLCS) is a benign dermatosis, histologically characterized by the presence of mature ectopic adipocytes in the dermis. We hereby report a case of a 10-year-old boy who presented with multiple huge swellings on the scapular regions and lower back. The lesions were surmounted by small papules, along with peau-d orange appearance at places. Histology showed features consistent with NLCS. The case is being reported for the unusual clinical presentation.

  3. Huge nevus lipomatosus cutaneous superficialis on back: An unusual presentation

    Directory of Open Access Journals (Sweden)

    Dipti Das

    2015-01-01

    Full Text Available Nevus lipomatosus cutaneous superficialis (NLCS is a benign dermatosis, histologically characterized by the presence of mature ectopic adipocytes in the dermis. We hereby report a case of a 10-year-old boy who presented with multiple huge swellings on the scapular regions and lower back. The lesions were surmounted by small papules, along with peau-d orange appearance at places. Histology showed features consistent with NLCS. The case is being reported for the unusual clinical presentation.

  4. Huge Intravascular Tumor Extending to the Heart: Leiomyomatosis

    Directory of Open Access Journals (Sweden)

    Suat Doganci

    2015-01-01

    Full Text Available Intravenous leiomyomatosis (IVL is a rare neoplasm characterized by histologically benign-looking smooth muscle cell tumor mass, which is growing within the intrauterine and extrauterine venous system. In this report we aimed to present an unusual case of IVL, which is originating from iliac vein and extended throughout to right cardiac chambers. A 49-year-old female patient, who was treated with warfarin sodium due to right iliac vein thrombosis, was admitted to our department with intermittent dyspnea, palpitation, and dizziness. Physical examination was almost normal except bilateral pretibial edema. On magnetic resonance venography, there was an intravenous mass, which is originated from right internal iliac vein and extended into the inferior vena cava. Transthoracic echocardiography and transesophageal echocardiography revealed a huge mass extending from the inferior vena cava through the right atrium, with obvious venous occlusion. Thoracic, abdominal, and pelvic MR showed an intravascular mass, which is concordant with leiomyomatosis. Surgery was performed through median sternotomy. A huge mass with 25-cm length and 186-gr weight was excised through right atrial oblique incision, on beating heart with cardiopulmonary bypass. Histopathologic assessment was compatible with IVL. Exact strategy for the surgical treatment of IVL is still controversial. We used one-stage approach, with complete resection of a huge IVL extending from right atrium to right iliac vein. In such cases, high recurrence rate is a significant problem; therefore it should be kept in mind.

  5. Multimodality treatment with radiotherapy for huge hepatocellular carcinoma.

    Science.gov (United States)

    Han, Hee Ji; Kim, Mi Sun; Cha, Jihye; Choi, Jin Sub; Han, Kwang Hyub; Seong, Jinsil

    2014-01-01

    For huge hepatocellular carcinoma (HCC), therapeutic decisions have varied from local therapy to systemic therapy, with radiotherapy (RT) playing only a palliative role. In this study, we investigated whether multimodality treatment involving RT could be effective in huge HCC. This study was performed in 116 patients with HCC >10 cm. The number of patients in stage II, III and IV was 12, 54 and 50, respectively. RT was given as a combined modality in most patients. The median dose was 45 Gy, with 1.8 Gy per fraction. The median overall survival (OS) and progression-free survival (PFS) were 14.8 and 6.5 months, respectively. The median infield PFS was not reached. Infield failure, outfield intrahepatic and extrahepatic failure were observed in 8.6, 18.1, and 12.1% of patients, respectively. For OS and PFS, number of tumors, initial alpha-fetoprotein (AFP) level, treatment response, percent AFP decrement, and hepatic resection were significant prognostic factors. Tumor characteristics and treatment response were significantly different between long-term survivors and the other patients. Although huge HCC presents an aggressive clinical course, multimodality approaches involving RT can offer an opportunity for prolonged survival. © 2014 S. Karger AG, Basel.

  6. Huge Intravascular Tumor Extending to the Heart: Leiomyomatosis.

    Science.gov (United States)

    Doganci, Suat; Kaya, Erkan; Kadan, Murat; Karabacak, Kubilay; Erol, Gökhan; Demirkilic, Ufuk

    2015-01-01

    Intravenous leiomyomatosis (IVL) is a rare neoplasm characterized by histologically benign-looking smooth muscle cell tumor mass, which is growing within the intrauterine and extrauterine venous system. In this report we aimed to present an unusual case of IVL, which is originating from iliac vein and extended throughout to right cardiac chambers. A 49-year-old female patient, who was treated with warfarin sodium due to right iliac vein thrombosis, was admitted to our department with intermittent dyspnea, palpitation, and dizziness. Physical examination was almost normal except bilateral pretibial edema. On magnetic resonance venography, there was an intravenous mass, which is originated from right internal iliac vein and extended into the inferior vena cava. Transthoracic echocardiography and transesophageal echocardiography revealed a huge mass extending from the inferior vena cava through the right atrium, with obvious venous occlusion. Thoracic, abdominal, and pelvic MR showed an intravascular mass, which is concordant with leiomyomatosis. Surgery was performed through median sternotomy. A huge mass with 25-cm length and 186-gr weight was excised through right atrial oblique incision, on beating heart with cardiopulmonary bypass. Histopathologic assessment was compatible with IVL. Exact strategy for the surgical treatment of IVL is still controversial. We used one-stage approach, with complete resection of a huge IVL extending from right atrium to right iliac vein. In such cases, high recurrence rate is a significant problem; therefore it should be kept in mind.

  7. Analyzing huge pathology images with open source software.

    Science.gov (United States)

    Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

    2013-06-06

    Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here

  8. A NOVEL APPROACH FOR PATTERN ANALYSIS FROM HUGE DATAWAREHOUSE

    Directory of Open Access Journals (Sweden)

    BABITA

    2014-05-01

    Full Text Available Due to the tremendous growth of data and large databases, efficient extraction of required data has become a challenging task. This paper propose a novel approach for knowledge discovery from huge unlabeled temporal databases by employing a combination of HMM and K-means technique. We propose to recursively divide the entire database into clusters having similar characteristics, this process is repeated until we get the cluster’s where no further diversification is possible. Thereafter, the clusters are labeled for knowledge extraction for various purposes.

  9. A young woman with a huge paratubal cyst

    Directory of Open Access Journals (Sweden)

    Ceren Golbasi

    2016-09-01

    Full Text Available Paratubal cysts are asymptomatic embryological remnants. These cysts are usually diagnosed during adolescence and reproductive age. In general, their sizes are small but can be complicated by rupture, torsion, or hemorrhage. Paratubal cysts are often discovered fortuitously on routine ultrasound examination. We report a 19-year-old female patient who presented with irregular menses and abdominal pain. Ultrasound examination revealed a huge cystic mass at the right adnexial area. The diagnosis was confirmed as paratubal cyst during laporotomy and, hence, cystectomy and right salpingectomy were performed. [Cukurova Med J 2016; 41(3.000: 573-576

  10. Modeling huge sound sources in a room acoustical calculation program

    DEFF Research Database (Denmark)

    Christensen, Claus Lynge

    1999-01-01

    A room acoustical model capable of modeling point sources, line sources, and surface sources is presented. Line and surface sources are modeled using a special ray-tracing algorithm detecting the radiation pattern of the surfaces of the room. Point sources are modeled using a hybrid calculation...... method combining this ray-tracing method with image source modeling. With these three source types it is possible to model huge and complex sound sources in industrial environments. Compared to a calculation with only point sources, the use of extended sound sources is shown to improve the agreement...

  11. A huge renal capsular leiomyoma mimicking retroperitoneal sarcoma

    Directory of Open Access Journals (Sweden)

    Lal Anupam

    2009-01-01

    Full Text Available A huge left renal capsular leiomyoma mimicking retroperitoneal sarcoma presented in a patient as an abdominal mass. Computed tomography displayed a large heterogeneous retro-peritoneal mass in the left side of the abdomen with inferior and medial displacement as well as loss of fat plane with the left kidney. Surgical exploration revealed a capsulated mass that was tightly adherent to the left kidney; therefore, total tumor resection with radical left nephrectomy was performed. Histopathology ultimately confirmed the benign nature of the mass. This is the largest leiomyoma reported in literature to the best of our knowledge.

  12. Huge pyometra in a postmenopausal age: a diagnostic dilemma

    Directory of Open Access Journals (Sweden)

    Pramila Yadav

    2015-10-01

    Full Text Available Pyometra in postmenopausal women is an extremely rare disease that hardly responds to the usual treatment of antibiotics therapy. Our case presented as a postmenopausal woman with a huge pyometra. Pyometra drainage was done with great difficulty after a blind biopsy. Endometrial and cervical biopsy followed by endometrial curettage was done. An intrauterine foley's catheter was kept for seven days and Histopathological report was suggestive of squamous cell carcinoma of cervix. [Int J Reprod Contracept Obstet Gynecol 2015; 4(5.000: 1549-1551

  13. Gene-Environment Research and Cancer Epidemiology

    Science.gov (United States)

    The Epidemiology and Genomics Research Program supports extramural research that investigates both genetic and environmental factors that may contribute to the etiology of cancer and/or impact cancer outcomes.

  14. Clinical Epidemiology Of Stroke

    Directory of Open Access Journals (Sweden)

    Nagaraja D

    2005-01-01

    Full Text Available Stroke is a huge public health problem because of its high morbidity and disability. The epidemiology of stroke is of relevance to construct practical paradigms to tackle this major health issue in the community. Recent data have shown that about 72-86% of strokes are ischemic, 9-18% are due to hemorrhage (intracerebral of subarachnoid and the rest are undefined. The risk factors for stroke are multiple and combined. At present, stroke is no more considered as unavoidable and untreatable. It is an emergency and specialized units and teams improve outcome and lower costs. Death related to stroke is declining in many countries and in both sexes. This decrease in multifactorial. The detection and more effective treatment of hypertension may play an important factor, as well as the improved medical care and improvement in diagnostic procedures. While stroke incidence appears stable and stroke mortality is slowly declining, the absolute magnitude of stroke is likely to grow over the next 30 years. as the population ages, the absolute number of stroke victims and demands on healthcare and other support systems is likely to increase substantially in the future. Keeping this in perspective, this chapter shall focus on the epidemiology of stroke in the world and in Indian, in particular.

  15. Errors in Seismic Hazard Assessment are Creating Huge Human Losses

    Science.gov (United States)

    Bela, J.

    2015-12-01

    The current practice of representing earthquake hazards to the public based upon their perceived likelihood or probability of occurrence is proven now by the global record of actual earthquakes to be not only erroneous and unreliable, but also too deadly! Earthquake occurrence is sporadic and therefore assumptions of earthquake frequency and return-period are both not only misleading, but also categorically false. More than 700,000 people have now lost their lives (2000-2011), wherein 11 of the World's Deadliest Earthquakes have occurred in locations where probability-based seismic hazard assessments had predicted only low seismic low hazard. Unless seismic hazard assessment and the setting of minimum earthquake design safety standards for buildings and bridges are based on a more realistic deterministic recognition of "what can happen" rather than on what mathematical models suggest is "most likely to happen" such future huge human losses can only be expected to continue! The actual earthquake events that did occur were at or near the maximum potential-size event that either already had occurred in the past; or were geologically known to be possible. Haiti's M7 earthquake, 2010 (with > 222,000 fatalities) meant the dead could not even be buried with dignity. Japan's catastrophic Tohoku earthquake, 2011; a M9 Megathrust earthquake, unleashed a tsunami that not only obliterated coastal communities along the northern Japanese coast, but also claimed > 20,000 lives. This tsunami flooded nuclear reactors at Fukushima, causing 4 explosions and 3 reactors to melt down. But while this history of huge human losses due to erroneous and misleading seismic hazard estimates, despite its wrenching pain, cannot be unlived; if faced with courage and a more realistic deterministic estimate of "what is possible", it need not be lived again. An objective testing of the results of global probability based seismic hazard maps against real occurrences has never been done by the

  16. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology.

    Science.gov (United States)

    Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K; Tiwari, Sumeet K; Baddam, Ramani; Ahmed, Niyaz

    2016-01-01

    A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

  17. Distributed and parallel approach for handle and perform huge datasets

    Science.gov (United States)

    Konopko, Joanna

    2015-12-01

    Big Data refers to the dynamic, large and disparate volumes of data comes from many different sources (tools, machines, sensors, mobile devices) uncorrelated with each others. It requires new, innovative and scalable technology to collect, host and analytically process the vast amount of data. Proper architecture of the system that perform huge data sets is needed. In this paper, the comparison of distributed and parallel system architecture is presented on the example of MapReduce (MR) Hadoop platform and parallel database platform (DBMS). This paper also analyzes the problem of performing and handling valuable information from petabytes of data. The both paradigms: MapReduce and parallel DBMS are described and compared. The hybrid architecture approach is also proposed and could be used to solve the analyzed problem of storing and processing Big Data.

  18. Anaethetic management of a neonate with huge cystic hygroma.

    Directory of Open Access Journals (Sweden)

    Bindi Palkhiwala

    2013-01-01

    Full Text Available We discuss here the case of a 7 day old neonate with huge cystic hygroma on the left side of the neck invading the major vessels of neck, facial nerve, strap muscles and sternocleidomastoid. Anasethtic implications in this case were maintaining airway patency after induction, difficult intubation, risk perioperative dislodgement of tube and judgement of proper time for extubation. Following gaseous induction and adequate mask ventilation, patient was intubated with muscle relaxant. peroperatively to avoid accidental extubation, we choose to manually hold the ET tube after fixing it. At the end of relatively uneventful surgery, we could extubate the patient in OT. patient was shifted to NICU for observation. Post operatively on 3rd day, facial palsy was observed. Ptient was discharged on 21st day.

  19. Huge Intracanal lumbar Disc Herniation: a Review of Four Cases

    Directory of Open Access Journals (Sweden)

    Farzad Omidi-Kashani

    2016-01-01

    Full Text Available Lumbar disc herniation (LDH is the most common cause of sciatica and only in about 10% of the affected patients, surgical intervention is necessary. The side of the patient (the side of most prominent clinical complaints is usually consistent with the side of imaging (the side with most prominent disc herniation on imaging scans. In this case series, we presented our experience in four cases with huge intracanal LDH that a mismatch between the patient’s side and the imaging’s side was present. In these cases, for deciding to do the operation, the physicians need to rely more on clinical findings, but for deciding the side of discectomy, imaging characteristic (imaging side may be a more important criterion.

  20. A parallel solver for huge dense linear systems

    Science.gov (United States)

    Badia, J. M.; Movilla, J. L.; Climente, J. I.; Castillo, M.; Marqués, M.; Mayo, R.; Quintana-Ortí, E. S.; Planelles, J.

    2011-11-01

    HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000). The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations. The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform. Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors. New version program summaryProgram title: Huge Dense System Solver (HDSS) Catalogue identifier: AEHU_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 87 062 No. of bytes in distributed program, including test data, etc.: 1 069 110 Distribution format: tar.gz Programming language: Fortran90, C Computer: Parallel architectures: multiprocessors, computer clusters Operating system

  1. A huge glandular odontogenic cyst occurring at posterior mandible

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Gi Chung; Han, Won Jeong; Kim, Eun Kyung [Dankook University College of Medicine, Seoul (Korea, Republic of)

    2004-12-15

    The glandular odontogenic cyst is a rare lesion described in 1987. It generally occurs at anterior region of mandible in adults over the age of 40 and has a slight tendency to recur. Histopathologically, a cystic cavity lined by a nonkeratinized, stratified squamous, or cuboidal epithelium varying in thickness is found including a superficial layer with glandular or pseudoglandular structures. A 21-year-old male visited Dankook University Dental Hospital with a chief complaint of swelling of the left posterior mandible. Radiographically, a huge multilocular radiolucent lesion involving impacted 3rd molar at the posterior mandible was observed. Buccolingual cortical expansion with partial perforation of buccal cortical bone was also shown. Histopathologically, this lesion was lined by stratified squamous epithelium with glandular structures in areas of plaque-like thickening. The final diagnosis was made as a glandular odontogenic cyst.

  2. Does China's Huge External Surplus Imply an Undervalued Renminbi?

    Institute of Scientific and Technical Information of China (English)

    Anthony J. Makin

    2007-01-01

    A pegged exchange rate regime has been pivotal to China's export-led development strategy. However, its huge trade surpluses and massive build up of international reserves have been matched by large deficits for major trading partners, creating acute policy concerns abroad, especially in the USA. This paper provides a straightforward conceptual framework for interpreting the effect of China's exchange rate policy on its own trade balance and that of trading partners in the context of discrepant economic growth rates. It shows how pegging the exchange rate when output is outstripping expenditure induces China's trade surpluses and counterpart deficits for its trading partners. An important corollary is that given its strictly regulated capital account, China's persistently large surpluses imply a significantly undervalued renminbi, which should gradually become more flexible.

  3. Molecular epidemiology of glanders, Pakistan.

    Science.gov (United States)

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O'Neill, Matthew; Deshazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera; Keim, Paul

    2009-12-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines.

  4. Molecular Epidemiology of Glanders, Pakistan

    OpenAIRE

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O’Neill, Matthew; DeShazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera; Keim, Paul

    2009-01-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines.

  5. Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

    Science.gov (United States)

    Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.

    2016-01-01

    The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to “frictional” effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the “cluster” and “cline” constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096

  6. Population Genomics and the Statistical Values of Race:An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

    Directory of Open Access Journals (Sweden)

    Koffi N. Maglo

    2016-02-01

    Full Text Available The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to frictional effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the cluster and cline constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin’s argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors and evolutionary forces affecting disease causation and treatment response.

  7. Epidemiology of gliomas.

    Science.gov (United States)

    Ostrom, Quinn T; Gittleman, Haley; Stetson, Lindsay; Virk, Selene M; Barnholtz-Sloan, Jill S

    2015-01-01

    Gliomas are the most common type of primary intracranial tumors. Some glioma subtypes cause significant mortality and morbidity that are disproportionate to their relatively rare incidence. A very small proportion of glioma cases can be attributed to inherited genetic disorders. Many potential risk factors for glioma have been studied to date, but few provide explanation for the number of brain tumors identified. The most significant of these factors includes increased risk due to exposure to ionizing radiation, and decreased risk with history of allergy or atopic disease. The potential effect of exposure to cellular phones has been studied extensively, but the results remain inconclusive. Recent genomic analyses, using the genome-wide association study (GWAS) design, have identified several inherited risk variants that are associated with increased glioma risk. The following chapter provides an overview of the current state of research in the epidemiology of intracranial glioma.

  8. Late Intervention-Related Complication - A Huge Subepicardial Hematoma.

    Science.gov (United States)

    Ko, Po-Yen; Chang, Chih-Ping; Yang, Chen-Chia; Lin, Jen-Jyh

    2013-05-01

    A 75-year-old man had a history of triple vessel coronary artery disease. In August 2009, he had undergone successful percutaneous coronary intervention to the left circumflex coronary artery (LCX) for management of an in-stent restenosis (ISR) lesion. However, in September 2010, he began experiencing recurrent episodes of exertional chest pain. Chest radiography showed the left cardiac border bulging upwards. Transthoracic echocardiography and chest computed tomography revealed a huge oval mass of about 10.4 cm × 7.9 cm × 8.6 cm, which showed calcification and was obliterating the LCX. Subsequent coronary angiography revealed significant instent restenosis, with extravasation of a small amount of contrast material at the stent location, suggesting that the coronary artery had ruptured. We implanted a polytetrafluoroethylene-covered stent to seal the coronary perforation and to release the occlusion. The patient was symptom-free and had an uneventful outcome until the 1-year follow up. Coronary artery perforation; Covered stent; Hematoma.

  9. A huge posteromedial mediastinal cyst complicated with vertebral dislodgment

    Directory of Open Access Journals (Sweden)

    Manoussaridis Jordan T

    2006-08-01

    Full Text Available Abstract Background Mediastinal cysts compromise almost 20% of all mediastinal masses with bronchogenic subtype accounting for 60% of all cystic lesions. Although compression of adjoining soft tissues is usual, spinal complications and neurological symptoms are outmost rare and tend to characterize almost exclusively the neuroenteric cysts. Case presentation A young patient with intermittent, dull pain in his back and free medical history presented in the orthopaedic department of our hospital. There, the initial clinical and radiologic evaluation revealed a mediastinal mass and the patient was referred to the thoracic surgery department for further exploration. The following computed tomography (CT and magnetic resonance imaging (MRI shown a huge mediastinal cyst compressing the T4-T6 vertebral bodies. The neurological symptoms of the patient were attributed to this specific pathology due to the complete agreement between the location of the cyst and the nervous rule area of the compressed thoracic vertebrae. Despite our strongly suggestions for surgery the patient denied any treatment. Conclusion In controversy with the common faith that the spine plays the role of the natural barrier to the further expansion of cystic lesions, our case clearly indicates that, exceptionally, mediastinal cysts may cause severe vertebral complications. Therefore, early excision should be considered especially in young patients or where close follow up is uncertain.

  10. Molecular epidemiology and genetic evolution of the whole genome of G3P[8] human rotavirus in Wuhan, China, from 2000 through 2013.

    Directory of Open Access Journals (Sweden)

    Yuan-Hong Wang

    Full Text Available Rotaviruses are a major etiologic agent of gastroenteritis in infants and young children worldwide. Since the latter of the 1990s, G3 human rotaviruses referred to as "new variant G3" have emerged and spread in China, being a dominant genotype until 2010, although their genomic evolution has not yet been well investigated.The complete genomes of 33 G3P[8] human rotavirus strains detected in Wuhan, China, from 2000 through 2013 were analyzed. Phylogenetic trees of concatenated sequences of all the RNA segments and individual genes were constructed together with published rotavirus sequences.Genotypes of 11 gene segments of all the 33 strains were assigned to G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, belonging to Wa genogroup. Phylogenetic analysis of the concatenated full genome sequences indicated that all the modern G3P[8] strains were assigned to Cluster 2 containing only one clade of G3P[8] strains in the US detected in the 1970s, which was distinct from Cluster 1 comprising most of old G3P[8] strains. While main lineages of all the 11 gene segments persisted during the study period, different lineages appeared occasionally in RNA segments encoding VP1, VP4, VP6, and NSP1-NSP5, exhibiting various allele constellations. In contrast, only a single lineage was detected for VP7, VP2, and VP3 genes. Remarkable lineage shift was observed for NSP1 gene; lineage A1-2 emerged in 2007 and became dominant in 2008-2009 epidemic season, while lineage A1-1 persisted throughout the study period.Chinese G3P[8] rotavirus strains have evolved since 2000 by intra-genogroup reassortment with co-circulating strains, accumulating more reassorted genes over the years. This is the first large-scale whole genome-based study to assess the long-term evolution of common human rotaviruses (G3P[8] in an Asian country.

  11. Epidemiological causality.

    Science.gov (United States)

    Morabia, Alfredo

    2005-01-01

    Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

  12. MRI Verification of a Case of Huge Infantile Rhabdomyoma

    Science.gov (United States)

    Ramadani, Naser; Kreshnike, Kreshnike Dedushi; Muçaj, Sefedin; Kabashi, Serbeze; Hoxhaj, Astrit; Jerliu, Naim; Bejiçi, Ramush

    2016-01-01

    Introduction: Cardiac rhabdomyoma is type of benign myocardial tumor that is the most common fetal cardiac tumor. Cardiac rhabdomyomas are usually detected before birth or during the first year of life. They account for over 60% of all primary cardiac tumors. Case report: A 6 month old child with coughing and obstruction in breathing, was hospitalized in the Pediatric Clinic in UCCK, Pristine. The difficulty of breathing was heard and the pathological noise of the heart was noticed from the pediatrician. In the echo of the heart at the posterior and apico-lateral part of the left ventricle a tumoral mass was presented with the dimensions of 56 × 54 mm that forwarded the contractions of the left ventricle, the mass involved also the left ventricle wall and was not vascularized. The right ventricle was deformed and with the shifting of the SIV on the right the contractility was preserved. Aorta, the left arch and AP were normal with laminar circulation. The pericard was presented free. Radiography of thoracic organs was made; it resulted on cardiomegaly and significant bronchovascular drawing. It was completed with an MRI and it resulted on: Cardiomegaly due to large tumoral mass lesion (60×34 mm) involving lateral wall of left ventricle. It was isointense to the muscle on T1W images, markedly hyperintense on T2W images. There were a few septa or bant like hypointensities within lesion. On postcontrast study it showed avid enhancement. The left ventricle volume was decreased. Mild pericardial effusion was also noted. Surgical intervention was performed and it resulted on the histopathological aspect as a huge infantile rhadbomyoma. Conclusion: In most cases no treatment is required and these lesions regress spontaneously. Patients with left ventricular outflow tract obstruction or refractory arrhythmias respond well to surgical excision. Rhabdomyomas are frequently diagnosed by means of fetal echocardiography during the prenatal period. PMID:27147810

  13. Single-Path Sigma from a Huge Dataset in Taiwan

    Science.gov (United States)

    Sung, Chih-Hsuan; Lee, Chyi-Tyi

    2014-05-01

    Ground-motion variability, which was used in the probabilistic seismic hazard analysis (PSHA) in computing annual exceedence probability, is composed of random variability (aleatory uncertainty) and model uncertainty (epistemic uncertainty). Finding random variability of ground motions has become an important issue in PSHA, and only the random variability can be used in deriving the annual exceedence probability of ground-motion. Epistemic uncertainty will be put in the logic tree to estimate the total uncertainty of ground-motion. In the present study, we used about 18,859 records from 158 shallow earthquakes (Mw > 3.0, focal depth ≤ 35 km, each station has at least 20 records) form the Taiwan Strong-Motion Instrumentation Program (TSMIP) network to analyse the random variability of ground-motion. First, a new ground-motion attenuation model was established by using this huge data set. Second, the residuals from the median attenuation were analysed by direct observation on inter-event variability and site-specific variability. Finally, the single-path variability was found by a moving-window method on either single-earthquake residuals or single-station residuals. A variogram method was also used to find minimum variability for intra-event residuals and inter-event residuals, respectively. Results reveal that 90% of the single-path sigma σSP are ranging from 0.219 to 0.254 (ln unit) and are 58% to 64% smaller than the total sigma (σT =0.601). The single-site sigma (σSS) are also 39%-43% smaller. If we use only random variability (single-path sigma) in PSHA, then the resultant hazard level would be 28% and 25% lower than the traditional one (using total sigma) in 475-year and in 2475-year return period, respectively, in Taipei.

  14. Epigenetic epidemiology of cancer.

    Science.gov (United States)

    Barrow, Timothy M; Michels, Karin B

    2014-12-05

    Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.

  15. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  16. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  17. Pulmonary hypertension with a huge thrombosis in main stem of pulmonary artery

    Institute of Scientific and Technical Information of China (English)

    杨萍; 曾红; 孟繁波; 赵林阳

    2001-01-01

    @@A huge thrombosis in the main stem of the pulmonary artery (PA) with pulmonary hypertension has rarely been reported. We present two cases diagnosed and treated in our hospital. One suffered from polyarteritis with a huge thrombus in PA revealed at autopsy. The second case had congenital heart disease of the patent artery duct; and the huge thrombus was found on echocardiogram and extirpated in surgery.

  18. Huge ascending aortic aneurysm with an intraluminal thrombus in an embolic event-free patient.

    Science.gov (United States)

    Parato, Vito Maurizio; Prifti, Edvin; Pezzuoli, Franco; Labanti, Benedetto; Baboci, Arben

    2015-03-01

    We present a case of an 87-year-old male patient with a huge ascending aortic aneurysm, filled by a huge thrombus most probably due to previous dissection. This finding was detected by two-dimensional transthoracic echocardiography and contrast-enhanced computed tomography (CT) angiography scan. The patient refused surgical treatment and was medically treated. Despite the huge and mobile intraluminal thrombus, the patient remained embolic event-free up to 6 years later, and this makes the case unique.

  19. [Precision medicine: new opportunities and challenges for molecular epidemiology].

    Science.gov (United States)

    Song, Jing; Hu, Yonghua

    2016-04-01

    Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.

  20. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies [v2; ref status: indexed, http://f1000r.es/5hl

    Directory of Open Access Journals (Sweden)

    Bjørn Fjukstad

    2015-06-01

    Full Text Available Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids.

  1. Efficacy of hepatic resection for huge (≥ 10 cm) hepatocellular carcinoma: good prognosis associated with the uninodular subtype.

    Science.gov (United States)

    Zhu, Shao-Liang; Chen, Jie; Li, Hang; Li, Le-Qun; Zhong, Jian-Hong

    2015-01-01

    The value of hepatic resection (HR) for huge hepatocellular carcinomas (HCC) (≥ 10 cm in diameter) remains controversial. The aim of this study is to evaluate the efficacy of hepatic resection (HR) for patients with huge HCC. A total of 739 patients with huge HCC (≥ 10 cm in diameter) (huge HCC group, n = 244) or small HCC (huge HCC were identified based on Cox regression analyses. The hospital mortality of these two groups were similar (P = 0.252). The 5-year OS of huge HCC group and small HCC group were 30.3% and 51.9%, respectively (P huge HCC had a significant higher 5-year OS (50.6%) than mutinodular huge HCC (26.9%) (P = 0.016). Multivariate analysis revealed that uninodular huge HCC and absence of PVTT independently predicted better OS for huge HCC patients. HR is a safe and effective approach for the treatment of huge HCC, especially for the uninodular subtype.

  2. Directed genome engineering for genome optimization.

    Science.gov (United States)

    D'Halluin, Kathleen; Ruiter, Rene

    2013-01-01

    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  3. Nanomedicine: tiny particles and machines give huge gains.

    Science.gov (United States)

    Tong, Sheng; Fine, Eli J; Lin, Yanni; Cradick, Thomas J; Bao, Gang

    2014-02-01

    Nanomedicine is an emerging field that integrates nanotechnology, biomolecular engineering, life sciences and medicine; it is expected to produce major breakthroughs in medical diagnostics and therapeutics. Nano-scale structures and devices are compatible in size with proteins and nucleic acids in living cells. Therefore, the design, characterization and application of nano-scale probes, carriers and machines may provide unprecedented opportunities for achieving a better control of biological processes, and drastic improvements in disease detection, therapy, and prevention. Recent advances in nanomedicine include the development of nanoparticle (NP)-based probes for molecular imaging, nano-carriers for drug/gene delivery, multifunctional NPs for theranostics, and molecular machines for biological and medical studies. This article provides an overview of the nanomedicine field, with an emphasis on NPs for imaging and therapy, as well as engineered nucleases for genome editing. The challenges in translating nanomedicine approaches to clinical applications are discussed.

  4. Report from the Maryland epidemiology schizophrenia linkage study: No evidence for linkage between schizophrenia and a number of candidate and other genomic regions using a complex dominant model

    Energy Technology Data Exchange (ETDEWEB)

    Karayiorgou, M.; Hwang, J.; Elango, R. [Massachusetts Institute of Technology, Cambridge, MA (United States)] [and others

    1994-12-15

    Our collaborative group has undertaken a linkage study of schizophrenia, using a systematic sample of patients admitted to Maryland hospitals. An initial sample of 39 families, each having two or more affecteds, was available for genotyping candidate genes, candidate regions, and highly polymorphic markers randomly distributed throughout the genome. We used a single complex dominant model (with a disease gene frequency of 0.005 and age-dependent penetrance for affected phenotype: for under 35, penetrance = .45; for 35 and older, penetrance = .85). We report here 130 markers which met the exclusion criteria of LOD score < -2.00 at theta > 0.01 in at least 10 informative families, and no evidence for heterogeneity. We also report here markers that were tested as candidates for linkage to the schizophrenic phenotype. They were selected based on the following criteria: (a) proximity to reported chromosomal rearrangements (both 5q and 11q), (b) suggestions of linkage from other families (5q), or (c) presence of a candidate gene (5q, 11q, 3q: dopamine receptors 1, 2, and 3, respectively). We also tested for mutations of codon 717 in exon 17 of the amyloid precursor protein (APP) gene and were unable to detect the C to T substitution in our schizophrenic group. 48 refs., 2 tabs.

  5. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

    Directory of Open Access Journals (Sweden)

    Khoury Muin J

    2007-11-01

    Full Text Available Abstract Background Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications – Literature Finder and Investigator Browser – as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Results Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. Conclusion The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.

  6. Efficient visualization of unsteady and huge scalar and vector fields

    Science.gov (United States)

    Vetter, Michael; Olbrich, Stephan

    2016-04-01

    The simulation of climate data tends to produce very large data sets, which hardly can be processed in classical post-processing visualization applications. Within the most traditional post-processing scenarios the visualization pipeline consisting of the processes data generation, visualization mapping and rendering is distributed into two parts over the network or separated via file transfer: the data generation on a supercomputer on the one hand and the other tasks on a special visualization system on the other hand. That way either temporary data sets with huge volume have to be transferred over the network, which leads to bandwidth bottlenecks and volume limitations. As an alternative all simulation and visualization processes are integrated in a monolithic application, where just 2D pixel data is stored, which reduces the user's possibilities for 3D interaction with visualization to frame skipping. Within the Climate Visualization Lab - as part of the Cluster of Excellence "Integrated Climate System Analysis and Prediction" (CliSAP at the University of Hamburg, in cooperation with the German Climate Computing Center (DKRZ) - we plan to integrate a different approach, which has been proven to be successful in former meteorology applications, e.g. PALM (Parallel Large Eddy Simulation Model). Our software framework DSVR is based on the separation of the process chain between the mapping and the rendering processes. We have developed a parallelized visualization library based on MPI and evaluated on various supercomputers. DSVR can be used to integrate the visualization into a parallel simulation model to support in-situ processing, resulting in a sequence of time-based geometric 3D objects which can be interactively rendered in a separate 3D viewer application. To meet the actual requirements (a) to visualize existing data sets, (b) to support more than rectilinear grids, and (c) to integrate in-situ processing in the ICON model, all based on our DSVR framework

  7. Epidemiology chapter.

    Science.gov (United States)

    Wolfram, J H; Butaev, M K; Duysheev, A; Gabbasova, A R; Khasanov, O S; Kulakov, Yu K; Mkrtchyan, A R; Myrzabekov, A M; Nurgaziev, R Z; Tsirel'son, L E; Willer, R D; Yaraev, R G; Zheludkov, M M

    2010-10-01

    This chapter outlines the epidemiology of brucellosis in the Russian Federation and in five countries bordering Russia. Since the Soviet Union's dissolution, Russia and the newly formed independent republics have failed to maintain policies to control brucellosis and other zoonotic diseases. Many of these republics, due to weak animal control and prevention systems and dangerous food preparation practices, are still burdened with the human cost of brucellosis. The final summary of this section provides an example of the successful transboundary cooperative efforts between Arizona and Mexico, which could be applied to the situation between Russia and the bordering independent republics.

  8. Fibrous dysplasia of the rib presenting as a huge chest wall tumor: report of a case.

    Science.gov (United States)

    Chang, B S; Lee, S C; Harn, H J

    1994-07-01

    Fibrous dysplasia of the rib is not uncommon, but is rarely demonstrated as a huge chest wall mass with severe clinical symptoms. A 59-year-old patient, presenting with a huge, rapidly expanding chest wall tumor compressing the lung, liver and heart accompanied by chest pain and dyspnea, is reported. The tumor was success-fully excised by local radical resection.

  9. Huge van Bordeeus : een ridder van Karel de Grote op avontuur in het Oosten

    NARCIS (Netherlands)

    Lens, Maria Johanna

    2004-01-01

    'Huge van Bordeeus' is de dissertatie van Maria Lens. Hierin doet zij verslag van haar onderzoek naar de Middelnederlandse overlevering van een Franse tekst, 'Huon de Bordeaux', over de ridder Huge van Bordeeus. Deze veertiende-eeuwse ridder, leenman van Karel de Grote, moet de baard en vier tanden

  10. Transarterial chemoembolization for huge hepatocellular carcinoma with diameter over ten centimeters: a large cohort study.

    Science.gov (United States)

    Xue, Tongchun; Le, Fan; Chen, Rongxin; Xie, Xiaoying; Zhang, Lan; Ge, Ningling; Chen, Yi; Wang, Yanhong; Zhang, Boheng; Ye, Shenglong; Ren, Zhenggang

    2015-03-01

    Patients with huge hepatocellular carcinoma >10 cm in diameter represent a special subgroup for treatment. To date, there are few data and little consensus on treatment strategies for huge hepatocellular carcinoma. In this study, we summarized the effects and safety of transarterial chemoembolization for huge hepatocellular carcinoma. A retrospective study was performed based on a large cohort of patients (n = 511) with huge hepatocellular carcinoma who underwent serial transarterial chemoembolization between January 2008 to December 2011 and were followed up until March 2013. We found median survival time was 6.5 months. On multivariate analysis, Child-Pugh class (A versus B) (p huge hepatocellular carcinoma and is recommended as a component of combination therapy. In addition, patients with good liver function and low alpha-fetoprotein levels may acquire greater survival benefits from transarterial chemoembolization.

  11. CASP-8 -652 6N ins/del polymorphism and cancer risk: A literature-based systematic HuGE review and meta-analysis.

    Science.gov (United States)

    Chen, DA; Ma, Tao; Liu, Xiao-Wei; Liu, Zhi

    2012-10-01

    Caspase-8 (encoded by the CASP-8 gene) is crucial in generating cell death signals and eliminating potentially malignant cells. Genetic variation in CASP8 may affect susceptibility to cancer. The CASP-8 -652 6N ins/del (rs3834129) polymorphism has been previously reported to influence the progression to several cancers. However, the overall reported studies have shown inconsistent conclusions. In this human genome epidemiology (HuGE) review and meta-analysis, the aim was to identify the association between CASP-8 -652 6N ins/del polymorphism and cancer risk. According to the inclusion criteria, 19 case-control studies with a total of 23,172 cancer cases and 26,532 healthy controls were retrieved. Meta-analysis results showed that the del allele, del allele carrier and ins/del genotype of -652 6N ins/del in the CASP-8 gene were negatively associated with cancer risk (OR=0.91, 95% CI=0.84-0.98, P=0.01; OR=0.88, 95% CI=0.80-0.96, P=0.005; OR=0.91, 95% CI=0.85-0.98, Pins/del and cancer risk (OR=0.89, 95% CI=0.79-1.01, P=0.08). In the subgroup analysis by ethnicity, the meta-analysis indicated that Caucasian populations harboring the del allele, del allele carriers and ins/del genotype had a lower cancer risk (OR=0.96, 95% CI=0.93-1.00, P=0.05; OR=0.86, 95% CI=0.75-1.00, P=0.05; OR=0.91, 95% CI=0.84-0.98, P=0.01; respectively). In addition, a negative association was found between the del allele of -652 6N ins/del in the CASP-8 gene and cancer risk in the Asian population (OR=0.89, 95% CI=0.83-0.97, P=0.005). In conclusion, this meta-analysis suggests that the del allele, del allele carrier and ins/del geno-type of the -652 6N ins/del polymorphism in the CASP-8 gene may be protective factors for cancer risk.

  12. A new holistic genome viewer for molecular genetics.

    NARCIS (Netherlands)

    H.J.F.M.M. Eussen (Bert); M.J. Moorhouse (Michael); M. Lesnussa (Michael); M. Muetgeert (Maarten); T.A. Knoch (Tobias)

    2006-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the

  13. A new holistic genome viewer for molecular genetics

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); L.V. de Zeeuw (Luc)

    2006-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of th

  14. Molecular Epidemiology of Amebiasis

    Science.gov (United States)

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis. PMID:18571478

  15. Mathematical epidemiology

    CERN Document Server

    Driessche, Pauline; Wu, Jianhong

    2008-01-01

    Based on lecture notes of two summer schools with a mixed audience from mathematical sciences, epidemiology and public health, this volume offers a comprehensive introduction to basic ideas and techniques in modeling infectious diseases, for the comparison of strategies to plan for an anticipated epidemic or pandemic, and to deal with a disease outbreak in real time. It covers detailed case studies for diseases including pandemic influenza, West Nile virus, and childhood diseases. Models for other diseases including Severe Acute Respiratory Syndrome, fox rabies, and sexually transmitted infections are included as applications. Its chapters are coherent and complementary independent units. In order to accustom students to look at the current literature and to experience different perspectives, no attempt has been made to achieve united writing style or unified notation. Notes on some mathematical background (calculus, matrix algebra, differential equations, and probability) have been prepared and may be downlo...

  16. Genomic DNA extraction from whole blood stored from 15- to 30-years at -20 °C by rapid phenol-chloroform protocol: a useful tool for genetic epidemiology studies.

    Science.gov (United States)

    Di Pietro, Fabio; Ortenzi, Francesco; Tilio, Martina; Concetti, Fabio; Napolioni, Valerio

    2011-02-01

    Long-term stored (LTS) whole blood collection can be an important source of DNA without collection costs, but there is a lack of information on methods useful to extract genomic DNA from such type of biological material. Here we report a simple and fast revisited phenol/chloroform extraction method from LTS whole blood. Protocol reliability was assessed by comparison with proteinase K and silica-gel membrane spin column-based DNA extraction methods using LTS -20 °C whole blood from 1980, and by testing it on 82 whole blood samples, collected from 1980 to 1995, with high quality (A(260/280) = 1.79 ± 0.32 O.D., A(260/230) = 1.45 ± 0.52 O.D.) and quantity results. Genotyping efficiency was also checked by performing RFLP-PCR and ASP-PCR of p53 Pro72Arg (rs1042522) SNP and hTERT MNS16A VNTR, respectively, resulting in 100% of samples successfully typed. In addition to the goodness and the efficiency of method proposed here, this protocol achieves working time reduction combining extraction and purification steps, allowing to work at room temperature. Furthermore, phenol is able to inactivate any potential nuclease and potential infective sources from the first step on. Based on these results we also conclude that LTS -20 °C whole blood samples may be considered a reliable and potential resource for future genotyping studies and retrospective analysis in a genetic epidemiological setting. Copyright © 2010 Elsevier Ltd. All rights reserved.

  17. Monitoring Antifungal Resistance in a Global Collection of Invasive Yeasts and Moulds: Application of CLSI Epidemiological Cutoff Values and Whole Genome Sequencing Analysis for Detection of Azole Resistance in Candida albicans.

    Science.gov (United States)

    Castanheira, Mariana; Deshpande, Lalitagauri M; Davis, Andrew P; Rhomberg, Paul R; Pfaller, Michael A

    2017-08-07

    The activity of 7 antifungal agents was evaluated against 3,557 invasive yeasts and moulds collected in 29 countries worldwide during 2014-2015. Epidemiological cutoff values (ECVs) published in the CLSI M59 document were applied for species with no clinical breakpoints. Echinocandin susceptibility rates were 95.9% to 100.0% for the 5 most common Candida species except anidulafungin and C. parapsilosis (88.7% susceptible/100.0% wild-type). Fluconazole resistance ranged from 8.0% for C. glabrata to 0.4% for C. albicans Seven Candida species displayed 100.0% wild-type amphotericin B and C. dubliniensis and C. lusitaniae exhibited wild-type echinocandin MIC results. The highest fluconazole, voriconazole, and posaconazole MIC values for Cryptococcus neoformansvar. grubii were 8 μg/mL, 0.12 μg/mL, and 0.25 μg/mL, respectively. A. fumigatus were 100.0% wild-type for caspofungin and amphotericin B, but 3 (0.8%) of these isolates were non- wild-type to itraconazole (2 isolates) or voriconazole (1 isolate). Mutations on FKS hotspots (HS) were detected among 13/20 Candida isolates (16/20 were C. glabrata) displaying echinocandin MIC>ECV. Most isolates carrying FKS HS mutations were resistant to 2 or more echinocandins. Five fluconazole-nonsusceptible C. albicans were submitted to whole genome sequencing analysis. Gain of function, Erg11 heterozygous, and Erg3 homozygous mutations were observed in 1 isolate each. One isolate displayed MDR1 promoter allele alterations associated with azole resistance. Elevated expression of MDR1 or CDR2 was observed among 3 and 1 isolates, respectively. Echinocandin and azole resistance is still uncommon among contemporary fungal isolates; however, resistance mechanisms to antifungals were observed among Candida spp. showing that resistance can emerge and monitoring is warranted. Copyright © 2017 American Society for Microbiology.

  18. Dairy consumption is associated with a lower incidence of the metabolic syndrome in middle-aged and older Korean adults: the Korean Genome and Epidemiology Study (KoGES).

    Science.gov (United States)

    Kim, Dasom; Kim, Jihye

    2017-01-01

    This cohort study examined the association between total and individual dairy products and the risk of developing the metabolic syndrome (MetS) and its components in Korean adults from the Korean Genome and Epidemiology Study. We prospectively analysed 5510 participants aged 40-69 years without the MetS at baseline during a 10-year follow-up period. Dairy consumption was assessed with a semi-quantitative FFQ at baseline and after 4 years. The MetS was defined according to the criteria by the National Cholesterol Education Program Adult Treatment Panel III. The Cox's proportional hazard model was used to examine the association between consumption of total dairy products, milk and yogurt in servings per week and the risk of incident MetS or individual components. A total of 2103 subjects developed the MetS (38·2 %) during an average follow-up of 67·4 months (range 17-104 months). Frequent dairy consumption (>7 servings of total dairy and milk/week, ≥4 servings of yogurt/week) was associated with a reduced risk of incident MetS and its components. In the multivariable adjusted model, hazard ratios for the MetS were 0·51 (95 % CI 0·43, 0·61) for total dairy products, 0·50 (95 % CI 0·38, 0·66) for milk and 0·67 (95 % CI 0·57, 0·78) for yogurt in frequent consumers compared with non-consumers. An inverse association between milk/yogurt and low HDL-cholesterol was shown only in women. In conclusion, high consumption of individual dairy products including milk and yogurt as well as total dairy were associated with a reduced risk of incident MetS and individual components in Korean adults.

  19. The system-biological GLOBE 3D Genome Platform. : A new holistic genome viewer for molecular genetics

    NARCIS (Netherlands)

    M. Lesnussa (Michael); F.N. Kepper (Nick); H.J.F.M.M. Eussen (Bert); T.A. Knoch (Tobias)

    2009-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the

  20. Mitochondrial genomes as living ‘fossils’

    OpenAIRE

    2013-01-01

    The huge variation between mitochondrial genomes makes untangling their evolutionary histories difficult. Richardson et al. report on the remarkably unaltered ‘fossil’ genome of the tulip tree, giving us many clues as to how the mitochondrial genomes of flowering plants have evolved over the last 150 million years, and raising questions about how such extraordinary sequence conservation can be maintained. See research article http://www.biomedcentral.com/1741-7007/11/29.

  1. Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium.

    Science.gov (United States)

    Wu, Jason H Y; Lemaitre, Rozenn N; Manichaikul, Ani; Guan, Weihua; Tanaka, Toshiko; Foy, Millennia; Kabagambe, Edmond K; Djousse, Luc; Siscovick, David; Fretts, Amanda M; Johnson, Catherine; King, Irena B; Psaty, Bruce M; McKnight, Barbara; Rich, Stephen S; Chen, Yii-Der I; Nettleton, Jennifer A; Tang, Weihong; Bandinelli, Stefania; Jacobs, David R; Browning, Brian L; Laurie, Cathy C; Gu, Xiangjun; Tsai, Michael Y; Steffen, Lyn M; Ferrucci, Luigi; Fornage, Myriam; Mozaffarian, Dariush

    2013-04-01

    BACKGROUND- Palmitic acid (16:0), stearic acid (18:0), palmitoleic acid (16:1n-7), and oleic acid (18:1n-9) are major saturated and monounsaturated fatty acids that affect cellular signaling and metabolic pathways. They are synthesized via de novo lipogenesis and are the main saturated and monounsaturated fatty acids in the diet. Levels of these fatty acids have been linked to diseases including type 2 diabetes mellitus and coronary heart disease. METHODS AND RESULTS- Genome-wide association studies were conducted in 5 population-based cohorts comprising 8961 participants of European ancestry to investigate the association of common genetic variation with plasma levels of these 4 fatty acids. We identified polymorphisms in 7 novel loci associated with circulating levels of ≥1 of these fatty acids. ALG14 (asparagine-linked glycosylation 14 homolog) polymorphisms were associated with higher 16:0 (P=2.7×10(-11)) and lower 18:0 (P=2.2×10(-18)). FADS1 and FADS2 (desaturases) polymorphisms were associated with higher 16:1n-7 (P=6.6×10(-13)) and 18:1n-9 (P=2.2×10(-32)) and lower 18:0 (P=1.3×10(-20)). LPGAT1 (lysophosphatidylglycerol acyltransferase) polymorphisms were associated with lower 18:0 (P=2.8×10(-9)). GCKR (glucokinase regulator; P=9.8×10(-10)) and HIF1AN (factor inhibiting hypoxia-inducible factor-1; P=5.7×10(-9)) polymorphisms were associated with higher 16:1n-7, whereas PKD2L1 (polycystic kidney disease 2-like 1; P=5.7×10(-15)) and a locus on chromosome 2 (not near known genes) were associated with lower 16:1n-7 (P=4.1×10(-8)). CONCLUSIONS- Our findings provide novel evidence that common variations in genes with diverse functions, including protein-glycosylation, polyunsaturated fatty acid metabolism, phospholipid modeling, and glucose- and oxygen-sensing pathways, are associated with circulating levels of 4 fatty acids in the de novo lipogenesis pathway. These results expand our knowledge of genetic factors relevant to de novo lipogenesis and

  2. Coccidioidomycosis: epidemiology

    Directory of Open Access Journals (Sweden)

    Brown J

    2013-06-01

    Full Text Available Jennifer Brown,1 Kaitlin Benedict,2 Benjamin J Park,2 George R Thompson III1,31Department of Internal Medicine, Division of Infectious Diseases, University of California, Davis Medical Center, Sacramento, CA, USA; 2Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA; 3Department of Medical Microbiology and Immunology, One Shields Avenue, Tupper Hall, Coccidioidomycosis Serology Laboratory, University of California, Davis, CA, USAAbstract: Coccidioidomycosis consists of a spectrum of disease, ranging from a mild, self-limited, febrile illness to severe, life-threatening infection. It is caused by the soil-dwelling fungi, Coccidioides immitis and C. posadasii, which are present in diverse endemic areas. Climate changes and environmental factors affect the Coccidioides lifecycle and influence infection rates. The incidence of coccidioidomycosis has risen substantially over the past two decades. The vast majority of Coccidioides infections occur in the endemic zones, such as California, Arizona, Mexico, and Central America. Infections occurring outside those zones appear to be increasingly common, and pose unique clinical and public health challenges. It has long been known that elderly persons, pregnant women, and members of certain ethnic groups are at risk for severe or disseminated coccidioidomycosis. In recent years, it has become evident that persons with immunodeficiency diseases, diabetics, transplant recipients, and prisoners are also particularly vulnerable.Keywords: coccidioidomycosis, Coccidioides, epidemiology, incidence, risk factors, geography

  3. Huge hepatocellular carcinoma with multiple intrahepatic metastases: An aggressive multimodal treatment

    Directory of Open Access Journals (Sweden)

    Satoshi Yasuda

    2015-01-01

    Conclusion: Multimodal treatment involving hepatectomy and TACE might be a good treatment strategy for patients with huge HCC with multiple intrahepatic metastases if the tumors are localized in the liver without distant or peritoneal metastasis.

  4. [Eco-epidemiology: towards epidemiology of complexity].

    Science.gov (United States)

    Bizouarn, Philippe

    2016-05-01

    In order to solve public health problems posed by the epidemiology of risk factors centered on the individual and neglecting the causal processes linking the risk factors with the health outcomes, Mervyn Susser proposed a multilevel epidemiology called eco-epidemiology, addressing the interdependence of individuals and their connection with molecular, individual, societal, environmental levels of organization participating in the causal disease processes. The aim of this epidemiology is to integrate more than a level of organization in design, analysis and interpretation of health problems. After presenting the main criticisms of risk-factor epidemiology focused on the individual, we will try to show how eco-epidemiology and its development could help to understand the need for a broader and integrative epidemiology, in which studies designed to identify risk factors would be balanced by studies designed to answer other questions equally vital to public health.

  5. A huge ovarian mucinous cystadenoma causing virilization, preterm labor, and persistent supine hypotensive syndrome during pregnancy.

    Science.gov (United States)

    Kucur, Suna Kabil; Acar, Canan; Temizkan, Osman; Ozagari, Aysim; Gozukara, Ilay; Akyol, Atif

    2016-01-01

    Mucinous cystadenoma (MC) of the ovary is an unilateral, multilocular cystic benign epithelial tumor. Supposed to be hormone responsive, MC reaches huge sizes during pregnancy. Aortocaval compression is common during pregnancy, especially when the pregnant woman is in the supine position. However, the compression recovers with a change in position. The authors report the first case of a huge mucinous cystadenoma of the ovary complicating pregnancy and causing virilization, premature labor, and persistent supine hypotensive syndrome.

  6. Robot-assisted laparoscopic resection of a huge pelvic tumor: A case report.

    Science.gov (United States)

    Jia, Zhuomin; Lyu, Xiangjun; Xu, Yong; Leonardi, Rosario; Zhang, Xu

    2016-07-04

    The traditional open surgery, for the treatment of huge tumor in the narrow space of pelvic cavity and in close proximity to pelvic organs and neurovascular structures, is very difficult and challenging. We report a case of huge neurilemmoma operated using the robot-assisted laparoscopy. We used interventional pre-operation embolization to control blood supply of tumor because MRI showed the tumor had a sufficient blood supply.

  7. The HUGE formula (hematocrit, urea and gender): association with cardiovascular risk.

    Science.gov (United States)

    Robles, N R; Felix, F J; Fernandez-Berges, D; Perez-Castán, J; Zaro, M J; Lozano, L; Alvarez-Palacios, P; Garcia-Trigo, A; Tejero, V; Morcillo, Y; Hidalgo, A B

    2013-07-01

    To evaluate the relationship between chronic renal failure (CFR) defined through HUGE (hematocrit, urea and gender) formula score and the patient's cardiovascular risk measured through cardiovascular disease antecedents such as ischemic cardiopathy, cerebrovascular disease and peripheral arterial disease. The sample consisted of 2,831 subjects. Mean age was 51.2±14.7 years and 53.5% were female. Serum creatinine, urea, hematocrit and 24h proteinuria were analyzed. HUGE score was calculated from gender, urea and hematocrit. GFR was estimated from uncalibrated serum creatinine using the abbreviated Modification of Diet in Renal Disease equation (MDRD-4). UAE was measured in first morning urine sample. Using HUGE formula 2.2% (n = 61) of subjects had CRF. Of them, 12 (19.7%) had cardiovascular disease history. Among patients without CRF (n = 2770), 194 subjects had history of previous cardiovascular diseases (0.07%; p HUGE definition of CRF was 3.25 (p = 0.001, Mantel-Haenszel test). CFR was associated to higher pulse pressure (PP) and increased urinary albumin excretion. A significant cardiovascular risk was associated to the diagnosis of CRF through HUGE formula. This relation was closer than the obtained using MDRD estimated GFR in spite of a bigger sample. HUGE formula seems to be a useful tool for diagnosing CRF and evaluate the cardiovascular risk of these patients.

  8. Newtonian self-gravitating system in a relativistic huge void universe model

    Science.gov (United States)

    Nishikawa, Ryusuke; Nakao, Ken-ichi; Yoo, Chul-Moon

    2016-12-01

    We consider a test of the Copernican Principle through observations of the large-scale structures, and for this purpose we study the self-gravitating system in a relativistic huge void universe model which does not invoke the Copernican Principle. If we focus on the the weakly self-gravitating and slowly evolving system whose spatial extent is much smaller than the scale of the cosmological horizon in the homogeneous and isotropic background universe model, the cosmological Newtonian approximation is available. Also in the huge void universe model, the same kind of approximation as the cosmological Newtonian approximation is available for the analysis of the perturbations contained in a region whose spatial size is much smaller than the scale of the huge void: the effects of the huge void are taken into account in a perturbative manner by using the Fermi-normal coordinates. By using this approximation, we derive the equations of motion for the weakly self-gravitating perturbations whose elements have relative velocities much smaller than the speed of light, and show the derived equations can be significantly different from those in the homogeneous and isotropic universe model, due to the anisotropic volume expansion in the huge void. We linearize the derived equations of motion and solve them. The solutions show that the behaviors of linear density perturbations are very different from those in the homogeneous and isotropic universe model.

  9. Colonic Angiodysplasia with a Huge Submucosal Hematoma in the Sigmoid Colon.

    Science.gov (United States)

    Shimizu, Takayuki; Koike, Daisuke; Nomura, Yukihiro; Ooe, Kenji

    2016-01-01

    Colonic angiodysplasia (AD) with bleeding as a comorbidity in the aging population is being increasingly reported. However, to our knowledge, there is no report on colonic AD accompanied by a huge hematoma. Herein, we report a case of colonic AD with a huge submucosal hematoma. A 75-year-old man with sudden melena was referred to our hospital. Helical computed tomographic angiography (CTA) revealed bleeding from the sigmoid colon. Additionally, colonoscopy showed a huge submucosal hematoma with bleeding in the sigmoid colon. As endoscopic hemostasis was difficult, sigmoidectomy was performed. The pathological diagnosis was colonic AD. The present case indicates that colonic AD should be considered in the differential diagnosis for melena. In addition, the case shows that helical CTA, which is a noninvasive imaging modality, is useful for the diagnosis of colonic AD and is as effective as colonoscopy and angiography for diagnosis.

  10. Robotic resection of huge presacral tumors: case series and comparison with an open resection.

    Science.gov (United States)

    Oh, Jae Keun; Yang, Moon Sool; Yoon, Do Heum; Rha, Koon Ho; Kim, Keung Nyun; Yi, Seong; Ha, Yoon

    2014-06-01

    Clinical case series and analysis. The purpose of the present study is to evaluate the advantages and disadvantages of robotic presacral tumor resection compared with conventional open approach. Conventional open approach for huge presacral tumors in the retroperitoneal space often demands excessive hospitalization and poor cosmesis. Furthermore, narrow surgical field sometimes interrupt delicate procedures. Nine patients with huge (diameter >10 cm) presacral tumors underwent surgery. Five patients among them had robotic procedure and the others had open transperitoneal tumor resection. Operation time, blood loss, hospitalization, and complications were analyzed. Robotic presacral tumor resection showed shorter operation time, less bleeding, and shorter hospitalization. Moreover, there was no complication related to abdominal adhesion. Although robotic resection for presacral tumor still has limitations technically and economically, robotic resection for huge presacral tumors demonstrated advantages over open resection specifically for benign neurogenic tumors.

  11. Giant pulmonary teratoma with huge splenic lymphangiomatosis: a very rare case.

    Science.gov (United States)

    Alsubaie, Hemail M; Alsubaie, Khaled M; Mahfouz, Mohammed Eid

    2017-09-01

    Teratomas are tumors composed of tissues derived from more than one germ cell line. They manifested with a great variety of clinical and radiological features. We report a case of a giant left hemithorax teratoma in a female with huge spleen tumor and review the relevant literature. A 38-year-old female with progressively aggravating dyspnea at rest from a mild trauma. Absent breath sounds on the left side. There was splenomegaly. Computed tomography scan revealed a huge mass (20 × 15 × 18 cm), containing elements of heterogeneous density in the left hemithorax. The spleen tumor was occupying most of the spleen without any other abdominal manifestations. The patient underwent left thoracotomy and laparoscopic splenectomy. Histopathological examination revealed a benign mature teratoma and cystic lymphangiomatosis of the spleen. To the best of our knowledge and after reviewing the available literature this is the first case of huge mature pulmonary teratoma with large cystic spleen lymphangiomatosis.

  12. Huge splenic epidermoid cyst with elevation of serum CA19-9 level.

    Science.gov (United States)

    Matsumoto, Sayo; Mori, Toshifumi; Miyoshi, Jinsei; Imoto, Yoshitaka; Shinomiya, Hirohiko; Wada, Satoshi; Nakao, Toshihiro; Shinohara, Hisamitsu; Yoshida, Sadahiro; Izumi, Keisuke; Okazaki, Jun; Muguruma, Naoki; Takayama, Tetsuji

    2015-01-01

    A 30-year-old female was referred to our hospital for further examination of liver dysfunction. A huge, soft mass was noted in her left upper quadrant on physical examination. Abdominal ultrasonography and computed tomography revealed a huge cystic tumor of 20 cm in the hilus of the spleen. Serum CA19-9 was 491 U/ml, and splenectomy was performed under suspicion of a malignant cystic tumor. The inner surface of the cyst was lined by squamous epithelial cells that were immunohistochemically positive for CA19-9. Serum CA19-9 level was normalized after the surgery. Our case of a very rare, huge epidermoid cyst of the spleen suggests that measurement of the serum CA19-9 level is useful for evaluating therapeutic efficacy of a splenic epidermoid cyst.

  13. Endovascular Treatment of a Huge Hepatic Artery Aneurysm by Coil Embolization Method: A Case Report.

    Science.gov (United States)

    Hemmati, Hossein; Karimian, Mehdi; Moradi, Habibollah; Farid Marandi, Kambiz; Haghdoost, Afrooz

    2015-07-01

    Hepatic artery aneurysms are rare but potentially life threatening. We describe a novel case of a successful endovascular coil embolization of a huge hepatic artery aneurysm. A 67-year-old woman presented with recent abdominal pain that had begun from 2 weeks before referring to our hospital. Sonographic and computerized tomographic (CT) findings revealed a huge hepatic artery aneurysm with 95 mm × 83 mm diameter. The patient underwent an endovascular technique. In aortic angiography, the celiac artery orifice and superior mesenteric artery were so narrow, so sonography was used in order to determine the exact position of the catheter in the celiac artery orifice. The aneurysm was thrombosed using coil embolization. Pulsation of the aneurysm immediately disappeared. Huge hepatic artery aneurysm can be safely treated using coil embolization.

  14. Collaborative treatment of huge intrathoracic meningoceles associated with neurofibromatosis type 1: a case report.

    Science.gov (United States)

    Cho, Deog Gon; Chang, Yong Jin; Cho, Kyu Do; Hong, Jae Taek

    2015-11-10

    An intrathoracic meningocele is a relatively rare disease, and it commonly accompanies neurofibromatosis type 1. Patients tend to have no symptom but if its size is too large and compresses a lung and neighboring organs, it needs shunt drainage or surgical resection. Herein, we present the case of a 52 year-old female patient with huge intrathoracic meningoceles associated with neurofibromatosis type 1, who has complained about chest discomfort and dyspnea at rest. As for a preliminary treatment, a neurosurgeon had performed a cystoperitoneal shunt, but the symptoms continued and the size of mass and the amount of pleural effusion did not change significantly. Therefore, the huge thoracic meningoceles were successfully treated through the thoracotomic approach in combination with lumbar puncture and cerebrospinal fluid drainage. It is reported that double huge intrathoracic meningoceles associated with neurofibromatosis type 1 was successfully treated by a shunting procedure followed by thoracotomic resection with collaboration of a neurosurgeon.

  15. International Lymphoma Epidemiology Consortium

    Science.gov (United States)

    The InterLymph Consortium, or formally the International Consortium of Investigators Working on Non-Hodgkin's Lymphoma Epidemiologic Studies, is an open scientific forum for epidemiologic research in non-Hodgkin's lymphoma.

  16. Ehrlichiosis: Statistics and Epidemiology

    Science.gov (United States)

    ... a tick Diseases transmitted by ticks Statistics and Epidemiology Recommend on Facebook Tweet Share Compartir On this ... Holman RC, McQuiston JH, Krebs JW, Swerdlow DL. Epidemiology of human ehrlichiosis and anaplasmosis in the United ...

  17. Huge Bilateral Paramesonephric Cysts in a 25 year old Nulliparous woman

    Science.gov (United States)

    Sagili, Haritha; Krishnan, Manikandan; Dasari, Papa

    2013-01-01

    Paraovarian cysts are uncommon adnexal masses which are usually asymptomatic. We describe a case of bilateral huge paramesonephric cysts in a nulliparous woman. A 25-year-old lady presented with abdominal distension for one year duration. Examination and imaging revealed large abdominopelvic cystic masses with no solid areas or septations. Intraoperatively there were huge bilateral paraovarian cysts which were excised. Histopathology revealed low cuboidal to ciliated columnar epithelium with no evidence of ovarian parenchyma suggestive of paramesonephric cyst. Paraovarian cyst should be included in the differential diagnosis of a cystic mass visualised on ultrasound. PMID:24392412

  18. Huge dissected ascending aorta associated with pseudo aneurysm and aortic coarctation feridoun.

    Science.gov (United States)

    Sabzi, Feridoun; Khosravi, Donya

    2015-07-01

    We report a unique case of chronic dissection of the ascending aorta complicated with huge and thrombotic pseudoaneurysm in a patient with coarctation of descending aorta. Preoperative investigations such as transesophageal echocardiography (TEE) confirmed the diagnosis of dissection. Intraoperative findings included a12 cm eccentric bulge of the right lateral side of dilated the ascending aorta filled with the clot and a circular shaped intimal tear communicating with an extended hematoma and dissection of the media layer. The rarity of the report is an association of the chronic dissection with huge pseudoaneurysm and coarctation. The patient underwent staged repair of an aneurysm and coarctation and had an uneventful postoperative recovery period.

  19. [Dermato-epidemiology].

    Science.gov (United States)

    Apfelbacher, C J; Diepgen, T L; Weisshaar, E

    2011-11-01

    Dermato-epidemiology is an important scientific discipline which investigates skin diseases using epidemiological methods. Epidemiology is the science of the distribution and determinants of disease in specified populations. We describe fundamental terms of dermato-epidemiology (measures of disease occurrence, measures of risk), different study types (observational studies, interventional studies), the selection of statistical tests, bias and confounding as well as the principles of evidence-based dermatology, and give illustrative examples.

  20. Chinese health care system and clinical epidemiology

    Science.gov (United States)

    Sun, Yuelian; Gregersen, Hans; Yuan, Wei

    2017-01-01

    China has gone through a comprehensive health care insurance reform since 2003 and achieved universal health insurance coverage in 2011. The new health care insurance system provides China with a huge opportunity for the development of health care and medical research when its rich medical resources are fully unfolded. In this study, we review the Chinese health care system and its implication for medical research, especially within clinical epidemiology. First, we briefly review the population register system, the distribution of the urban and rural population in China, and the development of the Chinese health care system after 1949. In the following sections, we describe the current Chinese health care delivery system and the current health insurance system. We then focus on the construction of the Chinese health information system as well as several existing registers and research projects on health data. Finally, we discuss the opportunities and challenges of the health care system in regard to clinical epidemiology research. China now has three main insurance schemes. The Urban Employee Basic Medical Insurance (UEBMI) covers urban employees and retired employees. The Urban Residence Basic Medical Insurance (URBMI) covers urban residents, including children, students, elderly people without previous employment, and unemployed people. The New Rural Cooperative Medical Scheme (NRCMS) covers rural residents. The Chinese Government has made efforts to build up health information data, including electronic medical records. The establishment of universal health care insurance with linkage to medical records will provide potentially huge research opportunities in the future. However, constructing a complete register system at a nationwide level is challenging. In the future, China will demand increased capacity of researchers and data managers, in particular within clinical epidemiology, to explore the rich resources. PMID:28356772

  1. Endovascular repair for a huge vertebral artery pseudoaneurysm caused by Behcet's disease

    Institute of Scientific and Technical Information of China (English)

    DONG Zhi-hui; FU Wei-guo; GUO Da-qiao; XU Xin; CHEN Bin; JIANG Jun-hao; YANG Jue; SHI Zheng-yu; WANG Yu-qi

    2006-01-01

    @@ Behcet's disease (BD), a multisystem chronic autoimmune process of unknown etiology,usually leads to arterial impairment. Isolated case reports have described BD-related arterial dissections, pseudoaneurysms or aneurysms.1-4 Recently, we successfully treated a huge vertebral artery pseudoaneurysm (VAPA) in a patient with BD by stent-grafting with preservation of the affected vertebral artery.

  2. Unusual Huge Keratoacanthoma in Sites of in the Previous Split-Thickness Skin Grafted Area

    Directory of Open Access Journals (Sweden)

    Fatih Uygur

    2009-09-01

    Full Text Available Keratoacanthoma (KA is a fairly common keratinizing, squamous neoplasm. The exact etiology of KA is unknown. However, ultraviolet radiation, trauma, chemical carcinogens, viral infections, immunosuppression, genetic factors, radiation and thermal burns have been accused of pathogenesis. In here, we represent an unusual huge KA arising from the previous reconstructed with split-thickness skin graft on the dorsal foot.

  3. Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization.

    Science.gov (United States)

    Li, Min; Zhang, John Zenghui; Xia, Fei

    2016-04-12

    Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10,000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems.

  4. Anatomic trisegmentectomy: An alternative treatment for huge or multiple hepatocellular carcinoma of right liver.

    Science.gov (United States)

    Jia, Changku; Weng, Jie; Qin, Qifan; Chen, Youke; Huang, Xiaolong; Fu, Yu

    2017-04-01

    The patients with huge (≥10cm) or multiple hepatocellular carcinoma (HCC) in the right liver and insufficient size of the remnant left liver can not be performed an operation of right hemihepatectomy because of that liver failure will occur post operation. We designed anatomic trisegmentectomy in right liver to increase the ratio of future liver remnant volume (%FLRV), thus increasing resectability of huge or multiple HCC. Thirteen patients were analyzed by preoperative CT scan for liver and tumor volumetries. If the right hemihepatectomy was done, %FLRV would be at the range of 29.6%-37.5%. However, if trisegmentectomy was done, %FLRV would increase by an average of 14.0%. So patients will not undergo postoperative liver failure due to sufficient %FLRV. Therefore, we designed anatomic trisegmentectomy, with retention of segment 5 or segment 8, to increase %FLRV and increase the resectability for huge or multiple HCC. After trisegmentectomy, the inflow and outflow of remnant liver were maintained well. Severe complications and mortality were not happened post operation. Of the 13 patients, 10 survived up to now. Of the 10 living cases, postoperative lung metastasis was found in 2 and intrahepatic recurrence was found in 1. These 3 patients survive with tumor after comprehensive therapies including oral administration of Sorafenib. Compared to right hemihepatectomy, anatomic trisegmentectomy in right liver guarantees the maximum preservation of %FLRV to increase the resectability of huge or multiple HCC, thus improving the overall resection rate. Copyright © 2017. Published by Elsevier Masson SAS.

  5. Huge hepatocellular carcinoma with multiple intrahepatic metastases: An aggressive multimodal treatment.

    Science.gov (United States)

    Yasuda, Satoshi; Nomi, Takeo; Hokuto, Daisuke; Yamato, Ichiro; Obara, Shinsaku; Yamada, Takatsugu; Kanehiro, Hiromichi; Nakajima, Yoshiyuki

    2015-01-01

    Huge hepatocellular carcinoma (HCC) possesses a potential risk for spontaneous rupture, which leads to a life-threatening complication with a high mortality rate. In addition, a large HCC is frequently accompanied by intrahepatic metastases. We describe, the case of a 74-year-old woman with a huge extrahepatically expanding HCC with multiple intrahepatic metastases who was treated by liver resection with repeated transcatheter arterial chemoembolization (TACE). To prevent tumor rupture or bleeding, we performed right hepatectomy. After the operation, TACE was applied for multiple intrahepatic metastases in the remnant liver. Furthermore, the elevated protein induced vitamin K absence (PIVKA II) level had decreased to limits within the normal range. Three months after the first TACE, computed tomography revealed several recurrences in the liver. TACE was applied for the second and third time and the tumors were well controlled. Although, liver resection is occasionally performed for patients with huge HCC to avoid spontaneous tumor rupture, only surgical approach might not be sufficient for such advanced HCC. To achieve long-term survival, it is necessary to control the residual intrahepatic tumors. We could control multiple intrahepatic metastases with repeated TACEs after hepatectomy. Multimodal treatment involving hepatectomy and TACE might be a good treatment strategy for patients with huge HCC with multiple intrahepatic metastases if the tumors are localized in the liver without distant or peritoneal metastasis. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Hepatic arterial infusion chemotherapy for patients with huge unresectable hepatocellular carcinoma.

    Science.gov (United States)

    Tsai, Wei-Lun; Lai, Kwok-Hung; Liang, Huei-Lung; Hsu, Ping-I; Chan, Hoi-Hung; Chen, Wen-Chi; Yu, Hsien-Chung; Tsay, Feng-Woei; Wang, Huay-Min; Tsai, Hung-Chih; Cheng, Jin-Shiung

    2014-01-01

    The optimal treatment for huge unresectable hepatocellular carcinoma (HCC) remains controversial. The outcome of transcatheter arterial chemoembolization (TACE) for patients huge unresectable HCC is generally poor and the survival benefit of TACE in these patients is unclear. The aim of the study is to compare the effect of hepatic arterial infusion chemotherapy (HAIC) versus symptomatic treatment in patients with huge unresectable HCC. Since 2000 to 2005, patients with huge (size >8 cm) unresectable HCC were enrolled. Fifty-eight patients received HAIC and 44 patients received symptomatic treatment. In the HAIC group, each patient received 2.4+1.4 (range: 1-6) courses of HAIC. Baseline characteristics and survival were compared between the HAIC and symptomatic treatment groups. The HAIC group and the symptomatic treatment group were similar in baseline characteristics and tumor stages. The overall survival rates at one and two years were 29% and 14% in the HAIC group and 7% and 5% in the symptomatic treatment group, respectively. The patients in the HAIC group had significantly better overall survival than the symptomatic treatment group (Phuge unresectable HCC.

  7. A Computational Method for Enabling Teaching-Learning Process in Huge Online Courses and Communities

    Science.gov (United States)

    Mora, Higinio; Ferrández, Antonio; Gil, David; Peral, Jesús

    2017-01-01

    Massive Open Online Courses and e-learning represent the future of the teaching-learning processes through the development of Information and Communication Technologies. They are the response to the new education needs of society. However, this future also presents many challenges such as the processing of online forums when a huge number of…

  8. A Huge Subcutaneous Hematoma in an Adult with Kasabach-Merritt Syndrome.

    Science.gov (United States)

    Wu, Kuan-Lin; Liao, Chiung-Ying; Chang, Chen-Kuang; Ho, Shang-Yun; Tyan, Yeu-Sheng; Huang, Yuan-Chun

    2017-06-19

    BACKGROUND Kasabach-Merritt syndrome is a potentially fatal disease that consists of hemangioma(s) with thrombocytopenia, microangiopathic hemolytic anemia, and coagulopathy. Extensive hemangiomatosis is rare. We present the radiological features and treatment strategy of a young adult suffering from Kasabach-Merritt syndrome with widespread hemangiomas and an infected huge hematoma in the right thigh. CASE REPORT A 33-year-old Taiwanese male presented with a painful 20-cm mass over his right thigh and gross hematuria for 2 days. Hemangiomatosis was bioptically proven in infancy and the patient was under regular follow-up. Physical examination revealed normal heart rate, respiratory rate, and body temperature. Multiple palpable lumps with brown and purple areas of skin over the neck, trunk, and right thigh were noted. Laboratory examinations revealed thrombocytopenia anemia and elevated fibrin degradation products. There were no signs of sepsis. Blood transfusion and steroid therapy were executed. Computed tomography showed a huge complicated subcutaneous hematoma in the right thigh. Drainage of the huge hematoma was performed and antibiotics were prescribed. After the local infection in the right thigh and the bleeding tendency were controlled, the patient was discharged in a stable condition two weeks later. CONCLUSIONS A huge infected hematoma and widespread hemangiomas are extremely rare complications of Kasabach-Merritt syndrome. There are no known treatment guidelines currently available. Our patient was successfully treated with steroids, drainage, and antibiotics.

  9. A Huge Ovarian Cyst in a Middle-Aged Iranian Female

    Directory of Open Access Journals (Sweden)

    Mohammad Kazem Moslemi

    2010-05-01

    Full Text Available A 38-year-old Iranian woman was found to have a huge ovarian cystic mass. Her presenting symptom was vague abdominal pain and severe abdominal distention. She underwent laparotomy and after surgical removal, the mass was found to be mucinous cystadenoma on histology.

  10. Huge right atrial myxoma causing fixed tricuspid stenosis with constitutional symptoms.

    Science.gov (United States)

    Kuralay, Erkan; Cingöz, Faruk; Günay, Celalettin; Demirkiliç, Ufuk; Tatar, Harun

    2003-01-01

    Nonspecific constitutional symptoms are reported mostly in patients with left-atrial myxomas, which occur five times as often as its right-atrial counterpart. We present huge right-atrial myxoma, which obstructs tricuspid orifice with nonspecific constitutional symptoms without any pulmonary embolism attack.

  11. Preserving stability of huge agriculture machines with internal mobilities: Application to a grape harvester

    OpenAIRE

    Dieumet, D.; Thuilot, B.; Lenain, R.; Berducat, M.

    2012-01-01

    International audience; This paper proposes an algorithm for estimating on-line the rollover risk of huge machine moving on natural ground. The approach is based on the reconstruction of lateral load transfer thanks to an observer, able to take into account terrain specificities (grip conditions and geometry). Capabilities are tested through experiments on a grape harvester.

  12. Engineering Relative Compression of Genomes

    CERN Document Server

    Grabowski, Szymon

    2011-01-01

    Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over a order of magnitude greater. One of the new successful ideas is augmenting the reference sequence with phrases from the other sequences, making more LZ-matches available.

  13. Biliary obstruction due to a huge simple hepatic cyst treated with laparoscopic resection.

    Science.gov (United States)

    Kaneya, Yohei; Yoshida, Hiroshi; Matsutani, Takeshi; Hirakata, Atsushi; Matsushita, Akira; Suzuki, Seiji; Yokoyama, Tadashi; Maruyama, Hiroshi; Sasajima, Koji; Uchida, Eiji

    2011-01-01

    Most hepatic cysts are asymptomatic, but complications occasionally occur. We describe a patient with biliary obstruction due to a huge simple hepatic cyst treated with laparoscopic resection. A 60-year-old Japanese woman was admitted to our hospital because of a nontender mass in the right upper quadrant of the abdomen. Laboratory tests revealed the following: serum total bilirubin, 0.6 mg/dL; serum aspartate aminotransferase, 100 IU/L; serum alanine aminotransferase, 78 IU/L; serum alkaline phosphatase, 521 IU/L; and serum gamma glutamic transpeptidase, 298 IU/L. Abdominal computed tomography, ultrasonography, and magnetic resonance cholangiopancreatography revealed a huge hepatic cyst, 13 cm in diameter, at the hepatic hilum, accompanied by dilatation of the intrahepatic bile duct and obstruction of the common bile duct. We diagnosed biliary obstruction due to a huge hepatic cyst at the hepatic hilum, and laparoscopic surgery was performed. A huge hepatic cyst was seen at the hepatic hilum. After needle puncture of the huge cyst, the anterior wall of the cyst was unroofed, and cholecystectomy was done. Intraoperative cholangiography through a cystic duct revealed stenosis of the duct. Subsequent decapsulation of the cyst was performed in front of the common bile duct. After this procedure, cholangiography revealed that the stenosis of the common bile duct had resolved. Histopathological examination of the surgical specimen confirmed the hepatic cyst was benign. The postoperative course was uneventful, and the results of liver function tests normalized. The patient was discharged 7 days after operation. Computed tomography 3 months after operation revealed disappearance of the hepatic cyst and no dilatation of the intrahepatic bile duct.

  14. [Future prospects of molecular epidemiology in tuberculosis].

    Science.gov (United States)

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    Before the availability of high-resolution genotyping tools in 1990s, there was a prevailing dogma of little genomic sequence diversity in Mycobacterium tuberculosis. Due to the low levels of genetic variation, it was assumed that M. tuberculosis exhibit very little phenotypic variation in immunologic and virulence factors. The fingerprinting method based on restriction fragment length polymorphisms (RFLP) of IS6110 insertion sequences had unveiled the underestimation of the sequence variation in M. tuberculosis and the importance of strain-to-strain variation for understanding pathogenesis, immune mechanisms, bacterial evolution, and host adaptation. This method became a gold standard for strain differentiation in the molecular epidemiological study. It had lead to a profusion of studies in molecular epidemiology such as the detection of unsuspected transmission, the estimation of the extent of recent transmission, the identification of laboratory cross-contamination, the identification of outbreaks, and distinction between reinfection and relapse. This, in 1990s, is the opening of the molecular epidemiology of tuberculosis. After the completion of genome project of the M. tuberculosis laboratory strain H37Rv, some of the clinical isolates were completely sequenced. This prompted the in silico genome comparison and identified various genomic markers which can give a unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis population. Of them, variable numbers of tandem repeats (VNTR) was found as the most promising PCR-based method which can provide adequate discrimination of M. tuberculosis strains in many cases, including the estimation of M. tuberculosis transmission and the identification of genetic lineages. PCR-based VNTR analysis is easy, rapid, and highly specific and can generate portable digit-based data, unlike the analog information obtained from IS6110 RFLP which is labor intensive. In this regards, investigators can

  15. G3DV: A new 3D genome browser and experimental data viewer.

    NARCIS (Netherlands)

    M.J. Moorhouse (Michael); H.J.F.M.M. Eussen (Bert); T.A. Knoch (Tobias); M. Lesnussa (Michael); A.D.M.E. Osterhaus (Albert); F.G. Grosveld (Frank); J.E.M.M. de Klein (Annelies)

    2006-01-01

    textabstractGenomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of t

  16. Report of the Integrative Molecular Cancer Epidemiology International Symposium, Lyon, France.

    Science.gov (United States)

    Raimondi, S

    2008-01-01

    An International Symposium on Integrative Molecular Cancer Epidemiology took place in Lyon, France, on 3-5 July 2008. The Symposium focused on aetiological and mechanistic aspects of molecular and genetic cancer epidemiology research and was divided into the following three sections: Molecular epidemiology-application of novel molecular markers to cancer epidemiology.Genomic epidemiology in the era of whole genome scan.INTEGRATIVE MOLECULAR EPIDEMIOLOGY: visions for the future.Participants included epidemiologists, geneticists, biochemical and molecular biologists, pharmacologists, pathologists and all researchers interested in this field. The Symposium provided a complete and clear overview of the present and future programmes in molecular cancer epidemiology. It also served to encourage international scientific collaboration between investigators working in this specific research field, and to stimulate transdisciplinary research with experts of other research areas. Highlights of each of the scientific presentations are summarized below.

  17. Performances Evaluation of a Novel Hadoop and Spark Based System of Image Retrieval for Huge Collections

    Directory of Open Access Journals (Sweden)

    Luca Costantini

    2015-01-01

    Full Text Available A novel system of image retrieval, based on Hadoop and Spark, is presented. Managing and extracting information from Big Data is a challenging and fundamental task. For these reasons, the system is scalable and it is designed to be able to manage small collections of images as well as huge collections of images. Hadoop and Spark are based on the MapReduce framework, but they have different characteristics. The proposed system is designed to take advantage of these two technologies. The performances of the proposed system are evaluated and analysed in terms of computational cost in order to understand in which context it could be successfully used. The experimental results show that the proposed system is efficient for both small and huge collections.

  18. A New Pixels Flipping Method for Huge Watermarking Capacity of the Invoice Font Image

    Directory of Open Access Journals (Sweden)

    Li Li

    2014-01-01

    Full Text Available Invoice printing just has two-color printing, so invoice font image can be seen as binary image. To embed watermarks into invoice image, the pixels need to be flipped. The more huge the watermark is, the more the pixels need to be flipped. We proposed a new pixels flipping method in invoice image for huge watermarking capacity. The pixels flipping method includes one novel interpolation method for binary image, one flippable pixels evaluation mechanism, and one denoising method based on gravity center and chaos degree. The proposed interpolation method ensures that the invoice image keeps features well after scaling. The flippable pixels evaluation mechanism ensures that the pixels keep better connectivity and smoothness and the pattern has highest structural similarity after flipping. The proposed denoising method makes invoice font image smoother and fiter for human vision. Experiments show that the proposed flipping method not only keeps the invoice font structure well but also improves watermarking capacity.

  19. Huge mucinous cystadenoma of ovary, describing a young patient: case report

    Directory of Open Access Journals (Sweden)

    Soheila Aminimoghaddam

    2017-08-01

    Conclusion: Ovarian cysts in young women who are associated with elevated levels of tumor markers and ascites require careful evaluation. Management of ovarian cysts depends on patient's age, size of the cyst, and its histopathological nature. Conservative surgery such as ovarian cystectomy or salpingo-oophorectomy is adequate in mucinous tumors of ovary. Multiple frozen sections are very important to know the malignant variation of this tumor and helps accurate patient management. Surgical expertise is required to prevent complications in huge tumors has distorted the anatomy, so gynecologic oncologist plays a prominent role in management. In this case, beside of the huge tumor and massive ascites uterine and ovaries were preserved by gynecologist oncologist and patient is well up to now.

  20. Huge gastric diospyrobezoars successfully treated by oral intake and endoscopic injection of Coca-Cola.

    Science.gov (United States)

    Chung, Y W; Han, D S; Park, Y K; Son, B K; Paik, C H; Jeon, Y C; Sohn, J H

    2006-07-01

    A diospyrobezoar is a type of phytobezoar that is considered to be harder than any other types of phytobezoars. Here, we describe a new treatment modality, which effectively and easily disrupted huge gastric diospyrobezoars. A 41-year-old man with a history of diabetes mellitus was admitted with lower abdominal pain and vomiting. Upper gastrointestinal endoscopy revealed three huge, round diospyrobezoars in the stomach. He was made to drink two cans of Coca-Cola every 6 h. At endoscopy the next day, the bezoars were partially dissolved and turned to be softened. We performed direct endoscopic injection of Coca-Cola into each bezoar. At repeated endoscopy the next day, the bezoars were completely dissolved.

  1. Successful Vaginal Delivery despite a Huge Ovarian Mucinous Cystadenoma Complicating Pregnancy: A Case Report

    Directory of Open Access Journals (Sweden)

    Dipak Mandi

    2013-12-01

    Full Text Available A 22-year-old patient with 9 months of amenorrhea and a huge abdominal swelling was admitted to our institution with an ultrasonography report of a multiloculated cystic space-occupying lesion, almost taking up the whole abdomen (probably of ovarian origin, along with a single live intrauterine fetus. She delivered vaginally a boy baby within 4 hours of admission without any maternal complication, but the baby had features of intrauterine growth restriction along with low birth weight. On the 8th postpartum day, the multiloculated cystic mass, which arose from the right ovary and weighed about 11 kg, was removed via laparotomy. A mucinous cystadenoma with no malignant cells in peritoneal washing was detected in histopathology examination. This report describes a rare case of a successful vaginal delivery despite a huge cystadenoma of the right ovary complicating the pregnancy.

  2. Huge Neck Masses Causing Respiratory Distress in Neonates: Two Cases of Congenital Cervical Teratoma.

    Science.gov (United States)

    Gezer, Hasan Özkan; Oğuzkurt, Pelin; Temiz, Abdulkerim; Bolat, Filiz Aka; Hiçsönmez, Akgün

    2016-12-01

    Congenital cervical teratomas are rare and usually large enough to cause respiratory distress in the neonatal period. We present two cases of congenital huge cystic neck masses in which distinguishing cervical cystic hygroma and congenital cystic teratoma was not possible through radiologic imaging techniques. Experience with the first case, which was initially diagnosed and treated as cystic hygroma by injection sclerotherapy, led to early suspicion and surgery in the second case. The masses were excised completely and histopathologic diagnoses were congenital teratoma in both patients. Our aim is to review congenital huge neck masses causing respiratory distress in early neonatal life to highlight this dilemma briefly with these interesting cases. Copyright © 2014. Published by Elsevier B.V.

  3. Huge echinococcal cyst of the liver managed by hepatectomy: Report of two cases.

    Science.gov (United States)

    Pavlidis, Efstathios T; Symeonidis, Nikolaos; Psarras, Kyriakos; Pavlidis, Theodoros E

    2017-01-01

    Echinococcocal cysts are predominantly located in the right liver. They are usually solitary and asymptomatic, but large cysts can cause compression symptoms. We report two cases of huge (25cm and 20cm in diameter, respectively) echinococcal cysts located in the left liver, which presented as a large palpable mass causing compression symptoms. Diagnosis was established with CT scan showing a cystic mass with the characteristic daughter cysts and reactive layer (pericystic wall) consisting of fibrous connective tissue and calcifications. Both patients were treated radically with left hepatectomy and had uneventful postoperative course and no recurrence upon follow-up. The treatment of liver echinococcal cysts represent a unique surgical challenge. Even though conservative approaches are less technically demanding, the radical approach with resection has better outcome with less recurrences, when performed by experienced surgeons. Resection rather than drainage is the management of choice for such huge liver echinococcal cysts. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. The huge Package for High-dimensional Undirected Graph Estimation in R

    Science.gov (United States)

    Zhao, Tuo; Liu, Han; Roeder, Kathryn; Lafferty, John; Wasserman, Larry

    2015-01-01

    We describe an R package named huge which provides easy-to-use functions for estimating high dimensional undirected graphs from data. This package implements recent results in the literature, including Friedman et al. (2007), Liu et al. (2009, 2012) and Liu et al. (2010). Compared with the existing graph estimation package glasso, the huge package provides extra features: (1) instead of using Fortan, it is written in C, which makes the code more portable and easier to modify; (2) besides fitting Gaussian graphical models, it also provides functions for fitting high dimensional semiparametric Gaussian copula models; (3) more functions like data-dependent model selection, data generation and graph visualization; (4) a minor convergence problem of the graphical lasso algorithm is corrected; (5) the package allows the user to apply both lossless and lossy screening rules to scale up large-scale problems, making a tradeoff between computational and statistical efficiency. PMID:26834510

  5. Mitral valve regurgitation due to annular dilatation caused by a huge and floating left atrial myxoma.

    Science.gov (United States)

    Kaya, Mehmet; Ersoy, Burak; Yeniterzi, Mehmet

    2015-09-01

    We describe a case of mitral valve annular dilatation caused by a huge left atrial myxoma obstructing the mitral valve orifice. A 50-year-old man presenting with palpitation was found to have a huge left atrial myxoma protruding into the left ventricle during diastole, causing severe mitral regurgitation. The diagnosis was made with echocardiogram. Transoesophageal echocardiography revealed a solid mass of 75 × 55 mm. During operation, the myxoma was completely removed from its attachment in the atrium. We preferred to place a mechanical heart valve after an annuloplasty ring because of severely dilated mitral annulus and chordae elongation. The patient had an uneventful recovery. Our case suggests that immediate surgery, careful evaluation of mitral valve annulus preoperatively is recommended.

  6. [Resection of a Huge Gastrointestinal Stromal Tumor of the Stomach Following Neoadjuvant Chemotherapy with Imatinib].

    Science.gov (United States)

    Sato, Yoshihiro; Karasawa, Hideaki; Aoki, Takeshi; Imoto, Hirofumi; Tanaka, Naoki; Watanabe, Kazuhiro; Abe, Tomoya; Nagao, Munenori; Ohnuma, Shinobu; Musha, Hiroaki; Takahashi, Masanobu; Motoi, Fuyuhiko; Naitoh, Takeshi; Ishioka, Chikashi; Unno, Michiaki

    2016-11-01

    We report a case of a huge gastric gastrointestinal stromal tumor(GIST)that was safely resected followingpreoperative imatinib therapy. A 72-year-old woman was hospitalized with severe abdominal distension. Computed tomography revealed a 27×17 cm tumor in the left upper abdominal cavity. The patient was diagnosed with high risk GIST by EUS-FNA. We initiated preoperative adjuvant chemotherapy with imatinib to achieve a reduction of operative risks and functional preservation. After 6 months of chemotherapy, CT showed a reduction in the tumor size and the patient underwent partial gastrectomy and partial resection of the diaphragm. Histologically, most of the tumor cells were replaced by hyalinized collagen and viable cells were scattered only around the blood vessels. Neoadjuvant chemotherapy with imatinib has the potential to become an important therapeutic option for the treatment of huge GISTs.

  7. Huge mass in right side of the heart: A rare case report.

    Science.gov (United States)

    Ghasemi, Reza; Ghanei-Motlagh, Fahimeh; Nazari, Susan; Yaghubi, Mohsen

    2016-11-01

    The presence of primary intracardiac tumors are scarce, and most of them are myxomas. We reported, in this paper, a case with huge mass in the right side of the heart. A 45-year-old man, with a complaint of bilateral lower limbs edema and exertional dyspnea, was admitted to intensive cardiac care unit. Cardiac auscultation revealed soft grade systolic murmur without any evidence of "tumor plop." Echocardiography showed a huge mobile mass in right side of the heart that suggested myxoma. Our patient underwent cardiac surgery with excision of 13 cm mass. Histopathological study was confirmed the diagnosis of mass type. In this case report, it shows that in the differential diagnosis of right-sided heart failure, the right sided myxoma must be considered. The preferable approach in patient with cardiac myxomas is surgical excision to alleviate symptoms, early identification, and removal.

  8. Huge Dissected Ascending Aorta Associated with Pseudo Aneurysm and Aortic Coarctation Feridoun

    Directory of Open Access Journals (Sweden)

    Feridoun Sabzi

    2015-10-01

    Full Text Available We report a unique case of chronic dissection of the ascending aorta complicated with huge and thrombotic pseudoaneurysm in a patient with coarctation of descending aorta. Preoperative investigations such as transesophageal echocardiography (TEE confirmed the diagnosis of dissection. Intraoperative findings included a12 cm eccentric bulge of the right lateral side of dilated the ascending aorta filled with the clot and a circular shaped intimal tear communicating with an extended hematoma and dissection of the media layer. The rarity of the report is an association of the chronic dissection with huge pseudoaneurysm and coarctation. The patient underwent staged repair of an aneurysm and coarctation and had an uneventful postoperative recovery period.

  9. A new pixels flipping method for huge watermarking capacity of the invoice font image.

    Science.gov (United States)

    Li, Li; Hou, Qingzheng; Lu, Jianfeng; Xu, Qishuai; Dai, Junping; Mao, Xiaoyang; Chang, Chin-Chen

    2014-01-01

    Invoice printing just has two-color printing, so invoice font image can be seen as binary image. To embed watermarks into invoice image, the pixels need to be flipped. The more huge the watermark is, the more the pixels need to be flipped. We proposed a new pixels flipping method in invoice image for huge watermarking capacity. The pixels flipping method includes one novel interpolation method for binary image, one flippable pixels evaluation mechanism, and one denoising method based on gravity center and chaos degree. The proposed interpolation method ensures that the invoice image keeps features well after scaling. The flippable pixels evaluation mechanism ensures that the pixels keep better connectivity and smoothness and the pattern has highest structural similarity after flipping. The proposed denoising method makes invoice font image smoother and fiter for human vision. Experiments show that the proposed flipping method not only keeps the invoice font structure well but also improves watermarking capacity.

  10. Air conditioning management of huge rooms; Gestion climatique des locaux de grande dimension

    Energy Technology Data Exchange (ETDEWEB)

    Guitton, P. [Electricite de France (EDF), 78 - Chatou (France); Izard, J.L. [Ecole d`Architecture de Marseille-Luminy, 13 - Marseille-Luminy (France); Wurtz, E. [La Rochelle Universite, 17 - La Rochelle, LEPTAB (France)] [and others

    1999-09-01

    This conference was organized by the section `air-conditioning engineering` of the French society of thermal engineers (SFT). This document comprises the abridged versions of the communications and deals with: air-conditioning using displacement: experience feedback on tertiary applications and development of a dimensioning tool, thermal response of linear atria, application of the zonal method to the description of the temperature field and flows pattern inside an auditorium, theoretical and experimental study of air renewal inside industrial rooms, management of huge rooms, design of new optimized buildings and use of the TAS software, can TRNSYS and Comis codes be used for huge spaces?, experimental study of the thermal-aeraulic conditions generated by a displacement air-conditioning device. (J.S.)

  11. Stochastic Huge-Resonance Caused by Coupling for a Globally Coupled Linear System

    Institute of Scientific and Technical Information of China (English)

    LI Jing-Hui

    2009-01-01

    In the paper, we investigate a globally coupled linear system with finite subunits subject to temporal periodic force and with multiplicative dichotomous noise.It is shown that, the global coupling among the subunits can hugely enhance the phenomenon of SR for the amplitude of the average mean field as the functions of the transition rate of the noise and that as the function of the frequency of the signal respectively.

  12. Therapeutic benefit of radiotherapy in huge (≥10 cm) unresectable hepatocellular carcinoma.

    Science.gov (United States)

    Kim, Kyung Hwan; Kim, Mi Sun; Chang, Jee Suk; Han, Kwang-Hyub; Kim, Do Young; Seong, Jinsil

    2014-05-01

    Huge (≥10 cm) hepatocellular carcinomas (HCCs) show dismal prognosis and only a limited number of cases are eligible for curative resection. We studied the therapeutic benefit of radiotherapy (RT) in patients with huge unresectable HCCs. Data from 283 patients with huge HCCs and preserved liver function who underwent non-surgical treatment from July 2001 to March 2012 were retrospectively reviewed. Patients were divided into 4 groups according to the initial treatment: Group A (N= 49), transarterial chemoembolization (TACE); Group B (N = 35), TACE + RT; Group C (N = 50), hepatic arterial infusion chemotherapy; and Group D (n = 149), concurrent chemoradiotherapy (CCRT). The median follow-up period was 27.8 months (range, 12.9-121.9 months). The median overall survival (OS) was longer in Groups B (15.3 months) and D (12.8 months) than in Groups A (7.5 months) and C (8.2 months; Group B vs. A, Bonferroni corrected P [P(c)] = 0.04; Group B vs. C, P(c) = 0.02; Group D vs. A, P(c) = 0.01; Group D vs. C, Pc = 0.006). Groups B and D also showed superior progression-free survival (PFS) and intrahepatic control than Groups A and C. In multivariate analysis, tumour multiplicity, serum alpha-foetoprotein level (≥200 ng/ml) and initial treatment were independent prognostic factors for OS and PFS. Patients with huge unresectable HCCs treated with RT, either as CCRT or in combination with TACE, showed excellent intrahepatic control and prolonged survival. RT could be considered a promising treatment modality in these patients. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. Interaction-induced huge magnetoresistance in a high mobility two-dimensional electron gas

    Energy Technology Data Exchange (ETDEWEB)

    Bockhorn, L.; Haug, R. J. [Institut für Festkörperphysik, Leibniz Universität Hannover, D-30167 Hannover (Germany); Gornyi, I. V. [Institut für Nanotechnologie, Karlsruher Institut of Technology, D-76021 Karlsruhe (Germany); Schuh, D. [Institut für Experimentelle und Angewandte Physik, Universität Regensburg, D-93053 Regensburg (Germany); Wegscheider, W. [ETH Zürich (Switzerland)

    2013-12-04

    A strong negative magnetoresistance is observed in a high-mobility two-dimensional electron gas in a GaAs/Al{sub 0.3}Ga{sub 0.7}As quantum well. We discuss that the negative magnetoresistance consists of a small peak induced by a combination of two types of disorder and a huge magnetoresistance explained by the interaction correction to the conductivity for mixed disorder.

  14. A HUGE SILENT INTRACRANIA L HYDATID CYST IN AN ADULT MALE: A CASE REPORT

    Directory of Open Access Journals (Sweden)

    Sonal

    2015-04-01

    Full Text Available Hydatid disease of the brain is a rare parasitic infestation caused by larval stage of Echinococcus granulosus. It has an insidious onset with a slow rate of growth resulting in late diagnosis. Its occurence is rare in India, being endemic in Mediterranean countries and Middle East. We report a case of a huge, slow - growing, silent intracranial left parieto - temporo - occipital hydatid cyst in an 18 year old male presenting as a large cystic space occupying lesion.

  15. Post-renal acute renal failure due to a huge bladder stone.

    Science.gov (United States)

    Celik, Orcun; Suelozgen, Tufan; Budak, Salih; Ilbey, Yusuf Ozlem

    2014-06-30

    A 63-year old male was referred to our emergency unit due to acute renal failure. The level of serum renal function tests levels, blood urea nitrogen (BUN)/creatinine, were 63 mmol/L/848 μmol/L. CT (Computarised Tomography) scan showed a huge bladder stone (5 cm x 6 cm x 5 cm) with increased bladder wall thickness. Post-renal acute renal failure due to bilateral ureterohydronephrosis was diagnosed. The huge bladder stone was considered to be the cause of ureterohydronephrosis and renal failure. The patient was catheterised and received haemodialysis immediately. He received haemodialysis four times during ten days of hospitalization and the level of serum renal function tests levels (BUN/ creatinine) decreased 18 mmol/L/123 μmol/L. After improvement of renal function, we performed cystoscopy that demonstrated normal prostatic urethra and bladder neck and bilaterally normal ureteral orifices. Bladder wall was roughly trabeculated and Bladder outlet was completely obstructed by a huge bladder stone. After cystoscopy open, cystolithotomy was performed to remove calcium phosphate and magnesium ammonium phosphate stone weighing 200 g removed. Four days after operation the patient was discharged uneventfully and urethral catheter was removed on the seventh day. Post-renal acute renal failure due to large bladder stones is rare in literature. According to the our knowledge; early diagnosis of the stone avoid growth to large size and prevent renal failure.

  16. Safety and efficacy of partial hepatectomy for huge (≥10 cm) hepatocellular carcinoma: A systematic review

    Science.gov (United States)

    Zhou, Yan-Ming; Li, Bin; Xu, Dong-Hui; Yang, Jia-Mei

    2011-01-01

    Summary Huge (≥10 cm) hepatocellular carcinoma (HCC) is not uncommon at clinical presentation, and the surgical outcomes of such tumors are poor. This systematic review aimed to assess the safety and efficacy of partial hepatectomy for huge HCC. We performed a search on Medline and PubMed databases for all relevant studies published prior to December 2009. After exclusions, 21 studies remained for appraisal and data extraction. All studies were classified as level-4 evidence. The median overall perioperative morbidity and mortality rates were 29.2% (range: 13.6–72%) and 3.5% (range: 0–18.2%), respectively. The overall median survival since the partial hepatectomy was 20.7 months (range: 10.1–32 months), with median 1-, 3- and 5-year survival of 60.7% (range: 41–72.2%), 34% (range: 0–60.3%) and 28.6% (range: 0–54%), respectively. The median disease-free survival since the partial hepatectomy was 11.3 months (range: 5.5–32months), with median 1-, 3- and 5-year disease-free survival rates of 48.7% (range: 32–65.4%), 27.5% (range: 14.1–49%) and 20.7% (range: 9.5–43%), respectively. Partial hepatectomy can be performed safely and is associated with long-term survival in a subset of patients with huge HCC, but the evidence of benefit is currently weak. PMID:21358616

  17. Huge focal nodular hyperplasia presenting in a 6-year-old child: A case presentation.

    Science.gov (United States)

    Zhuang, Lin; Ni, Chuangye; Din, Wenbing; Zhang, Feng; Zhuang, Yi; Sun, Yawei; Xi, Dong

    2016-01-01

    Focal nodular hyperplasia (FNH) is a benign lesion of the liver which is usually found in healthy adults, however, FNH is rare in children, and comprises only 2% of all pediatric liver tumors. Herein, we report the case of a 6-year-old child (male) with a huge FNH which size is more than 10cm. This could be the biggest FNH among all children's FNH cases ever reported. A 6-year-old boy was found a hepatic space-occupying lesion two years ago. As the time went by, the lesion became bigger gradually. The last CT examination showed the size of the tumor to be 10.5×9.9cm in the right hepatic lobe. This child underwent surgical resection of the tumor which was confirmed as FNH (11×8×7cm) by pathology. FNH is a benign lesion of the liver, and it is characterized by hepatocyte hyperplasia and a central stellate scar. It is uncommon for FNH to be diagnosed in children. Such huge FNH (about 11cm) is extremely rare. Surgical operation may be the effective method to cure huge FNH. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Modified concentric craniotomy for the removal of a huge calvarial metastatic tumor: technical note.

    Science.gov (United States)

    Kao, Ying; Yang, Shih-Hung; Kuo, Meng-Fai

    2016-02-01

    It is challenging for neurosurgeons to remove huge tumors involving the skull that may possibly invade the dura or intracranial neural tissue. In this situation, excision of the tumor may cause profound blood loss, unexpected opening of the dura, or neurological injury. We describe a technique of craniotomy in a pediatric patient to avoid surgical complications. A 15-year-old boy had a huge metastatic calvarial Ewing's sarcoma. We removed the tumor successfully with modified concentric craniotomy. First, two oval burr holes are made on both sides of the tumor. The inner craniotomy uses the internal margin of the oval holes, while the outer cut uses the outer margins. The skull bone in between the two craniotomies is removed easily in two pieces and the dura surrounding the tumor can be exposed early in the procedure. In this way, the huge skull tumor can be removed en bloc under direct vision to avoid unwanted complications. Minimal blood and bone loss can be achieved. Blood transfusion was not necessary during the surgery. The patient did not have new neurological symptoms and signs after surgery. The goal of the modified concentric craniotomy is to develop an accessible margin of the dura surrounding the bulky tumor in the early phase of surgery. Blood and bone loss can be reduced significantly.

  19. Intraoperative fluorescent cholangiography using indocyanine green for laparoscopic fenestration of nonparasitic huge liver cysts.

    Science.gov (United States)

    Kitajima, Toshihiro; Fujimoto, Yasuhiro; Hatano, Etsuro; Mitsunori, Yusuke; Tomiyama, Koji; Taura, Kojiro; Mizumoto, Masaki; Uemoto, Shinji

    2015-02-01

    Bile duct injury is one of the known serious complications of laparoscopic fenestration for nonparasitic liver cysts. Herein, we report the case of a huge liver cyst for which we performed laparoscopic fenestration using intraoperative fluorescent cholangiography with indocyanine green. A 71-year-old woman with abdominal distention was referred to our hospital. CT demonstrated a 17 × 11.5-cm simple cyst replacing the right lobe of the liver, so laparoscopic fenestration was performed. Although the biliary duct could not be detected because of compression by the huge cyst, fluorescent cholangiography with indocyanine green through endoscopic naso-biliary drainage tube clearly delineated the intrahepatic bile duct in the remaining cystic wall. The patient had no complications at 3 months after surgery. Fluorescent cholangiography using indocyanine green is a safe and effective procedure to avoid bile duct injury during laparoscopic fenestration, especially in patients with a huge liver cyst. © 2015 Japan Society for Endoscopic Surgery, Asia Endosurgery Task Force and Wiley Publishing Asia Pty Ltd.

  20. Efficacy of hepatic resection vs transarterial chemoembolization for solitary huge hepatocellular carcinoma.

    Science.gov (United States)

    Zhu, Shao-Liang; Zhong, Jian-Hong; Ke, Yang; Ma, Liang; You, Xue-Mei; Li, Le-Qun

    2015-08-28

    To compare the efficacy of hepatic resection (HR) and transarterial chemoembolization (TACE) for patients with solitary huge (≥ 10 cm) hepatocellular carcinoma (HCC). Records were retrospectively analyzed of 247 patients with solitary huge HCC, comprising 180 treated by HR and 67 by TACE. Long-term overall survival (OS) was compared between the two groups using the Kaplan-Meier method, and independent predictors of survival were identified by multivariate analysis. These analyses were performed using all patients in both groups and/or 61 pairs of propensity score-matched patients from the two groups. OS at 5 years was significantly higher in the HR group than the TACE group, across all patients (P = 0.002) and across propensity score-matched pairs (36.4% vs 18.2%, P = 0.039). The two groups showed similar postoperative mortality and morbidity. Multivariate analysis identified alpha-fetoprotein ≥ 400 ng/mL, presence of vascular invasion and TACE treatment as independent predictors of poor OS. Our findings suggest that HR can be safe and more effective than TACE for patients with solitary huge HCC.

  1. Huge Intramural Hematoma in a Thrombosed Middle Cerebral Artery Aneurysm: A Case Report.

    Science.gov (United States)

    Kim, Hak Jin; Lee, Sang Won; Lee, Tae Hong; Kim, Young Soo

    2015-09-01

    We describe a case of a huge intramural hematoma in a thrombosed middle cerebral artery aneurysm. A 47-year-old female patient with liver cirrhosis and thrombocytopenia presented to the neurosurgical unit with a 5-day history of headache and cognitive dysfunction. Magnetic resonance imaging and computed tomography of the brain showed a thrombosed aneurysm located in the right middle cerebral artery with a posteriorly located huge intramural hematoma mimicking an intracerebral hematoma. Imaging studies and cerebrospinal fluid analysis showed no evidence of subarachnoid hemorrhage. Angiography showed a partially thrombosed aneurysm at the origin of the right anterior temporal artery and an incidental aneurysm at the bifurcation of the right middle cerebral artery. Both aneurysms were embolized by coiling. After embolization, the thrombosed aneurysmal sac and intramural hematoma had decreased in size 4 days later and almost completely disappeared 8 months later. This is the first reported case of a nondissecting, nonfusiform aneurysm with a huge intramural hematoma, unlike that of a dissecting aneurysm.

  2. Disaster Characteristics and Mitigation Measures of Huge Glacial Debris Flows along the Sichuan-Tibet Railway

    Science.gov (United States)

    Liu, Jinfeng; You, Yong; Zhang, Guangze; Wang, Dong; Chen, Jiangang; Chen, Huayong

    2017-04-01

    The Ranwu-Tongmai section of the Sichuan-Tibet Railway passes through the Palongzangbu River basin which locates in the southeast Qinghai-Tibetan Plateau. Due to widely distributed maritime glacier in this area, the huge glacier debris flows are very developed. Consequently, the disastrous glacier debris flows with huge scale (106-108 m3 for one debris flow event) and damage become one of the key influencing factors for the route alignment of the Sichuan-Tibet Railway. The research on disaster characteristics and mitigation measures of huge glacial debris flows in the study area were conducted by the remote sensing interpretation, field investigation, parameter calculation and numerical simulation. Firstly, the distribution of the glaciers, glacier lakes and glacier debris flows were identified and classified; and the disaster characteristics for the huge glacier debris flow were analyzed and summarized. Secondly, the dynamic parameters including the flood peak discharge, debris flow peak discharge, velocity, total volume of a single debris flow event were calculated. Based on the disaster characteristics and the spatial relation with the railway, some mitigation principles and measures were proposed. Finally, the Guxiang Gully, where a huge glacier debris flow with 2*108m3 in volume occurred in 1953, was selected as a typical case to analyze its disaster characteristics and mitigation measures. The interpretation results show that the glacier area is about 970 km2 which accounts for 19% of the total study area. 130 glacier lakes and 102 glacier debris flows were identified and classified. The Sichuan-Tibet Railway passes through 43 glacier debris flows in the study area. The specific disaster characteristics were analyzed and corresponding mitigation measures were proposed for the route selection of the railway. For the Guxiang Gully, a numerical simulation to simulate the deposition condition at the alluvial fan was conducted. the simulation results show that the

  3. [Epidemiology and public policies].

    Science.gov (United States)

    Barata, Rita Barradas

    2013-03-01

    The present essay deals with the relation between epidemiology and public policies, highlighting the epidemiology position in the public health field, analyzing the impact of public policies over epidemiological profile and contributions from epidemiology to the lay down, implementation and evaluation of public health policies. In the first title, the essay debates the links between the epidemiology and public health field, the social determinants and political action framework proposed by the WHO's Commission on Social Determinants of Health, and different approaches of health policies. In the second title the essay analyses the reduction of child stunting in Brazil as an example of public policies that impact epidemiological profile. The third title presents three strategic topics for the application of public health policies: reduction of social inequalities in health, health promotion and regulation of products and services that have impact over health. The fourth title discusses the possibilities and difficulties to combine the epidemiological knowledge in the lay down, implementation and evaluation of public policies and, finally, material examples of such relation between epidemiology and public policies are presented.

  4. Metabolomic Approaches in Cancer Epidemiology

    Directory of Open Access Journals (Sweden)

    Mukesh Verma

    2015-08-01

    Full Text Available Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS and nuclear magnetic resonance spectroscopy (NMR that can measure hundreds of thousands of unique chemical entities (UCEs. The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other “omics” include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs. In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them.

  5. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

    NARCIS (Netherlands)

    J.M. Bryant (Josephine); A. Schürch (Anita); H. van Deutekom (Henk); S.R. Harris (Simon); J.L. de Beer (Jessica); V. de Jager (Victor); K. Kremer (Kristin); S.A.F.T. van Hijum (Sacha); R.J. Siezen (Roland); M.W. Borgdorff (Martien ); S.D. Bentley (Stephen); J. Parkhill (Julian); D. van Soolingen (Dick)

    2013-01-01

    textabstractBackground: Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate kno

  6. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

    NARCIS (Netherlands)

    Bryant, J.M.; Schürch, A.C.; Deutekom, van H.; Harris, S.R.; Beer, de J.L.; Jager, de V.C.L.; Kremer, K.; Hijum, van S.A.F.T.; Siezen, R.J.; Borgdorff, M.; Bentley, S.D.; Parkhill, J.; Soolingen, van D.

    2013-01-01

    BACKGROUND: Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of th

  7. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.

    NARCIS (Netherlands)

    Bryant, J.M.; Schurch, A.C.; Deutekom, H. van; Harris, S.R.; Beer, J.L. de; Jager, V. de; Kremer, K.; Hijum, S.A.F.T. van; Siezen, R.J.; Borgdorff, M.; Bentley, S.D.; Parkhill, J.; Soolingen, D. van

    2013-01-01

    BACKGROUND: Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of th

  8. Welcome to epidemiology and health.

    Science.gov (United States)

    Choi, Bo Youl

    2009-10-29

    The Korean Society of Epidemiology publishes a scholarly journal titled 'Korean Journal of Epidemiology', which announces and discusses the results of epidemiological studies from the past 30 yr. Since its first publication in 1979, the journal has contributed to the advancement of epidemiology as well as the prevention and control of disease, and the promotion of health in Korea.In 2009, the editorial board has decided to publish the journal in English to contribute internationally, and change the journal's name. The new name of the journal is 'Epidemiology and Health'.The abstract and full text of articles will be published as an open access online journal, which will be posted onto the homepage (http://www.e-epih.org/) in real time for anyone in the world to access free of charge. Our editorial policy is that 'Epidemiology and Health' is open to every researcher in fields related to epidemiology, regardless of membership, his or her major and nationality.Editorials, lectures, review papers, original articles, epidemic and case investigations, brief communications and letters will be published to generate active discussion through the journal along with the publication of the papers.'Epidemiology and Health' welcomes articles from various fields of epidemiology, such as 1) infectious diseases epidemiology, 2) chronic diseases epidemiology, 3) nutritional epidemiology, 4) clinical epidemiology, 5) pharmacoepidemiology, 6) genetic or molecular epidemiology, 7) social epidemiology, 8) environmental or occupational epidemiology, 9) epidemiological methods and biostatistics, 10) disease prevention and control, 11) health promotion and, 12) all other fields related to epidemiology.

  9. Severe progressive scoliosis due to huge subcutaneous cavernous hemangioma: A case report

    Directory of Open Access Journals (Sweden)

    Toyama Yoshiaki

    2011-03-01

    Full Text Available Abstract Cavernous hemangioma consists mainly of congenital vascular malformations present before birth and gradually increasing in size with skeletal growth. A small number of patients with cavernous hemangioma develop scoliosis, and surgical treatment for the scoliosis in such cases has not been reported to date. Here we report a 12-year-old male patient with severe progressive scoliosis due to a huge subcutaneous cavernous hemangioma, who underwent posterior correction and fusion surgery. Upon referral to our department, radiographs revealed a scoliosis of 85° at T6-L1 and a kyphosis of 58° at T4-T10. CT and MR images revealed a huge hemangioma extending from the subcutaneous region to the paraspinal muscles and the retroperitoneal space and invading the spinal canal. Posterior correction and fusion surgery using pedicle screws between T2 and L3 were performed. Massive hemorrhage from the hemangioma occurred during the surgery, with intraoperative blood loss reaching 2800 ml. The scoliosis was corrected to 59°, and the kyphosis to 45° after surgery. Seven hours after surgery, the patient suffered from hypovolemic shock and disseminated intravascular coagulation due to postoperative hemorrhage from the hemangioma. The patient developed sensory and conduction aphasia caused by cerebral hypoxia during the shock on the day of the surgery. At present, two years after the surgery, although the patient has completely recovered from the aphasia. This case illustrates that, in correction surgery for scoliosis due to huge subcutaneous cavernous hemangioma, intraoperative and postoperative intensive care for hemodynamics should be performed, since massive hemorrhage can occur during the postoperative period as well as the intraoperative period.

  10. High platelet counts increase metastatic risk in huge hepatocellular carcinoma undergoing transarterial chemoembolization.

    Science.gov (United States)

    Xue, Tong-Chun; Ge, Ning-Ling; Xu, Xin; Le, Fan; Zhang, Bo-Heng; Wang, Yan-Hong

    2016-09-01

    Accumulating evidence suggests platelets play critical roles in tumor metastasis. Moreover, the role of platelets in metastasis is partially correlated with inflammation. However, evidence regarding the contribution of platelets to hepatocellular carcinoma (HCC) metastasis is lacking. This study investigated the association between platelets and metastatic risk in HCC. We used huge HCC (diameter over 10 cm), a tumor subgroup with a strong inflammatory background, as a model to evaluate the potential predictive role of platelets and platelet-related biomarkers for metastasis in HCC patients undergoing transarterial chemoembolization. A logistic regression model was used to analyze risk factors for metastasis. Patients with huge HCC (n = 178) were enrolled, and 24.7% (44/178) of patients had remote metastases after treatment. Univariate analyses showed high platelet counts (P = 0.012), pretreatment platelet-to-lymphocyte ratios (pre-PLR) of 100 or more (P = 0.018) and post-PLR of 100 or more (P = 0.013) were potential risk factors for metastasis. Furthermore, multivariate analyses showed high platelet counts (odds ratio, 2.18; 95% confidence interval, 1.074-4.443; P = 0.031) and platelet-related biomarkers were independent risk factors for HCC metastasis. Particularly, the risk of metastasis in patients with high post-PLR values was significantly greater than patients with low post-PLR values. For tumor response and survival, patients with high platelet counts had faster disease progression (P = 0.002) and worse survival (P huge HCC undergoing chemoembolization, which supply clinical verification of the association between high platelet counts and HCC metastasis. © 2016 The Japan Society of Hepatology.

  11. The efficacy of stereotactic body radiation therapy on huge hepatocellular carcinoma unsuitable for other local modalities.

    Science.gov (United States)

    Que, Jenny Y; Lin, Li-Ching; Lin, Kuei-Li; Lin, Chia-Hui; Lin, Yu-Wei; Yang, Ching-Chieh

    2014-05-28

    To evaluate the safety and efficacy of Cyberknife stereotactic body radiation therapy (SBRT) and its effect on survival in patients with unresectable huge hepatocellular carcinoma (HCC) unsuitable of other standard treatment option. Between 2009 and 2011, 22 patients with unresectable huge HCC (≧10 cm) were treated with SBRT. dose ranged from 26 Gy to 40 Gy in five fractions. Overall survival (OS) and disease-progression free survival (DPFS) were determined by Kaplan-Meier analysis. Tumor response and toxicities were also assessed. After a median follow-up of 11.5 month (range 2-46 months). The objective response rate was achieved in 86.3% (complete response (CR): 22.7% and partial response (PR): 63.6%). The 1-yr. local control rate was 55.56%. The 1-year OS was 50% and median survival was 11 months (range 2-46 months). In univariate analysis, Child-Pugh stage (p = 0.0056) and SBRT dose (p = 0.0017) were significant factors for survival. However, in multivariate analysis, SBRT dose (p = 0.0072) was the most significant factor, while Child-Pugh stage of borderline significance. (p = 0.0514). Acute toxicities were mild and well tolerated. This study showed that SBRT can be delivered safely to huge HCC and achieved a substantial tumor regression and survival. The results suggest this technique should be considered a salvage treatment. However, local and regional recurrence remain the major cause of failure. Further studies of combination of SBRT and other treatment modalities may be reasonable.

  12. The big, large and huge case of state-building

    DEFF Research Database (Denmark)

    Harste, Gorm

      Using communication theory as point of departure, it is not evident how to study macro phenomena. Michel Foucault limited his studies to a non-Grand Theory when studying discursive events. At the same time, Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when trying...... to establish a perspective on a macro phenomena as European state formation. With Luhmann's system theory, the claim is that there is no such contradiction between Grand evolution and particular semantic history. Passing through some classic studies of the historical establishment of interaction systems...

  13. The  Big, Large and Huge Case of State-Building

    DEFF Research Database (Denmark)

    Harste, Gorm

    2009-01-01

      Using communication theory as point of departure it is not evident how to study macro phenomena. Michel Foucault delimited his studies to a non-Grand Theory when he studied discursive events. At the same time Charles Tilly wrote about Big Structures, Large Processes, Huge Comparisons when he...... tried to establish a perspective on a macro phenomena as European state formation. With Luhmann's system theory, the claim is that there is no such contradiction between Grand evolution and particular semantic history. Passing through some classic studies of the historical establishment of interaction...

  14. Huge malignant phyllodes breast tumor: a real entity in a new era of early breast cancer.

    Science.gov (United States)

    Testori, Alberto; Meroni, Stefano; Errico, Valentina; Travaglini, Roberto; Voulaz, Emanuele; Alloisio, Marco

    2015-02-27

    Phyllodes tumor is an extremely rare tumor of the breast. It occurs in females in the third and fourth decades. The difficulty in distinguishing between phyllodes tumors and benign fibroadenoma may lead to misdiagnosis. Lymph node involvement is rarely described in phyllodes tumors; for this reason, sentinel node biopsy may be warranted. We present a case of a 33-year-old woman affected by huge tumor of the right breast with ulceration in the skin with a rapid tumor growth and with omolateral axillary metastasis.

  15. Huge Benign Ovarian Cystic Teratoma in a Patient with a History of Hansen's Disease.

    Science.gov (United States)

    Okonta, Patrick I; Mofon, Chukwuemeke

    2014-01-01

    Mature ovarian cystic teratomas are common benign ovarian neoplasm derived from germ cells. With increasing availability of ultrasound services even in developing countries, the diagnosis of benign ovarian tumour is made earlier and the size of the ovarian tumour at diagnosis is relatively small. It is unusual to find an ovarian cystic teratoma larger than 10 cm. We report a huge mature ovarian cystic teratoma in a multipara with a history of Hansen's disease. We conclude that, in circumstances where women have restricted access to health care, the unusual finding of mature ovarian cystic teratoma larger than 10 cm is possible due to delayed presentation for diagnosis and treatment.

  16. Creating and Exploring Huge Parameter Spaces: Interactive Evolution as a Tool for Sound Generation

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2001-01-01

    of huge synthesis parameter spaces, and presents a possibility for the sound artist to create new sound engines customized for this kind of creation and exploration – sound engines too complex to control in any other way. Different sound engines are presented, together with a discussion of compositional......In this paper, a program is presented that applies interactive evolution to sound generation, i.e., preferred individuals are repeatedly selected from a population of genetically bred sound objects, created with various synthesis and pattern generation algorithms. This simplifies aural exploration...

  17. Huge capacity fiber-optic sensing network based on ultra-weak draw tower gratings

    Science.gov (United States)

    Yang, Minghong; Bai, Wei; Guo, Huiyong; Wen, Hongqiao; Yu, Haihu; Jiang, Desheng

    2016-03-01

    This paper reviews the work on huge capacity fiber-optic sensing network based on ultra-weak draw tower gratings developed at the National Engineering Laboratory for Fiber Optic Sensing Technology (NEL-FOST), Wuhan University of Technology, China. A versatile drawing tower grating sensor network based on ultra-weak fiber Bragg gratings (FBGs) is firstly proposed and demonstrated. The sensing network is interrogated with time- and wavelength-division multiplexing method, which is very promising for the large-scale sensing network.

  18. En bloc resection of huge cemento-ossifying fibroma of mandible: avoiding lower lip split incision.

    Science.gov (United States)

    Ayub, Tahera; Katpar, Shahjahan; Shafique, Salman; Mirza, Talat

    2011-05-01

    Cemento-ossifying Fibroma (COF) is an osteogenic benign neoplasm affecting the jaws and other craniofacial bones. It commonly presents as a progressively slow growing pathology, which can sometimes attain an enormous size, causing facial deformity. A case of a huge cemento-ossifying fibroma, appearing as a mandibular dumbell tumour in a male patient is documented, which caused massive bone destruction and deformity. It was surgically removed by performing en bloc resection of mandible avoiding the splitting of lower lip incision technique, thereby maintaining his normal facial appearance.

  19. Huge Intrathoracic Malignant Peripheral Nerve Sheath Tumor in an Adolescent with Neurofibromatosis Type 1

    Directory of Open Access Journals (Sweden)

    Jong Hyung Yoon

    2014-01-01

    Full Text Available Malignant peripheral nerve sheath tumor (MPNST is a rare soft tissue malignancy usually found in patients with neurofibromatosis type 1 (NF1 with a poor outcome. Although MPNST can be found in any part of the body including head and neck or extremities, intrathoracic MPNST with or without NF1 is uncommon, especially in children or adolescents. Reported herein is a case of huge intrathoracic MPNST in a 16-year-old girl with NF1, and a brief review of the literature.

  20. Huge gastric bezoar caused by honeycomb, an unusual complication of health faddism: a case report

    Science.gov (United States)

    Katsinelos, Panagiotis; Pilpilidis, Ioannis; Katsinelos, Taxiarchis; Lazaraki, Georgia; Fasoulas, Kostas; Zavos, Christos; Kountouras, Jannis

    2009-01-01

    We report a young healthy woman, who believed that the consumption of large amounts of honeycomb would lead to good health and who finally developed a huge gastric bezoar of hard consistency. The conventional endoscopic techniques failed to manage the bezoar. Using the combination of injection of hydrogen peroxide 3% solution inside the bezoar to induce disintegration and a special designed needle-knife sphincterotome (bezotome) we managed to remove the bezoar in fragments. To the best of our knowledge this is the first reported bezoar caused by honeycomb. PMID:19829904

  1. A huge chondromyxoid fibroma of the nasal cavity in a newborn baby.

    Science.gov (United States)

    Yoo, Young Tae; Park, Joo Hyun; Sunwoo, Woong Sang; Rhee, Chae-Seo

    2012-08-01

    Chondromyxoid fibroma is a rare benign tumor that usually occurs in the long bones. A 2-month newborn presented with huge masses in the both nasal cavities, which turned out to be chondromyxoid fibroma. The masses originated from both inferior turbinates. Total turbinectomy on the left side and submucosal mass excision on the right side were performed. No recurrence or new lesion was observed during the 2 years of follow up. We report here on a rare case of nasal cavity chondromyxoid fibroma in a neonate and we review the relevant literature.

  2. Totally laparoscopic gastrectomy for early gastric cancer accompanied by huge hiatal hernia: A case report.

    Science.gov (United States)

    Hagiwara, Chie; Yajima, Kazuhito; Iwasaki, Yoshiaki; Oohinata, Ryouki; Yuu, Ken; Ishiyama, Satoshi; Amaki, Misato; Nakano, Daisuke; Yamaguchi, Tatsuro; Matsumoto, Hiroshi; Takahashi, Keiichi

    2016-02-01

    We herein present a case in which we used a totally laparoscopic approach for early gastric cancer accompanied by a huge hiatal hernia. An 80-year-old Japanese woman was referred with a chief complaint of dysphagia. A clinical diagnosis of early gastric cancer, T1b (SM) N0M0, stage IA, accompanied by hiatal hernia, was made. Distal gastrectomy with D1 plus lymphadenectomy was carried out. After the gastrectomy, the hernial sac was excised and the hernial orifice was closed. Reconstruction using the Roux-en-Y method was selected. The postoperative course was uneventful and she was discharged on postoperative day 10.

  3. Huge aneurysm and coronary-cameral fistula from right coronary branch: First case.

    Science.gov (United States)

    Ahmad, Tanveer; Pasarad, Ashwini Kumar; Kishore, Kolkebaile Sadanand; Maheshwarappa, Nandakumar Neralakere

    2016-02-01

    Coronary-cameral fistulas are rare cardiovascular anomalies. A giant coronary artery aneurysm associated with a coronary-cameral fistula is a very rare condition, with an estimated prevalence of 0.02%. We report the case of middle-aged woman who presented with a huge extracardiac aneurysmal mass and a coronary-cameral fistula from a right coronary artery branch. It was successfully repaired by ligation and excision plus marsupialization of the aneurysm. We believe this is the first such a case reported in literature.

  4. Design of a superluminal ring laser gyroscope using multilayer optical coatings with huge group delay.

    Science.gov (United States)

    Qu, Tianliang; Yang, Kaiyong; Han, Xiang; Wu, Suyong; Huang, Yun; Luo, Hui

    2014-01-01

    We propose and analyze a superluminal ring laser gyroscope (RLG) using multilayer optical coatings with huge group delay (GD). This GD assisted superluminal RLG can measure the absolute rotation with a giant sensitivity-enhancement factor of ~10(3); while, the broadband FWHM of the enhancement factor can reach 20 MHz. This superluminal RLG is based on a traditional RLG with minimal re-engineering, and beneficial for miniaturization according to theoretical calculation. The idea of using GD coatings as a fast-light medium will shed lights on the design and application of fast-light sensors.

  5. Evolution and social epidemiology.

    Science.gov (United States)

    Nishi, Akihiro

    2015-11-01

    Evolutionary biology, which aims to explain the dynamic process of shaping the diversity of life, has not yet significantly affected thinking in social epidemiology. Current challenges in social epidemiology include understanding how social exposures can affect our biology, explaining the dynamics of society and health, and designing better interventions that are mindful of the impact of exposures during critical periods. I review how evolutionary concepts and tools, such as fitness gradient in cultural evolution, evolutionary game theory, and contemporary evolution in cancer, can provide helpful insights regarding social epidemiology.

  6. Long-term survival after surgical resection for huge hepatocellular carcinoma: comparison with transarterial chemoembolization after propensity score matching.

    Science.gov (United States)

    Min, Yang Won; Lee, Jun Hee; Gwak, Geum-Youn; Paik, Yong Han; Lee, Joon Hyoek; Rhee, Poong-Lyul; Koh, Kwang Cheol; Paik, Seung Woon; Yoo, Byung Chul; Choi, Moon Seok

    2014-05-01

    Surgical resection (SR) and transarterial chemoembolization (TACE) have been commonly applied for patients with huge hepatocellular carcinoma (HCC). However, optimal treatment has not been established. Between 2000 and 2009, 267 patients with huge HCC (≥ 10 cm) underwent TACE and 84 underwent SR as the first treatment. Propensity score matching generated a matched cohort composed of 152 patients. We investigated overall survival and possible prognostic factors. At baseline, the surgery group showed a tendency to have solitary tumor (72.6% vs 39.3%, P huge HCC. © 2013 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  7. Survey Definitions of Gout for Epidemiologic Studies: Comparison With Crystal Identification as the Gold Standard

    NARCIS (Netherlands)

    Dalbeth, N.; Schumacher, H.R.; Fransen, J.; Neogi, T.; Jansen, T.L; Brown, M.; Louthrenoo, W.; Vazquez-Mellado, J.; Eliseev, M.; McCarthy, G.; Stamp, L.K.; Perez-Ruiz, F.; Sivera, F.; Ea, H.K.; Gerritsen, M.; Scire, C.A.; Cavagna, L.; Lin, C.; Chou, Y.Y.; Tausche, A.K.; Rocha Castelar-Pinheiro, G. da; Janssen, M; Chen, J.H.; Cimmino, M.A.; Uhlig, T.; Taylor, W.J.

    2016-01-01

    OBJECTIVE: To identify the best-performing survey definition of gout from items commonly available in epidemiologic studies. METHODS: Survey definitions of gout were identified from 34 epidemiologic studies contributing to the Global Urate Genetics Consortium (GUGC) genome-wide association study.

  8. A huge 6.2 kilogram uterine myoma coinciding with omental leiomyosarcoma: case report.

    Science.gov (United States)

    Ruan, C W; Lee, C L; Yen, C F; Wang, C J; Soong, Y K

    1999-12-01

    Surgery for massive abdominal tumors is both interesting and challenging. We present a case involving a multiple uterine myoma weighing 6.2 Kg which coincided with omental leiomyosarcoma. To our knowledge, this is the first report of this type of condition in the English literature. A 44-year-old nulliparous woman had suffered from abdominal pain for a long time. A huge abdominal mass was palpated on physical examination. Computed tomography scanning revealed a huge pelvic-abdominal mass with the possibility of small bowel loops invaded by the mass. A 6-cm omental mass was incidentally found during the subsequent hysterectomy procedure. Perforation of the urinary bladder occurred during the dissection of adhesion. Resection of the omental mass, wide wedge resection of the invaded small bowel, primary repair of the bladder, and hysterectomy were performed. The final pathologic diagnosis was uterine leiomyomata with omental leiomyosarcoma. The patient returned home on postoperative day 14 and was well at the 18-month follow-up examination. The challenge of these tumors lies in their proper diagnosis and surgical management. More case reports and follow-up studies are needed to confirm the efficacy of their management.

  9. Treatment of Huge Hepatocellular Carcinoma Using Cinobufacini Injection in Transarterial Chemoembolization: A Retrospective Study

    Directory of Open Access Journals (Sweden)

    Jun Dong

    2016-01-01

    Full Text Available The aim of this study is to examine the safety and efficacy of Cinobufacini injection in transarterial chemoembolization (TACE for treatment of huge hepatocellular carcinoma (HCC. Clinical data of 56 consecutive patients with HCC larger than 10 cm who had been treated with TACE between December 2010 and August 2014 were retrospectively analyzed. Among these patients, 31 belonged to the Cinobufacini group and 25 belonged to the epirubicin group. The clinical efficacy, survival time, and adverse events in patients in the two groups were compared. The objective response rate in the Cinobufacini group was significantly higher than that in the epirubicin group (53.6% versus 23.1%, P=0.022. The median survival time (10.6 versus 14.1 months, χ2=0.092, P=0.762 and the median time to progression (4.9 versus 5.7 months, χ2=0.097, P=0.756 were similar between the groups. The incidence rate of adverse events was lower in the Cinobufacini group than in the epirubicin group (P<0.05. The short-term clinical efficacy of Cinobufacini is better than that of epirubicin in TACE for treating huge HCC, while their long-term clinical efficacy is similar. However, lower incidence of adverse events was noted in TACE using Cinobufacini rather than epirubicin.

  10. Surgical resection of a huge cemento-ossifying fibroma in skull base by intraoral approach.

    Science.gov (United States)

    Cheng, Xiao-Bing; Li, Yun-Peng; Lei, De-Lin; Li, Xiao-Dong; Tian, Lei

    2011-03-01

    Cemento-ossifying fibroma, also known as ossifying fibroma, usually occurs in the mandible and less commonly in the maxilla. The huge example in the skull base is even rare. We present a case of a huge cemento-ossifying fibroma arising below the skull base of a 30-year-old woman patient. Radiologic investigations showed a giant, lobulated, heterogeneous calcified hard tissue mass, which is well circumscribed and is a mixture of radiolucent and radiopaque, situated at the rear of the right maxilla to the middle skull base. The tumor expands into the right maxillary sinus and the orbital cavity, fusing with the right maxilla at the maxillary tuberosity and blocking the bilateral choanas, which caused marked proptosis and blurred vision. The tumor was resected successfully by intraoral approach, and pathologic examination confirmed the lesion to be a cemento-ossifying fibroma. This case demonstrates that cemento-ossifying fibroma in the maxilla, not like in the mandible, may appear more aggressive because the extensive growth is unimpeded by anatomic obstacles and that the intraoral approach can be used to excise the tumor in the skull base.

  11. The technical research on the huge glazed brick from the relic of Nanyue Kingdom Palace

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    'Qin brick and Han tile' has a great worldwide reputation in the architectural history of China. According to the former archaeological materials, the big hollow brick is usually one meter long and thirty to forty centimeters wide, while the solid brick is generally much smaller. But in 1995, large scale vestiges and structures were unearthed at the center of Guangzhou's old district, from the relic of Nanyue Kingdom Palace, which was built some 2000 years ago during the Western-Han Dynasty, A great number of earthen structural members were discovered, especially the solid glazed bricks in various beautiful patterns with an astonishing thickness and size. Some of them are one meter square, more than 20 centimeters thick, and weight half a ton, which are named ‘Brick No.1 in the world' by excavators. People have shown great interest in how to make these huge glazed bricks at the ancient technical conditions, because it is very difficult to manufacture such huge bricks even with the modern technology. At the request of Guangdong Nanyue Kingdom Palace Museum, Shanghai Institute of Ceramics carried out systematical measurements and analysis on these bricks and studied the physical and chemical forming mechanisms from their chemical compositions, structure, and physical characteristics. Here the technical characteristics of the bricks are also discussed.

  12. The technical research on the huge glazed brick from the relic of Nanyue Kingdom Palace

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    ‘Qin brick and Han tile’ has a great worldwide reputation in the architectural history of China. According to the former archaeological materials, the big hollow brick is usually one meter long and thirty to forty centimeters wide, while the solid brick is generally much smaller. But in 1995, large scale vestiges and structures were un- earthed at the center of Guangzhou’s old district, from the relic of Nanyue Kingdom Palace, which was built some 2000 years ago during the Western-Han Dynasty. A great number of earthen structural members were discovered, especially the solid glazed bricks in various beautiful patterns with an astonishing thickness and size. Some of them are one meter square, more than 20 centimeters thick, and weight half a ton, which are named ‘Brick No.1 in the world’ by excavators. People have shown great interest in how to make these huge glazed bricks at the ancient tech- nical conditions, because it is very difficult to manufacture such huge bricks even with the modern technology. At the request of Guangdong Nanyue Kingdom Palace Museum, Shanghai Institute of Ceramics carried out systematical measurements and analysis on these bricks and studied the physical and chemical forming mechanisms from their chemical compositions, structure, and physical character- istics. Here the technical characteristics of the bricks are also discussed.

  13. Treatment of Huge Hepatocellular Carcinoma Using Cinobufacini Injection in Transarterial Chemoembolization: A Retrospective Study.

    Science.gov (United States)

    Dong, Jun; Zhai, Xiaofeng; Chen, Zhe; Liu, Qun; Ye, Hua; Chen, Wei; Ling, Changquan

    2016-01-01

    The aim of this study is to examine the safety and efficacy of Cinobufacini injection in transarterial chemoembolization (TACE) for treatment of huge hepatocellular carcinoma (HCC). Clinical data of 56 consecutive patients with HCC larger than 10 cm who had been treated with TACE between December 2010 and August 2014 were retrospectively analyzed. Among these patients, 31 belonged to the Cinobufacini group and 25 belonged to the epirubicin group. The clinical efficacy, survival time, and adverse events in patients in the two groups were compared. The objective response rate in the Cinobufacini group was significantly higher than that in the epirubicin group (53.6% versus 23.1%, P = 0.022). The median survival time (10.6 versus 14.1 months, χ (2) = 0.092, P = 0.762) and the median time to progression (4.9 versus 5.7 months, χ (2) = 0.097, P = 0.756) were similar between the groups. The incidence rate of adverse events was lower in the Cinobufacini group than in the epirubicin group (P huge HCC, while their long-term clinical efficacy is similar. However, lower incidence of adverse events was noted in TACE using Cinobufacini rather than epirubicin.

  14. Addressing huge spatial heterogeneity induced by virus infections in lentil breeding trials.

    Science.gov (United States)

    Kargiotidou, Anastasia; Vlachostergios, Dimitrios N; Tzantarmas, Constantinos; Mylonas, Ioannis; Foti, Chrysanthi; Menexes, George; Polidoros, Alexios; Tokatlidis, Ioannis S

    2016-12-01

    Spatial heterogeneity can have serious effects on the precision of field experimentation in plant breeding. In the present study the capacity of the honeycomb design (HD) to sample huge spatial heterogeneity was appraised. For this purpose, four trials were conducted each comprising a lentil landrace being screened for response to viruses. Huge spatial heterogeneity was reflected by the abnormally high values for coefficient of variation (CV) of single-plant yields, ranging 123-162 %. At a given field area, increasing the number of simulated entries was followed by declined effectiveness of the method, on account of the larger circular block implying greater intra-block heterogeneity; a hyperbolic increasing pattern of the top to bottom entry mean gap (TBG) indicated that a number of more than 100 replicates (number of plants per entry) is the crucial threshold to avoid significant deterioration of the sampling degree. Nevertheless, the honeycomb model kept dealing with variation better than the randomized complete block (RCB) pattern, thanks to the circular shape and standardized type of block that ensure the less possible extra heterogeneity with expanding the area of the block. Owing to the even and systematic entry allocation, breeders do not need to be concerned with the extra spatial heterogeneity that might induce the extra surface needed to expand the size of the block when many entries are considered. Instead, they could improve accuracy of comparisons with increasing the number of replicates (circular blocks) despite the concomitant greater overall spatial heterogeneity.

  15. Challenging the time complexity of exact subgraph isomorphism for huge and dense graphs with VF3.

    Science.gov (United States)

    Carletti, Vincenzo; Foggia, Pasquale; Saggese, Alessia; Vento, Mario

    2017-04-24

    Graph matching is essential in several fields that use structured information, such as biology, chemistry, social networks, knowledge management, document analysis and others. Except for special classes of graphs, graph matching has in the worst-case an exponential complexity; however, there are algorithms that show an acceptable execution time, as long as the graphs are not too large and not too dense. In this paper we introduce a novel subgraph isomorphism algorithm, VF3, particularly efficient in the challenging case of graphs with thousands of nodes and a high edge density. Its performance, both in terms of time and memory, has been assessed on a large dataset of 12700 random graphs with a size up to 10000 nodes, made publicly available. VF3 has been compared with four other state-of-the-art algorithms, and the huge experimentation required more than two years of processing time. The results confirm that VF3 definitely outperforms the other algorithms when the graphs become huge and dense, but also has a very good performance on smaller or sparser graphs.

  16. Strontium-89 therapy for the treatment of huge osseous metastases in prostate carcinoma: A case report.

    Science.gov (United States)

    Zhang, Wenjie; Zhao, Weiwei; Jia, Zhiyun; Deng, Houfu

    2013-02-01

    Prostate cancer is a growing public health problem. The palliation of pain in patients with painful bone metastases is of primary importance in the clinical management of advanced cancer. Internal therapy with radionuclides, which concentrate at sites of increased bone turnover, is used to control pain and improve quality of life as an alternative to conventional therapies. In the present study, we report the case of a 52-year-old male who had been diagnosed with prostate cancer. The patient presented with severe pain in multiple areas, but particularly in the right hip. A whole-body bone scan revealed that the right hip, ilium and ischium were covered with huge metastatic lesions. Treatment with radionuclide strontium-89 chloride ((89)Sr) resulted in a partial response which was confirmed by the successful relief of pain and other imaging modalities. No significant change in the leukocyte or thrombocyte levels was observed. The results of the present study indicate that systemic radionuclide therapy using (89)Sr is an effective, well-tolerated and safe palliative treatment in patients with huge osseous metastases in prostate carcinoma.

  17. Resection of Huge Liver Cancer Involving the Second Porta Hepatis:A Report of 55 Cases

    Institute of Scientific and Technical Information of China (English)

    CHENHan; WUMengchao; WANGYi; WEIGongtian; HULei

    2002-01-01

    Objective To investigate the possibility and surgical procedures for huge liver cancer involving the second porta hepatis.Methods 55 cases of huge liver cancer, with the diameter of 8-28 cm(mean 12.7 cm) were studied. Right subcostal or “rooftop” incision was made, the liver ligments were divided, good exposure of the tumor and access to retrohepatic inferior vena cava were achieved.Hepatectomies were completed under intermittent interruption of first porta hepatis. Occluding tape around vena cava was applied before liver resection if necessary.Results All tumors were successfully resected without death during operation.The longest survival time was now 4 years in one case. The 1-4 year postoperative survival rates were 63%,50%,50% and 30% respectively.Conclusion Young patients with solitary large liver tumor, which grows slowly over a long period on basis of non-cirrhotic or mild cirrhotic liver, should undergo an exploration in an attempt of resection irrespective of the image contraindication, provided that there is no extra-hepatic metastasis.

  18. [One case of huge cyst at the back end of nasal septum].

    Science.gov (United States)

    Zang, Jian; Liu, Qian; Jiang, Xuejun

    2014-04-01

    A male of 17 years old complained of bilateral nasal congestion with mouth breathing for half a year. The physical examination showed patency of bilateral nasal cavity. Nasopharyngeal fiberscope revealed a huge spherical smooth reddish mass at the nasopharyngeal posterior wall and the back-end of nasal cavity blocking the entire postnaris and contacting with bilateral tubal tori, the size of which is about 3.5 cm x 2.5 cm. The nasopharyngeal 3D-CT showed a low density cystic mass area in the nasopharynx with smooth edges, and the CT value is approximately 32.4 HU. No exact enhancement was observed. The cystic mass originated from and compressed the back end of nasal septum. A semicircular defect in the leading edge of clivus was observed, and the inferior wall of sphenoid sinus is compressed uplifted upwards. The nasopharyngeal MR showed that the nasopharyngeal lesion presented short T1 and long T2 signals with multiple small wall nodules around. Neither the lesion nor the peripheral nodules can be significantly enhanced by enhancement scan. After a nasal endoscopic surgery, the case was definitely diagnosed as nasal septum back-end huge cyst.

  19. Cancer Epidemiology Cohorts

    Science.gov (United States)

    Cohort studies are fundamental for epidemiological research by helping researchers better understand the etiology of cancer and provide insights into the key determinants of this disease and its outcomes.

  20. Occupational cancer epidemiology.

    Science.gov (United States)

    Boffetta, Paolo

    2011-01-01

    Occupational cancer epidemiology has led to the identification of more than 40 agents, groups of agents, and exposure circumstances which cause cancer in humans. This evidence has been followed by preventive and control measures. There are four areas where occupational cancer epidemiology may contribute important results in the future: surveillance of workers exposed to carcinogens, identification of new carcinogens and target organs, study of interactions, and research on special exposure circumstances.

  1. Ethics, big data and computing in epidemiology and public health.

    Science.gov (United States)

    Salerno, Jennifer; Knoppers, Bartha M; Lee, Lisa M; Hlaing, WayWay M; Goodman, Kenneth W

    2017-05-01

    This article reflects on the activities of the Ethics Committee of the American College of Epidemiology (ACE). Members of the Ethics Committee identified an opportunity to elaborate on knowledge gained since the inception of the original Ethics Guidelines published by the ACE Ethics and Standards of Practice Committee in 2000. The ACE Ethics Committee presented a symposium session at the 2016 Epidemiology Congress of the Americas in Miami on the evolving complexities of ethics and epidemiology as it pertains to "big data." This article presents a summary and further discussion of that symposium session. Three topic areas were presented: the policy implications of big data and computing, the fallacy of "secondary" data sources, and the duty of citizens to contribute to big data. A balanced perspective is needed that provides safeguards for individuals but also furthers research to improve population health. Our in-depth review offers next steps for teaching of ethics and epidemiology, as well as for epidemiological research, public health practice, and health policy. To address contemporary topics in the area of ethics and epidemiology, the Ethics Committee hosted a symposium session on the timely topic of big data. Technological advancements in clinical medicine and genetic epidemiology research coupled with rapid advancements in data networks, storage, and computation at a lower cost are resulting in the growth of huge data repositories. Big data increases concerns about data integrity; informed consent; protection of individual privacy, confidentiality, and harm; data reidentification; and the reporting of faulty inferences. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Comparative Microbial Genomics and Forensics.

    Science.gov (United States)

    Massey, Steven E

    2016-08-01

    Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

  3. The HUGE formula (hematocrit, urea, gender) for screening for chronic kidney disease in elderly patients: a study of diagnostic accuracy.

    Science.gov (United States)

    Musso, Carlos G; de Los Rios, Eduardo; Vilas, Manuel; Terrasa, Sergio; Bratti, Griselda; Varela, Federico; Diez, Guillermo Rosa; Jauregui, Jose; Luna, Daniel

    2017-04-01

    Chronically reduced glomerular filtration rate (GFR) in old people does not always mean that they suffer from chronic kidney disease (CKD) since their GFR can just be reduced by aging. The HUGE equation has been recently described and validated in Spain for screening CKD without taking into account the patient's GFR value. This equation is based on patient's hematocrit, plasma urea levels and gender. The present study documented that the HUGE equation had and acceptable performance for screening CKD in elderly Argentine patients.

  4. 巨大阑尾黏液性囊腺瘤1例%1 case of huge appendiceal mucinous cystadenoma

    Institute of Scientific and Technical Information of China (English)

    王磊; 刘雯雯

    2016-01-01

    Huge appendiceal mucinous cystadenoma is rare in clinic,and the preoperative misdiagnosis rate is high.The data of 1 case of huge appendiceal mucinous cystadenoma was introduced in this paper.%巨大阑尾黏液性囊腺瘤临床较少见,术前误诊率高。本文对巨大阑尾黏液性囊腺瘤1例的病例资料进行介绍。

  5. Huge hepatocellular carcinoma greater than 10 cm in diameter worsens prognosis by causing distant recurrence after curative resection.

    Science.gov (United States)

    Wakayama, Kenji; Kamiyama, Toshiya; Yokoo, Hideki; Orimo, Tatsuya; Shimada, Shingo; Einama, Takahiro; Kamachi, Hirofumi; Taketomi, Akinobu

    2017-03-01

    This study aimed to evaluate the impact of huge (≥10 cm) hepatocellular carcinoma (HCC) to the recurrence pattern and the prognosis after hepatectomy. 574 patients who underwent hepatectomy by 17 surgeons (Open 536 and Laparoscopic 38) for HCC without major vascular invasion from 1990 to 2013 at single institute were retrospectively analyzed. Huge tumor, age, HCV, multiple tumors and microscopic portal invasion are independent risk factors for overall survival (OS), and huge tumor, ICGR15 ≥16%, multiple tumors, moderate/poor histology, microscopic portal invasion and a positive pathological margin are risk factors for relapse-free survival (RFS). The 5-year OS and RFS of patients with huge HCC (n = 53) (42.9 and 14.2%) were significantly worse than those of patients with HCC Huge tumor is an independent risk factor for initial extra-hepatic recurrence (Hazard ratio 7.86, P Huge HCC (≥10 cm) is an independent risk factor due to a high risk for initial extra-hepatic recurrence. Future systemic adjuvant therapy is needed for these patients. J. Surg. Oncol. 2017;115:324-329. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. Treatment of huge hypertensive putaminal hemorrhage by surgery and cerebrospinal fluid drainage.

    Science.gov (United States)

    Zhang, Hong-Tian; Xue, Sha; Li, Pei-Jian; Fu, Yan-Bin; Xu, Ru-Xiang

    2013-09-01

    There is limited information available regarding the treatment of huge hypertensive putaminal hemorrhage (HPH). This study aimed to evaluate our experience of 33 patients with huge HPH who were treated by open surgery (decompressive craniectomy and hematoma evacuation) and external cerebrospinal fluid (CSF) drainage. We reviewed the records of 33 consecutive patients admitted to our hospital with huge HPH (≥ 60 cm(3)). All patients were treated by decompressive craniectomy, hematoma evacuation, and CSF drainage. Data collected included age, gender, blood pressure at admission, Glasgow Coma Scale (GCS) score, intracranial hemorrhage (ICH) location, ICH volume, degree of midline shift, presence/absence of basal cistern obliteration at admission and before surgery, and presence/absence of intraventricular hemorrhage (IVH). Outcome was assessed by the Glasgow Outcome Scale score at 30 days after surgery. The median GCS score was 5.0 at admission, and improved to 8.0 at 1 week after surgery. The median ICH volume was 95 cm(3) before surgery and 4 cm(3) after surgery. IVH was observed in 93.9% of patients. The overall survival rate to discharge was 75.6% (25/33), including 15.1% (4/33) with good function, 36.4% (12/33) with disability, and 24.3% (8/33) in a vegetative state. The mortality rate was 24.3% (8/33). Patients with right-sided ICH had better outcomes than those with left-sided ICH. No patients with GCS score ≤ 6 and ICH volume ≥ 90cm(3) at admission achieved good postoperative function. Operative time was significantly shorter with hematoma evacuation via the transcortical approach than via the transsylvian approach (3.41 ± 0.75 h vs. 4.14 ± 0.59 h, Phuge HPH by decompressive craniectomy, hematoma evacuation, and CSF drainage is life-saving. Patients with GCS score 7-8, ICH volume 60-90 cm(3), and right-sided ICH may achieve good recovery. The transcortical approach appears to be more effective than the transsylvian approach for rapid decompression of

  7. Huge pelvic parachordoma: fine needle aspiration cytology and histological differential diagnosis

    Directory of Open Access Journals (Sweden)

    Mona A. Kandil

    2012-10-01

    Full Text Available Parachordoma is an extremely rare soft tissue tumor of unknown lineage. Parachordoma develops most often on the extremities. Only 2 cases have been reported as pelvic parachordoma. A 46-year old Egyptian woman with a huge painful pelvic mass was found to have a parachordoma with ectopic pelvic right kidney. There is only one report in the literature of fine needle aspiration cytology in this setting. The microscopic picture of parachordoma is not new to pathologists but the gross picture of this rare tumor has not previously been published; not even in the World Health Organization classification of soft tissues tumors. Diagnosis was confirmed by immuno-histochemistry. The patient is in good clinical condition without any evidence of recurrence or metastasis after 84 months of follow up.

  8. Shape Memory and Huge Superelasticity in Ni–Mn–Ga Glass-Coated Fibers

    Directory of Open Access Journals (Sweden)

    Lei Shao

    2017-01-01

    Full Text Available Ni–Mn–Ga polycrystalline alloy fibers with diameters of 33 μm are reported to exhibit significantly improved ductility and huge superelastic and shape memory strains in comparison to conventional brittle bulk polycrystalline alloys. Particularly, the recoverable strain of the Ni54.9–Mn23.5–Ga21.6 fiber can be as high as 10% at 40 °C. Such optimized behavior has been achieved by a suitable fabrication process via a glass-coating melt spinning method. The superelastic properties at different temperatures and the shape memory effect of Ni54.9–Mn23.5–Ga21.6 fibers were investigated.

  9. Tiny grains give huge gains: nanocrystal-based signal amplification for biomolecule detection.

    Science.gov (United States)

    Tong, Sheng; Ren, Binbin; Zheng, Zhilan; Shen, Han; Bao, Gang

    2013-06-25

    Nanocrystals, despite their tiny sizes, contain thousands to millions of atoms. Here we show that the large number of atoms packed in each metallic nanocrystal can provide a huge gain in signal amplification for biomolecule detection. We have devised a highly sensitive, linear amplification scheme by integrating the dissolution of bound nanocrystals and metal-induced stoichiometric chromogenesis, and demonstrated that signal amplification is fully defined by the size and atom density of nanocrystals, which can be optimized through well-controlled nanocrystal synthesis. Further, the rich library of chromogenic reactions allows implementation of this scheme in various assay formats, as demonstrated by the iron oxide nanoparticle linked immunosorbent assay (ILISA) and blotting assay developed in this study. Our results indicate that, owing to the inherent simplicity, high sensitivity and repeatability, the nanocrystal based amplification scheme can significantly improve biomolecule quantification in both laboratory research and clinical diagnostics. This novel method adds a new dimension to current nanoparticle-based bioassays.

  10. Development of a huge varix following endovascular embolization for cerebellar arteriovenous malformation

    Energy Technology Data Exchange (ETDEWEB)

    Mineura, K.; Sasajima, H.; Itoh, Y.; Kowada, M. [Akita Univ. Hospital (Japan). Neurosurgical Service; Tomura, N. [Akita Univ. Hospital (Japan). Dept. of Radiology; Goto, K. [Iizuka Hospital, Fukuoka (Japan). Dept. of Interventional Neuroradiology

    1998-03-01

    We report on the case of a huge varix that developed after the endovascular embolization of a cerebellar arteriovenous malformation (AVM) with a single drainer. A 21-year-old male presented with trigeminal neuralgia which was caused by the dilated drainer of the AVM. A varix was found at the basal vein of Rosenthal 2 months after an initial stage of embolization with polyvinyl alcohol particles; it diminished after the surgical extirpation of the AVM. The varix formation might have been facilitated by the stenosis in the vein of Galen and by the dynamic changes that followed the embolization. This rare complication should be kept in mind when embolization is performed for AVMs with impaired venous outlets. (orig.).

  11. Huge spin-transfer torque in a magnetic tunnel junction by a superlattice barrier

    Science.gov (United States)

    Chen, C. H.; Tseng, P.; Ko, C. W.; Hsueh, W. J.

    2017-09-01

    Huge spin-transfer torque (STT) in a magnetic tunnel junction (MTJ) achieved by superlattice barrier composed of alternate layers of a nonmagnetic metal and an insulator is proposed. The magnitude of the STT depends on the number of cells in the superlattice barrier and the nonmagnetic metal layer's thickness. The result shows that the STT of the novel superlattice-barrier MTJ can reach values up to four orders of magnitude greater than those of traditional single-barrier stacks based on three cells superlattice by designing the nonmagnetic metal layer's thickness. In addition, the spin-transfer torque of the proposed MTJ can also be thousands of magnitude greater than those of traditional double-barrier MTJs.

  12. Unusual Large Sporadic Angiomyolipoma Co-existing with Huge Simple Renal Cyst

    Directory of Open Access Journals (Sweden)

    Sunil V Jagtap

    2011-07-01

    Full Text Available Renal Angiomyolipoma (AML is an unusual benign mesenchymal tumor with no malignant potential. It is composed of adipose tissue, smooth muscle and abnormal thick walled blood vessels. It can occur sporadically or may be associated with tuberous sclerosis. Sporadic angiomyolipoma (AML coexisting with simple renal cyst is extremely rare and only one case report is available in the literature. In our case, unique combination of sporadic AML along with simple renal cyst with huge size and weight was noted. To the best of our knowledge, ours is the second such case and first case from India. Due to its large size, complete nephrectomy was performed to avoid chances of rupture and retroperitoneal hemorrhage. Post-operative period was uneventful and the patient ahs been on regular follow-up.

  13. Bilateral ureteral complete obstruction with huge spontaneous urinoma formation in a patient with advanced bladder cancer.

    Science.gov (United States)

    Jou, Yeong-Chin; Shen, Cheng-Huang; Cheng, Ming-Chin; Lin, Chang-Te; Chen, Pi-Che

    2012-02-01

    Spontaneous rupture of the collecting system with extravasation of urine and urinoma formation is usually associated with urinary tract obstruction by a ureteral calculus. Tumor growth is an extremely rare cause of urinary extravasation. Here we report a case of bilateral obstructive uropathy with a huge spontaneous left retroperitoneal urinoma caused by advanced infiltrative transitional cell carcinoma of the urinary bladder. The point of leakage was located in the left renal pelvis. The urinary leakage ceased after percutaneous nephrostomy drainage, and the patient subsequently underwent radical cystoprostatectomy. Histopathology revealed a high-grade urothelial carcinoma of the urinary bladder with pelvic lymph node metastasis. The patient refused any adjuvant treatment and expired 6 months after the operation from disseminated metastasis from bladder cancer. Copyright © 2011. Published by Elsevier B.V.

  14. Bilateral ureteral complete obstruction with huge spontaneous urinoma formation in a patient with advanced bladder cancer

    Directory of Open Access Journals (Sweden)

    Yeong-Chin Jou

    2012-02-01

    Full Text Available Spontaneous rupture of the collecting system with extravasation of urine and urinoma formation is usually associated with urinary tract obstruction by a ureteral calculus. Tumor growth is an extremely rare cause of urinary extravasation. Here we report a case of bilateral obstructive uropathy with a huge spontaneous left retroperitoneal urinoma caused by advanced infiltrative transitional cell carcinoma of the urinary bladder. The point of leakage was located in the left renal pelvis. The urinary leakage ceased after percutaneous nephrostomy drainage, and the patient subsequently underwent radical cystoprostatectomy. Histopathology revealed a high-grade urothelial carcinoma of the urinary bladder with pelvic lymph node metastasis. The patient refused any adjuvant treatment and expired 6 months after the operation from disseminated metastasis from bladder cancer.

  15. Genome-wide Association Studies from the Cancer Genetic Markers of Susceptibility (CGEMS) Initiative | Office of Cancer Genomics

    Science.gov (United States)

    CGEMS identifies common inherited genetic variations associated with a number of cancers, including breast and prostate. Data from these genome-wide association studies (GWAS) are available through the Division of Cancer Epidemiology & Genetics website.

  16. PRS: PERSONNEL RECOMMENDATION SYSTEM FOR HUGE DATA ANALYSIS USING PORTER STEMMER

    Directory of Open Access Journals (Sweden)

    T N Chiranjeevi

    2016-04-01

    Full Text Available Personal recommendation system is one which gives better and preferential recommendation to the users to satisfy their personalized requirements such as practical applications like Webpage Preferences, Sport Videos preferences, Stock selection based on price, TV preferences, Hotel preferences, books, Mobile phones, CDs and various other products now use recommender systems. The existing Pearson Correlation Coefficient (PCC and item-based algorithm using PCC, are called as UPCC and IPCC respectively. These systems are mainly based on only the rating services and does not consider the user personal preferences, they simply just give the result based on the ratings. As the size of data increases it will give the recommendations based on the top rated services and it will miss out most of user preferences. These are main drawbacks in the existing system which will give same results to the users based on some evaluations and rankings or rating service, they will neglect the user preferences and necessities. To address this problem we propose a new approach called, Personnel Recommendation System (PRS for huge data analysis using Porter Stemmer to solve the above challenges. In the proposed system it provides a personalized service recommendation list to the users and recommends the most useful services to the users which will increase the accuracy and efficiency in searching better services. Particularly, a set of suggestions or keywords are provided to indicate user preferences and we used Collaborative Filtering and Porter Stemmer algorithm which gives a suitable recommendations to the users. In real, the broad experiments are conducted on the huge database which is available in real world, and outcome shows that our proposed personal recommender method extensively improves the precision and efficiency of service recommender system over the KASR method. In our approach mainly consider the user preferences so it will not miss out the any of the data

  17. Huge epithelial nonparasitic splenic cyst: A case report and a review of treatment methods.

    Science.gov (United States)

    Farhangi, Bahman; Farhangi, Arezo; Firouzjahi, Alireza; Jahed, Babak

    2016-01-01

    Splenic cysts are rare in all age groups and there are a few reports in the world literature. Primary cysts occur most frequently in children and young adults, comprising around 25% of all nonparasitic splenic cysts. Various techniques are suggested for the treatment of splenic cysts. In this case report, a huge epithelial splenic cyst in a 17-year-old female is presented and different treatment methods of splenic cysts are evaluated. A 17-year-old female presented with progressive abdominal mass in left upper quadrant associated with abdominal pain and food intolerance of duration of several months. There was no history of trauma. On physical examination, there was a huge mass located in the upper left side of abdomen. Computerized tomography scan revealed that a large cystic lesion had occupied the spleen with dimensions of 32x21xI5.6 cm. After patient preparation laparotomy was performed and complete cyst excision was done with splenectomy, patient was discharged after 2 days. This is a report of a case of epithelial splenic cyst of the spleen in a 17-year old female. The management of splenic cysts continues to evolve and the optimum treatment of patients with nonparasitic splenic cysts is controversial, as a principle preservation technique of the spleen with minimally invasive methods such as laparoscopy is preferred to splenectomy with the exception of very large cysts and when splenic hilum is involved in cyst wall. However, significant cyst recurrences were encountered with these techniques. Recently open partial splenectomy has been proposed as a safe and effective method in the management of NPSCs it ensures complete cyst removal, lack of cyst recurrence, and preservation of the spleen functions.

  18. Bioinspired oil strider floating at the oil/water interface supported by huge superoleophobic force.

    Science.gov (United States)

    Liu, Xueli; Gao, Jun; Xue, Zhongxin; Chen, Li; Lin, Ling; Jiang, Lei; Wang, Shutao

    2012-06-26

    Oil pollution to aquatic devices, especially to those oil-cleaning devices and equipment-repairing robots during oil spill accidents, has drawn great attention and remains an urgent problem to be resolved. Developing devices that can move freely in an oil/water system without contamination from oil has both scientific and practical importance. In nature, the insect water strider can float on water by utilizing the superhydrophobic supporting force received by its legs. Inspired by this unique floating phenomenon, in this article, we designed a model device named "oil strider" that could float stably at the oil/water interface without contamination by oil. The floating capability of the oil strider originated from the huge underwater superoleophobic supporting force its "legs" received. We prepared the micro/nanohierarchical structured copper-oxide-coated copper wires, acting as the artificial legs of oil strider, by a simple base-corrosion process. The surface structures and hydrophilic chemical components of the coatings on copper wires induced the huge superoleophobic force at the oil/water interface, to support the oil strider from sinking into the oil. Experimental results and theoretical analysis demonstrate that this supporting force is mainly composed of three parts: the buoyancy force, the curvature force, and the deformation force. We anticipate that this artificial oil strider will provide a guide for the design of smart aquatic devices that can move freely in an oil/water system with excellent oil repellent capability, and be helpful in practical situations such as oil handling and oil spill cleanup.

  19. [Epidemiological imaginary in Campania Region].

    Science.gov (United States)

    Greco, Pietro

    2012-01-01

    The interviews on the epidemiological imaginary, collected within the framework of the project Sebiorec,(1) clearly demonstrate that also in Campania, on the border between the provinces of Naples and Caserta - where the issue of waste and land devastation take forms that are unprecedented compared to any other part of Europe - there is a widespread, strong, sacrosanct demand of participation in environment and health management. The request of deliberative ecological democracy is pressing.(2) There is an urgent need to meet that plethora of rights emerging in the "knowledge society" and in the "risk society" that someone has called "rights for scientific citizenship."(3) This request of the population of Campania, net of local cultural specificity, it is quite similar to that of the people of any other region of Europe. The context in which this request of participation is expressed, however, is quite different. Not only and not just for that real or perceived social pre-modern and familist web that would replace a modern civil society in Campania and all across the Southern Italian regions, but also and especially for some structural causes that we here try to list. Campania is a unique region in Europe - in many ways different even from other regions of southern Italy - due to the conjunction of at least five factors, not independent from each other. 1) The presence of a widespread organized crime which, in many areas, metropolitan and non-metropolitan alike, and especially in the provinces of Naples and Caserta, is a sort of state against the State and has one of its main levers of power and a major source of its wealth in the illegal control of the territory, in its different dimensions (military, but also economic, social and even cultural). 2) A huge social and economic disintegration, exacerbated in the last twenty years by a process of deindustrialization (until the early nineties Naples was the fifth industrial city of Italy, today it is a desert where

  20. Fluorescent In Situ Hybridization (FISH) on Pachytene Chromosomes as a Tool for Genome Characterization. In: Legume Genomics

    NARCIS (Netherlands)

    Geurts, R.; Jong, de J.H.S.G.M.

    2013-01-01

    A growing number of international genome consortia have initiated large-scale sequencing projects for most of the major crop species. This huge amount of information not only boosted genetic and physical mapping research, but it also enabled novel applications on the level of chromosome biology incl

  1. Fluorescent In Situ Hybridization (FISH) on Pachytene Chromosomes as a Tool for Genome Characterization. In: Legume Genomics

    NARCIS (Netherlands)

    Geurts, R.; Jong, de J.H.S.G.M.

    2013-01-01

    A growing number of international genome consortia have initiated large-scale sequencing projects for most of the major crop species. This huge amount of information not only boosted genetic and physical mapping research, but it also enabled novel applications on the level of chromosome biology

  2. The platelet-to-lymphocyte ratio predicts poor survival in patients with huge hepatocellular carcinoma that received transarterial chemoembolization.

    Science.gov (United States)

    Xue, Tong-Chun; Jia, Qing-An; Ge, Ning-Ling; Zhang, Bo-Heng; Wang, Yan-Hong; Ren, Zheng-Gang; Ye, Sheng-Long

    2015-08-01

    Inflammation is particularly strong in huge hepatocellular carcinoma (HCC). However, it is unclear whether the platelet-to-lymphocyte ratio (PLR), as an inflammatory-related marker, can predict survival of patients with huge HCC. In this study, we enrolled 291 patients with huge HCC (diameter over 10 cm) who were undergoing repeated transarterial chemoembolization (TACE) at our institute. The baseline PLR was calculated from complete serum blood counts before the first chemoembolization. We found that a baseline PLR cutoff value over 150 best predicted huge HCC survival. The 12, 24, and 36 months survival rates in the high PLR group (22.6, 8.1, and 4.1 %, respectively) were significantly lower than in the low PLR group (35.6, 22.4, and 14 %, respectively). Thus, a significant difference was found in overall survival (log-rank test, p huge HCC, a high baseline PLR is a useful predictor of poor survival in patients undergoing chemoembolization. Additional anti-inflammatory or anti-platelet treatments, in combination with TACE, may improve survival in HCC patients with high PLR.

  3. The value of a formula including haematocrit, blood urea and gender (HUGE) as a screening test for chronic renal insufficiency.

    Science.gov (United States)

    Alvarez-Gregori, J A; Robles, N R; Mena, C; Ardanuy, R; Jauregui, R; Macas-Nu Nunez, J F

    2011-06-01

    Despite increasing use in clinical practice, an estimated glomerular filtration rate value (eGFR) of HUGE formula. A formula including haematocrit , blood urea, and gender (HUGE), diagnoses CRI regardless of the variables of age, blood creatinine, creatinine clearance, or other eGFR. The HUGE formula is: L = 2.505458 - (0.264418 x Hematocrit) + (0.118100 x Urea) [+ 1.383960 if male]. If L is a negative number the individual does not have CRI; if L is a positive number, CRI is present. Our data demonstrate that the HUGE formula is more reliable than MDRD and CKD-EPI, particularly in persons aged over 70. Our HUGE screening formula offers a straightforward, easily available and inexpensive method for differentiating between CRI and eGFR < 60 ml/min/1.73 m2 that will prevent a considerable number of aged healthy persons, as much as 1.700.000 in Spain and 2.600.000 in U.K., to be excluded from clinical assays or treatments contraindicated in CRI.

  4. Clinical Interpretation of Genomic Variations.

    Science.gov (United States)

    Sayitoğlu, Müge

    2016-09-05

    Novel high-throughput sequencing technologies generate large-scale genomic data and are used extensively for disease mapping of monogenic and/or complex disorders, personalized treatment, and pharmacogenomics. Next-generation sequencing is rapidly becoming routine tool for diagnosis and molecular monitoring of patients to evaluate therapeutic efficiency. The next-generation sequencing platforms generate huge amounts of genetic variation data and it remains a challenge to interpret the variations that are identified. Such data interpretation needs close collaboration among bioinformaticians, clinicians, and geneticists. There are several problems that must be addressed, such as the generation of new algorithms for mapping and annotation, harmonization of the terminology, correct use of nomenclature, reference genomes for different populations, rare disease variant databases, and clinical reports.

  5. [COMBINED POSTERIOR AND ANTERIOR APPROACHES FOR RESECTION OF THORACOLUMBAR SPINAL HUGE DUMBBELL-SHAPED TUMOR].

    Science.gov (United States)

    Shi, Jiandang; Zhao, Chen; Ding, Huiqiang; Fu, Bin; Niu, Ningkui; Yue, Xuefeng; Yang, Zongqiang; He, Yin

    2016-02-01

    To investigate the surgical outcome of combined posterior and anterior approaches for the resection of thoracolumbar spinal canal huge dumbbell-shaped tumor. Between January 2009 and March 2015, 12 patients with thoracolumbar spinal canal huge dumbbell-shaped tumor were treated by posterior approach and anterolateral approach through diaphragmatic crura and thoracoabdominal incision for complete resection. There were 9 males and 3 females, with an average age of 45 years (range, 30-65 years). The disease duration was 8-64 weeks (mean, 12.7 weeks). The tumor was located at T(12), L1 in 6 cases, at L(1,2) in 5 cases, and at L(2,3) in 1 case. The tumor size ranged from 4.3 cm x 4.0 cm x 3.5 cm to 7.5 cm x 6.3 cm x 6.0 cm. According to tumor outside the spinal involvement scope and site and based on the typing of Eden, 5 cases were rated as type b, 2 cases as type d, 4 cases as type e, and 1 case as type f in the transverse direction; two segments were involved in 8 cases, and more than two segments in 4 cases. The degree of tumor excision, tumor recurrence, and the spine stability were observed during follow-up. The verbal rating scale (VRS) was used to evaluate pain improvement. The average surgical time was 170 minutes (range, 150-230 minutes); the average intraoperative blood loss was 350 mL (range, 270-600 mL). All incisions healed by first intention, and no thoracic cavity infection and other operation related complication occurred. Of 12 cases, 10 were histologically confirmed as schwannoma, and 2 as neurofibroma. The patients were followed up 6 months to 6 years (mean, 31 months). Neurological symptoms were significantly improved in all patients, without lower back soreness. The thoracolumbar X-ray film and MRI showed no tumor residue. No tumor recurrence, internal fixator loosening, scoliosis, and other complications were observed during follow-up. VRS at last follow-up was significantly improved to grade 0 (10 cases) or grade 1 (2 cases) from preoperative

  6. Genomic dysregulation in gastric tumors.

    Science.gov (United States)

    Janjigian, Yelena Y; Kelsen, David P

    2013-03-01

    Gastric cancer is among the most common human malignancies and the second leading cause of cancer-related death. The different epidemiologic and histopathology of subtypes of gastric cancer are associated with different genomic patterns. Data suggests that gene expression patterns of proximal, distal gastric cancers-intestinal type, and diffuse/signet cell are well separated. This review summarizes the genetic and epigenetic changes thought to drive gastric cancer and the emerging paradigm of gastric cancer as three unique disease subtypes.

  7. Partial reactivation of a huge deep-seated ancient rock slide: recognition, formation mechanism, and stability

    Science.gov (United States)

    Tang, Minggao; Xu, Qiang; Li, Yusheng; Huang, Runqiu; Rengers, Niek; Zhu, Xing

    2016-08-01

    About 18 years ago, a large-scale discontinuous layer in properties and colour was found in the new Fengjie town at the shore of the Three Gorges Reservoir area in China. There are many resettled residents and buildings on the sloping area, the safety of which is potentially affected by this layer, so it has become the focus of attention. Before this study started there were two viewpoints regarding the origin of this layer. One was that is was from a huge ancient slide and the other was that is was from a fault graben. In order to find out how it was formed and to be able to carry out a stability analysis of the slope the authors have carried out a research program, including geological field investigations and mapping, a deep drilling hole, a geotechnical centrifuge model test, and a simulation analysis. The results of the research led to the conclusion that the layer is the sliding plane of a huge deep-seated ancient rock slide, which we called the Sanmashan landslide. An important argument for the conclusion is the recognition of a regional compressive tectonic stress field in this area, which cannot lead to the formation of a fault graben because it needs a tensional tectonic stress field. Moreover, numerous unique geological features, sliding marks, and other relics of the ancient slide have been discovered in the field. The formation process of the ancient slide could be repeated in a large geotechnical centrifuge model test. The test shows that a deformation and failure process of "creep-crack-cut" has occurred. The type of the ancient slide can be classified as a "successive rotational rock slide". Finally, the role of seepage in the stability of the Sanmashan landslide has been analysed. Our final conclusions are that, during rainfall and filling-drawdown cycles in the Three Gorges Reservoir, the Sanmashan landslide as a whole is dormant and stable and the secondary landslides in the toe area of the slope are presently stable but can be reactivated. This

  8. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  9. Ophthalmic epidemiology in Europe

    DEFF Research Database (Denmark)

    Delcourt, Cécile; Korobelnik, Jean-François; Buitendijk, Gabriëlle H S

    2016-01-01

    The European Eye Epidemiology (E3) consortium is a recently formed consortium of 29 groups from 12 European countries. It already comprises 21 population-based studies and 20 other studies (case-control, cases only, randomized trials), providing ophthalmological data on approximately 170,000 Euro...

  10. Inflammatory bowel disease epidemiology

    DEFF Research Database (Denmark)

    Burisch, Johan; Munkholm, Pia

    2013-01-01

    The occurrence of inflammatory bowel disease (IBD) is increasing worldwide, yet the reasons remain unknown. New therapeutic approaches have been introduced in medical IBD therapy, but their impact on the natural history of IBD remains uncertain. This review will summarize the recent findings in t...... in the epidemiology of IBD....

  11. Phylogenetically resolving epidemiologic linkage.

    Science.gov (United States)

    Romero-Severson, Ethan O; Bulla, Ingo; Leitner, Thomas

    2016-03-08

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.

  12. [Toxoplasmosis: Epidemiology, Diagnosis, Treatment].

    Science.gov (United States)

    Khryanin, A A; Reshetnikov, O V; Kuvshinova, I N

    2015-01-01

    The up-to-date literature and original data on the epidemiology, diagnosis and treatment of toxoplasmosis are presented. Particular attention is paid to the parasite infection during pregnancy. Spiramycin is the drug of choice for acute toxoplasmosis in pregnant women.

  13. Molecular epidemiology of ascariasis

    DEFF Research Database (Denmark)

    Betson, Martha; Halstead, Fennella; Nejsum, Peter

      We are using molecular epidemiology techniques to study the population structure of Ascaris obtained from humans and pigs. Worms were obtained from human hosts on Zanzibar and in Uganda, Bangladesh, Guatemala and Nepal and Ascaris from pigs were collected from in Uganda, Tanzania, Denmark...

  14. Epidemiology of Down Syndrome

    Science.gov (United States)

    Sherman, Stephanie L.; Allen, Emily G.; Bean, Lora H.; Freeman, Sallie B.

    2007-01-01

    Down syndrome (DS) is the most commonly identified genetic form of mental retardation and the leading cause of specific birth defects and medical conditions. Traditional epidemiological studies to determine the prevalence, cause, and clinical significance of the syndrome have been conducted over the last 100 years. DS has been estimated to occur…

  15. Triangulation in aetiological epidemiology.

    Science.gov (United States)

    Lawlor, Debbie A; Tilling, Kate; Davey Smith, George

    2016-12-01

    Triangulation is the practice of obtaining more reliable answers to research questions through integrating results from several different approaches, where each approach has different key sources of potential bias that are unrelated to each other. With respect to causal questions in aetiological epidemiology, if the results of different approaches all point to the same conclusion, this strengthens confidence in the finding. This is particularly the case when the key sources of bias of some of the approaches would predict that findings would point in opposite directions if they were due to such biases. Where there are inconsistencies, understanding the key sources of bias of each approach can help to identify what further research is required to address the causal question. The aim of this paper is to illustrate how triangulation might be used to improve causal inference in aetiological epidemiology. We propose a minimum set of criteria for use in triangulation in aetiological epidemiology, summarize the key sources of bias of several approaches and describe how these might be integrated within a triangulation framework. We emphasize the importance of being explicit about the expected direction of bias within each approach, whenever this is possible, and seeking to identify approaches that would be expected to bias the true causal effect in different directions. We also note the importance, when comparing results, of taking account of differences in the duration and timing of exposures. We provide three examples to illustrate these points. © The Author 2017. Published by Oxford University Press on behalf of the International Epidemiological Association.

  16. The Epidemiology of Pheochromocytoma

    DEFF Research Database (Denmark)

    Ladefoged Ebbehøj, Andreas

    2017-01-01

    Pheochromocytoma and catecholamine secreting paraganglioma (PPGL) are exceedingly rare endocrine tumours, but remain a frequent diagnostic dilemma due to their potential life-threatening nature. Reliable data on the epidemiology of PPGL is lacking and no time trends in incidence rates (IR) have...

  17. Epidemiology of burns

    NARCIS (Netherlands)

    Dokter, Jan

    2016-01-01

    The aim of this thesis is to understand the epidemiology, treatment and outcomes of specialized burn care in The Netherlands. This thesis is mainly based on historical data of the burn centre in Rotterdam from 1986, combined with historical data from the burn centres in Groningen and Beverwijk from

  18. Future perspectives, applications and challenges of genomic epidemiology studies for food-borne pathogens: A case study of Enterohemorrhagic Escherichia coli (EHEC) of the O157:H7 serotype.

    Science.gov (United States)

    Eppinger, Mark; Cebula, Thomas A

    2015-01-01

    The shiga-toxin (Stx)-producing human pathogen Escherichia coli serotype O157:H7 is a highly pathogenic subgroup of Stx-producing E. coli (STEC) with food-borne etiology and bovine reservoir. Each year in the U. S., approximately 100,000 patients are infected with enterohemorrhagic E. coli (EHEC) of the O157:H7 serotype. This food-borne pathogen is a global public health threat responsible for widespread outbreaks of human disease. Since its initial discovery in 1982, O157:H7 has rapidly become the dominant EHEC serotype in North America. Hospitalization rates among patients as high as 50% have been reported for severe outbreaks of human disease. Symptoms of disease can rapidly deteriorate and progress to life-threatening complications such as Hemolytic Uremic Syndrome (HUS), the leading cause of kidney failure in children, or Hemorrhagic Colitis. In depth understanding of the genomic diversity that exists among currently circulating EHEC populations has broad applications for improved molecular-guided biosurveillance, outbreak preparedness, diagnostic risk assessment, and development of alternative toxin-suppressing therapeutics.

  19. Modified simultaneous integrated boost radiotherapy for an unresectable huge refractory pelvic tumor diagnosed as a rectal adenocarcinoma.

    Science.gov (United States)

    Nomiya, Takuma; Akamatsu, Hiroko; Harada, Mayumi; Ota, Ibuki; Hagiwara, Yasuhito; Ichikawa, Mayumi; Miwa, Misako; Kawashiro, Shouhei; Hagiwara, Motohisa; Chin, Masahiro; Hashizume, Eiji; Nemoto, Kenji

    2014-12-28

    A clinical trial of radiotherapy with modified simultaneous integrated boost (SIB) technique against huge tumors was conducted. A 58-year-old male patient who had a huge pelvic tumor diagnosed as a rectal adenocarcinoma due to familial adenomatous polyposis was enrolled in this trial. The total dose of 77 Gy (equivalent dose in 2 Gy/fraction) and 64.5 Gy was delivered to the center of the tumor and the surrounding area respectively, and approximately 20% dose escalation was achieved with the modified SIB technique. The tumor with an initial maximum size of 15 cm disappeared 120 d after the start of the radiotherapy. Performance status of the patient improved from 4 to 0. Radiotherapy with modified SIB may be effective for patients with a huge tumor in terms of tumor shrinkage/disappearance, improvement of QOL, and prolongation of survival.

  20. MR-based truncation and attenuation correction in integrated PET/MR hybrid imaging using HUGE with continuous table motion.

    Science.gov (United States)

    Lindemann, Maike E; Oehmigen, Mark; Blumhagen, Jan O; Gratz, Marcel; Quick, Harald H

    2017-09-01

    The objective of this study was to introduce and evaluate a method for MR-based attenuation and truncation correction in phantom and patient measurements to improve PET quantification in PET/MR hybrid imaging. The fully MR-based method HUGE (B0 Homogenization using gradient enhancement) provides field-of-view extension in MR imaging, which can be used for truncation correction and improved PET quantification in PET/MR hybrid imaging. The HUGE method in this recent implementation is combined with continuously moving table data acquisition to provide a seamless nontruncated whole-body data set of the outer patient contours to complete the established standard MR-based Dixon-VIBE data for attenuation correction. The method was systematically evaluated in NEMA standard phantom experiments to investigate the impact of HUGE truncation correction on PET quantification. The method was then applied to 24 oncologic patients in whole-body PET/MR hybrid imaging. The impact of MR-based truncation correction with HUGE on PET data was compared to the impact of the established PET-based MLAA algorithm for contour detection. In phantom and in all patient measurements, the standard Dixon-VIBE attenuation correction data show geometric distortions and signal truncations at the edges of the MR imaging field-of-view. In contrast, the Dixon-VIBE-based attenuation correction data additionally extended by applying HUGE shows significantly less distortion and truncations and due to the continuously moving table acquisition robustly provides smooth outer contours of the patient arms. In the investigated patient cases, MLAA frequently showed an overestimation of arm volume and associated artifacts limiting contour detection. When applying HUGE, an average relative increase in SUVmean in patients' lesion of 4.2% and for MLAA of 4.6% were measured, when compared to standard Dixon-VIBE only. In specific lesions maximal differences in SUVmean up to 13% for HUGE and 14% for MLAA were measured

  1. Huge nanodielectric effects in polyimide/boron nitride nanocomposites revealed by the nanofiller size

    Science.gov (United States)

    Diaham, S.; Saysouk, F.; Locatelli, M.-L.; Lebey, T.

    2015-09-01

    The dielectric properties of polyimide/boron nitride (PI/BN) nanocomposite films are investigated as a function of the BN nanofiller size from 20 to 350 °C and at low filler content (1-2 vol.%). The role of the BN nanofiller size on the large reduction of the electrode polarization relaxation phenomenon due to ionic movements is reported. For the two smallest BN nanoparticles (95 nm and 35 nm), the permittivity, dielectric losses and dc conductivity are strongly attenuated above 200 °C by a factor of 10 to 1000 compared to neat PI. Thus, the dc conductivity at 350 °C is reduced from 4   ×   10-8 Ω-1 cm-1 for neat PI to 3   ×   10-11 Ω-1 cm-1 for PI/BN (35 nm). Moreover, a further decrease is obtained by functionalizing the nanofiller surface with a silane coupling agent which improves the grafting of PI chains on those latter nanoparticles. These results highlight the trapping efficiency in the interphase region introduced by the small BN nanofillers (<100 nm) and provides evidence as to the huge nanodielectric effects on the charge carrier transport controlled by the nanoparticle diameter. This finding should be of great importance for advanced high temperature electrical insulation in the future.

  2. Huge thermal conductivity enhancement in boron nitride – ethylene glycol nanofluids

    Energy Technology Data Exchange (ETDEWEB)

    Żyła, Gaweł, E-mail: gzyla@prz.edu.pl [Department of Physics and Medical Engineering, Rzeszow University of Technology, Rzeszow, 35-905 (Poland); Fal, Jacek; Traciak, Julian [Department of Physics and Medical Engineering, Rzeszow University of Technology, Rzeszow, 35-905 (Poland); Gizowska, Magdalena; Perkowski, Krzysztof [Department of Nanotechnology, Institute of Ceramics and Building Materials, Warsaw, 02-676 (Poland)

    2016-09-01

    Paper presents the results of experimental studies on thermophysical properties of boron nitride (BN) plate-like shaped particles in ethylene glycol (EG). Essentially, the studies were focused on the thermal conductivity of suspensions of these particles. Nanofluids were obtained with two-step method (by dispersing BN particles in ethylene glycol) and its’ thermal conductivity was analyzed at various mass concentrations, up to 20 wt. %. Thermal conductivity was measured in temperature range from 293.15 K to 338.15 K with 15 K step. The measurements of thermal conductivity of nanofluids were performed in the system based on a device using the transient line heat source method. Studies have shown that nanofluids’ thermal conductivity increases with increasing fraction of nanoparticles. The results of studies also presented that the thermal conductivity of nanofluids changes very slightly with the increase of temperature. - Highlights: • Huge thermal conductivity enhancement in BN-EG nanofluid was reported. • Thermal conductivity increase very slightly with increasing of the temperature. • Thermal conductivity increase linearly with volume concentration of particles.

  3. Synovial sarcoma presenting with huge mediastinal mass: a case report and review of literature

    Science.gov (United States)

    2013-01-01

    Background Synovial sarcoma presenting in the mediastinum is exceedingly rare. Furthermore, data addressing optimal therapy is limited. Herein we present a case where an attempt to downsize the tumor to a resectable state with chemotherapy was employed. Case presentation A 32 year female presented with massive pericardial effusion and unresectable huge mediastinal mass. Computed axial tomography scan - guided biopsy with adjunctive immunostains and molecular studies confirmed a diagnosis of synovial sarcoma. Following three cycles of combination Ifosfamide and doxorubicin chemotherapy, no response was demonstrated. The patient refused further therapy and had progression of her disease 4 months following the last cycle. Conclusion Synovial sarcoma presenting with unresectable mediastinal mass carry a poor prognosis. Up to the best of our knowledge there are only four previous reports where primary chemotherapy was employed, unfortunately; none of these cases had subsequent complete surgical resection. Identification of the best treatment strategy for patients with unresectable disease is warranted. Our case can be of benefit to medical oncologists and thoracic surgeons who might be faced with this unique and exceedingly rare clinical scenario. PMID:23800262

  4. Unexpected Huge Dimerization Ratio in One-Dimensional Carbon Atomic Chains.

    Science.gov (United States)

    Lin, Yung-Chang; Morishita, Shigeyuki; Koshino, Masanori; Yeh, Chao-Hui; Teng, Po-Yuan; Chiu, Po-Wen; Sawada, Hidetaka; Suenaga, Kazutomo

    2017-01-11

    Peierls theory predicted atomic distortion in one-dimensional (1D) crystal due to its intrinsic instability in 1930. Free-standing carbon atomic chains created in situ in transmission electron microscope (TEM)1-3 are an ideal example to experimentally observe the dimerization behavior of carbon atomic chain within a finite length. We report here a surprisingly huge distortion found in the free-standing carbon atomic chains at 773 K, which is 10 times larger than the value expected in the system. Such an abnormally distorted phase only dominates at the elevated temperatures, while two distinct phases, distorted and undistorted, coexist at lower or ambient temperatures. Atom-by-atom spectroscopy indeed shows considerable variations in the carbon 1s spectra at each atomic site but commonly observes a slightly downshifted π* peak, which proves its sp(1) bonding feature. These results suggest that the simple model, relaxed and straight, is not fully adequate to describe the realistic 1D structure, which is extremely sensitive to perturbations such as external force or boundary conditions.

  5. A Huge Capital Drop with Compression of Femoral Vessels Associated with Hip Osteoarthritis

    Directory of Open Access Journals (Sweden)

    Tomoya Takasago

    2015-01-01

    Full Text Available A capital drop is a type of osteophyte at the inferomedial portion of the femoral head commonly observed in hip osteoarthritis (OA, secondary to developmental dysplasia. Capital drop itself is typically asymptomatic; however, symptoms can appear secondary to impinge against the acetabulum or to irritation of the surrounding tissues, such as nerves, vessels, and tendons. We present here a case of unilateral leg edema in a patient with hip OA, caused by a huge bone mass occurring at the inferomedial portion of the femoral head that compressed the femoral vessels. We diagnosed this bone mass as a capital drop secondary to hip OA after confirming that the mass occurred at least after the age of 63 years based on a previous X-ray. We performed early resection and total hip arthroplasty since the patient’s hip pain was due to both advanced hip OA and compression of the femoral vessels; moreover, we aimed to prevent venous thrombosis secondary to vascular compression considering the advanced age and the potent risk of thrombosis in the patient. A large capital drop should be considered as a cause of vascular compression in cases of unilateral leg edema in OA patients.

  6. Acute abdomen in early pregnancy caused by torsion of bilateral huge multiloculated ovarian cysts

    Directory of Open Access Journals (Sweden)

    Sathiyakala Rajendran

    2015-10-01

    Full Text Available The association of pregnancy and torsion of bilateral huge benign ovarian cyst is rare. We report a case of multigravida at 13 weeks of pregnancy presenting with acute onset of lower abdominal pain. Ultrasound revealed bilateral multiloculated ovarian cysts of size 10x10 cm on right side and 15x10cm on left side with evidence of torsion and a single live intrauterine fetus of gestational age 13 weeks 4 days. Emergency laparotomy was done with vaginal susten 200 mg as perioperative tocolysis. Intra operatively, uterus was enlarged to 14 weeks size. Both ovaries were replaced with multiloculated cysts of size 15x10 cm on left side and 10x10 cm on right side. Ovarian pedicle was found to be twisted once on right side and twice on left side. On right side, untwisting of pedicle was done and the ovarian cyst was punctured at multiple sites to drain the clear fluid. Biopsy was taken from the right ovarian cyst wall. On left side, ovariotomy was done. Histopathology revealed mucinous cyst adenoma of left ovary and multiple corpus luteum in right ovarian biopsy specimen. The patient was followed up with regular antenatal check-ups and ultrasound to rule out the recurrence of ovarian cyst on right side. The patient successfully delivered a term male baby at 39 weeks. [Int J Reprod Contracept Obstet Gynecol 2015; 4(5.000: 1598-1601

  7. Propranolol in Treatment of Huge and Complicated Infantile Hemangiomas in Egyptian Children

    Directory of Open Access Journals (Sweden)

    Basheir A. Hassan

    2014-01-01

    Full Text Available Background. Infantile hemangiomas (IHs are the most common benign tumours of infancy. Propranolol has recently been reported to be a highly effective treatment for IHs. This study aimed to evaluate the efficacy and side effects of propranolol for treatment of complicated cases of IHs. Patients and Methods. This prospective clinical study included 30 children with huge or complicated IHs; their ages ranged from 2 months to 1 year. They were treated by oral propranolol. Treatment outcomes were clinically evaluated. Results. Superficial cutaneous hemangiomas began to respond to propranolol therapy within one to two weeks after the onset of treatment. The mean treatment period that was needed for the occurrence of complete resolution was 9.4 months. Treatment with propranolol was well tolerated and had few side effects. No rebound growth of the tumors was noted when propranolol dosing stopped except in one case. Conclusion. Propranolol is a promising treatment for IHs without obvious side effects. However, further studies with longer follow-up periods are needed.

  8. Computational AstroStatistics Fast and Efficient Tools for Analysing Huge Astronomical Data Sources

    CERN Document Server

    Nichol, R C; Connolly, A J; Davies, S; Genovese, C; Hopkins, A M; Miller, C J; Moore, A W; Pelleg, D; Richards, G T; Schneider, J; Szapudi, I; Wasserman, L H

    2001-01-01

    I present here a review of past and present multi-disciplinary research of the Pittsburgh Computational AstroStatistics (PiCA) group. This group is dedicated to developing fast and efficient statistical algorithms for analysing huge astronomical data sources. I begin with a short review of multi-resolutional kd-trees which are the building blocks for many of our algorithms. For example, quick range queries and fast n-point correlation functions. I will present new results from the use of Mixture Models (Connolly et al. 2000) in density estimation of multi-color data from the Sloan Digital Sky Survey (SDSS). Specifically, the selection of quasars and the automated identification of X-ray sources. I will also present a brief overview of the False Discovery Rate (FDR) procedure (Miller et al. 2001a) and show how it has been used in the detection of ``Baryon Wiggles'' in the local galaxy power spectrum and source identification in radio data. Finally, I will look forward to new research on an automated Bayes Netw...

  9. Distributed data organization and parallel data retrieval methods for huge laser scanner point clouds

    Science.gov (United States)

    Hongchao, Ma; Wang, Zongyue

    2011-02-01

    This paper proposes a novel method for distributed data organization and parallel data retrieval from huge volume point clouds generated by airborne Light Detection and Ranging (LiDAR) technology under a cluster computing environment, in order to allow fast analysis, processing, and visualization of the point clouds within a given area. The proposed method is suitable for both grid and quadtree data structures. As for distribution strategy, cross distribution of the dataset would be more efficient than serial distribution in terms of non-redundant datasets, since a dataset is more uniformly distributed in the former arrangement. However, redundant datasets are necessary in order to meet the frequent need of input and output operations in multi-client scenarios: the first copy would be distributed by a cross distribution strategy while the second (and later) would be distributed by an iterated exchanging distribution strategy. Such a distribution strategy would distribute datasets more uniformly to each data server. In data retrieval, a greedy algorithm is used to allocate the query task to a data server, where the computing load is lightest if the data block needing to be retrieved is stored among multiple data servers. Experiments show that the method proposed in this paper can satisfy the demands of frequent and fast data query.

  10. Molecular Epidemiology of Foodborne Pathogens

    Science.gov (United States)

    Chen, Yi; Brown, Eric; Knabel, Stephen J.

    The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".

  11. Current challenges in genome annotation through structural biology and bioinformatics.

    Science.gov (United States)

    Furnham, Nicholas; de Beer, Tjaart A P; Thornton, Janet M

    2012-10-01

    With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry. Copyright © 2012. Published by Elsevier Ltd.

  12. Longevity studies in GenomEUtwin

    DEFF Research Database (Denmark)

    Skytthe, Axel; Pedersen, Nancy L; Kaprio, Jaakko

    2003-01-01

    for the Danish 1870-1900 twin cohorts to include the new 1901-1910 cohorts, which are consistent with the previous findings. The size of the twin cohorts in GenomEUtwin and the existence of population-based, nationwide health and death registers make epidemiological studies of longevity very powerful...

  13. Epidemiological studies on syncope

    DEFF Research Database (Denmark)

    Ruwald, Martin Huth

    2013-01-01

    of the patients play an essential role. In epidemiology these factors have major impact on the outcome of the patients. Until recently, even the definition of syncope differed from one study to another which has made literature reviews difficult. Traditionally the data on epidemiology of syncope has been taken...... from smaller studies from different clinical settings with wide differences in patient morbidity. Through the extensive Danish registries we examined the characteristics and prognosis of the patients hospitalized due to syncope in a nationwide study. The aims of the present thesis were to investigate......, prevalence and cardiovascular factors associated with the risk of syncope, 4) the prognosis in healthy individuals discharged after syncope, and 5) the prognosis of patients after syncope and evaluation of the CHADS2 score as a tool for short- and long-term risk prediction. The first studies of the present...

  14. Epidemiology of colorectal cancer

    Science.gov (United States)

    Marley, Andrew R; Nan, Hongmei

    2016-01-01

    Colorectal cancer is currently the third deadliest cancer in the United States and will claim an estimated 49,190 U.S. lives in 2016. The purpose of this review is to summarize our current understanding of this disease, based on nationally published statistics and information presented in peer-reviewed journal articles. Specifically, this review will cover the following topics: descriptive epidemiology (including time and disease trends both in the United States and abroad), risk factors (environmental, genetic, and gene-environment interactions), screening, prevention and control, and treatment. Landmark discoveries in colorectal cancer risk factor research will also be presented. Based on the information reviewed for this report, we suggest that future U.S. public health efforts aim to increase colorectal cancer screening among African American communities, and that future worldwide colorectal cancer epidemiology studies should focus on researching nutrient-gene interactions towards the goal of improving personalized treatment and prevention strategies.

  15. Endovascular Treatment of the Huge Dissecting Aneurysms Involving the Basilar Artery by the Internal Trapping Technique: Technical Note

    Directory of Open Access Journals (Sweden)

    Shi-Qing Mu

    2015-01-01

    Full Text Available Background: The endovascular strategy of the huge dissecting aneurysms involving the basilar artery (BA is controversial and challenging. This study was to investigate the clinical and angiographic outcomes of the treatment of the huge dissecting aneurysms involving the BA by the internal trapping (IT technique. Methods: We retrospectively studied 15 patients with the huge dissecting aneurysms involving the BA treated by the IT technique between September 2005 and September 2014 in Department of Interventional Neuroradiology of Beijing Tiantan Hospital. Clinical and angiographic data were reviewed and evaluated. Results: All patients were treated by the IT technique. That meant the dissecting artery and aneurysm segments were completed occlusion. After the procedure, the angiography demonstrated that all the dissecting artery and aneurysm segments were completed occlusion. Follow-up angiography was performed at 3-6 months or 12-18 months after the endovascular treatment (median 8 months, 14 patients had a good recovery. Re-canalization occurred in one patient whose aneurysm involved in bilateral vertebral arteries and the two third of the middle-lower BA. After the second treatment, the patient died by the ventricular tachycardia. Conclusions: The IT technique is a technically feasible and safe alternative for the treatment of BA dissecting aneurysms, but it is not necessarily the safest or most definitive treatment modality. The ideal treatment of the huge dissecting aneurysms involving the BA remains debatable and must be investigated on a case-by-case basis.

  16. Endovascular Treatment of the Huge Dissecting Aneurysms Involving the Basilar Artery by the Internal Trapping Technique: Technical Note

    Institute of Scientific and Technical Information of China (English)

    Shi-Qing Mu; Xin-Jian Yang; You-Xiang Li; Chu-Han Jiang; Zhong-Xue Wu

    2015-01-01

    Background:The endovascular strategy of the huge dissecting aneurysms involving the basilar artery (BA) is controversial and challenging.This study was to investigate the clinical and angiographic outcomes of the treatment of the huge dissecting aneurysms involving the BA by the internal trapping (IT) technique.Methods:We retrospectively studied 15 patients with the huge dissecting aneurysms involving the BA treated by the IT technique between September 2005 and September 2014 in Department of lnterventional Neuroradiology of Beijing Tiantan Hospital.Clinical and angiographic data were reviewed and evaluated.Results:All patients were treated by the IT technique.That meant the dissecting artery and aneurysm segments were completed occlusion.After the procedure,the angiography demonstrated that all the dissecting artery and aneurysm segments were completed occlusion.Follow-up angiography was performed at 3-6 months or 12-18 months after the endovascular treatment (median 8 months),14 patients had a good recovery.Re-canalization occurred in one patient whose aneurysm involved in bilateral vertebral arteries and the two third of the middle-lower BA.After the second treatment,the patient died by the ventricular tachycardia.Conclusions:The IT technique is a technically feasible and safe alternative for the treatment of BA dissecting aneurysms,but it is not necessarily the safest or most definitive treatment modality.The ideal treatment of the huge dissecting aneurysms involving the BA remains debatable and must be investigated on a case-by-case basis.

  17. Treating Huge Tear-Drop Fracture of Axis With Trapezoidal Bone: A Case Report and Literature Review.

    Science.gov (United States)

    Yang, Xiaobin; Zheng, Bolong; Hao, Dingjun; Liu, Benyin; Yan, Liang; He, Baorong

    2015-11-01

    Case report and review of relevant literature. To discuss the surgical strategies and clinical outcome of managing huge tear drop fracture of axis. Teardrop fracture of axis is rarely seen, especially the huge type. The surgical technique is demanding because of the special anatomical structure and difficulty with bone grafting. Moreover, the surgical approach is controversial in the literature. A 51-year-old male patient suffered from neck pain after falling from the bicycle, neck movement was limited with no neurological compromise. X-ray suggested huge tear-drop fracture of anterior-inferior corner of axis, narrowing of C2/3 intervertebral disc. Fusion with self-designed tricortical trapezoidal iliac bone was performed. Treating huge teardrop fracture of axis by anterior bone grafting with self-designed tricortical trapezoidal iliac bone is effective and stable. A 3-month follow-up showed fusion was achieved, upper cervical curvature was restored, and neck pain disappeared. Self-designed tricortical trapezoidal iliac bone provided adequate fusion area of bone grafting, restoring the normal intervertebral height and cervical alignment, and the midterm outcome is satisfactory. 5.

  18. Huge pseudomyxoma peritonei: Surgical strategies and procedures to employ to optimize the rate of complete cytoreductive surgery.

    Science.gov (United States)

    Benhaim, L; Honoré, C; Goéré, D; Delhorme, J-B; Elias, D

    2016-04-01

    Complete cytoreductive surgery (CCRS) plus Hyperthermic Intraperitoneal Chemotherapy (HIPEC) is the best-known treatment for pseudomyxoma peritonei (PMP). In 30% of the cases, PMP realize a widespread involvement of the peritoneal cavity. In these extreme situations, we developed, devoted strategies to optimize the feasibility and safety of CCRS. This study describes the surgical resections required for CCRS and the consequent approaches that we propose to achieve CCRS. We defined "huge PMP" by a peritoneal cancer index (PCI) ≥ 28. Surgical procedures of patients operated on between 1994 and 2014 were retrospectively reviewed from a prospective database in a single institution. During this period, 311 patients were operated on and 247 (79%) underwent CCRS + HIPEC. Among them, 100 patients presented "huge" PMP and 54 patients underwent CCRS + HIPEC. In patients with "huge" PMP, the rate of CCRS + HIPEC was 25% before 2002 and reached 71% between 2011 and 2014. We identified 3 conditions for CCRS 1) to guaranty a sufficient length of residual small bowel 2) to preserve the left gastric vessels in order to preserve the superior third of the stomach 3) to ensure that the hepatic pedicle can be entirely cleared from its tumor involvement. None of the other peritonectomy procedures were decisional for CCRS. Our learning curve improved the selection and completion rate of CCRS + HIPEC for "huge PMP". Some anatomical and physiological prerequisites guarantee the feasibility and safety of such extensive surgeries. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Endovascular Treatment of the Huge Dissecting Aneurysms Involving the Basilar Artery by the Internal Trapping Technique: Technical Note.

    Science.gov (United States)

    Mu, Shi-Qing; Yang, Xin-Jian; Li, You-Xiang; Jiang, Chu-Han; Wu, Zhong-Xue

    2015-07-20

    The endovascular strategy of the huge dissecting aneurysms involving the basilar artery (BA) is controversial and challenging. This study was to investigate the clinical and angiographic outcomes of the treatment of the huge dissecting aneurysms involving the BA by the internal trapping (IT) technique. We retrospectively studied 15 patients with the huge dissecting aneurysms involving the BA treated by the IT technique between September 2005 and September 2014 in Department of Interventional Neuroradiology of Beijing Tiantan Hospital. Clinical and angiographic data were reviewed and evaluated. All patients were treated by the IT technique. That meant the dissecting artery and aneurysm segments were completed occlusion. After the procedure, the angiography demonstrated that all the dissecting artery and aneurysm segments were completed occlusion. Follow-up angiography was performed at 3-6 months or 12-18 months after the endovascular treatment (median 8 months), 14 patients had a good recovery. Re-canalization occurred in one patient whose aneurysm involved in bilateral vertebral arteries and the two third of the middle-lower BA. After the second treatment, the patient died by the ventricular tachycardia. The IT technique is a technically feasible and safe alternative for the treatment of BA dissecting aneurysms, but it is not necessarily the safest or most definitive treatment modality. The ideal treatment of the huge dissecting aneurysms involving the BA remains debatable and must be investigated on a case-by-case basis.

  20. Is hepatectomy for huge hepatocellular carcinoma (≥ 10 cm in diameter) safe and effective? A single-center experience.

    Science.gov (United States)

    Yang, Jian; Li, Chuan; Wen, Tian-Fu; Yan, Lu-Nan; Li, Bo; Wang, Wen-Tao; Yang, Jia-Yin; Xu, Ming-Qing

    2014-01-01

    This retrospective study aimed to validate the safety and effectiveness of hepatectomy for huge hepatocellular carcinoma (HCC). Data of patients who underwent hepatectomy for HCC between January 2006 and December 2012 were reviewed. The patients were divided into three groups: huge HCC(≥ 10 cm in diameter), large HCC(≥ 5 buthuge and large HCC groups were lower than that of the small HCC group (OS: 32.5% vs 36.3% vs 71.2%, p=0.000; DFS: 20.0% vs 24.8% vs 40.7%, p=0.039), but there was no difference between the huge and large HCC groups (OS: 32.5% vs 36.3%, p=0.667; DFS: 20.0% vs 24.8%, p=0.540). In multivariate analysis, five independent poor prognostic factors that affected OS were significantly associated with worse survival (phuge HCC is similar to that for large and small HCC; and this approach for huge HCC may achieve similar long-term survival and disease-free survival as for large HCC.

  1. Flume tests to study the initiation of huge debris flows after the Wenchuan earthquake in S-WChina

    NARCIS (Netherlands)

    Hu, Wei; Xu, Qiang; van Asch, Theo.W.J.; Zhua, X; Xu, Q.Q.

    2014-01-01

    In the Wenchuan area in the southwest of China, a huge amount of loose co-seismic landslide material was deposited on slopes during the Wenchuan earthquake of May 2008. These loose deposits formed the source material for rainfall-induced debris flows or shallow landslides in the years after the eart

  2. The Epidemiology of Sarcoma

    OpenAIRE

    Burningham Zachary; Hashibe Mia; Spector Logan; Schiffman Joshua D

    2012-01-01

    Abstract Sarcomas account for over 20% of all pediatric solid malignant cancers and less than 1% of all adult solid malignant cancers. The vast majority of diagnosed sarcomas will be soft tissue sarcomas, while malignant bone tumors make up just over 10% of sarcomas. The risks for sarcoma are not well-understood. We evaluated the existing literature on the epidemiology and etiology of sarcoma. Risks for sarcoma development can be divided into environmental exposures, genetic susceptibility, a...

  3. Privacy preserving processing of genomic data: A survey.

    Science.gov (United States)

    Akgün, Mete; Bayrak, A Osman; Ozer, Bugra; Sağıroğlu, M Şamil

    2015-08-01

    Recently, the rapid advance in genome sequencing technology has led to production of huge amount of sensitive genomic data. However, a serious privacy challenge is confronted with increasing number of genetic tests as genomic data is the ultimate source of identity for humans. Lately, privacy threats and possible solutions regarding the undesired access to genomic data are discussed, however it is challenging to apply proposed solutions to real life problems due to the complex nature of security definitions. In this review, we have categorized pre-existing problems and corresponding solutions in more understandable and convenient way. Additionally, we have also included open privacy problems coming with each genomic data processing procedure. We believe our classification of genome associated privacy problems will pave the way for linking of real-life problems with previously proposed methods. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Perspectives of Integrative Cancer Genomics in Next Generation Sequencing Era

    Directory of Open Access Journals (Sweden)

    So Mee Kwon

    2012-06-01

    Full Text Available The explosive development of genomics technologies including microarrays and next generation sequencing (NGS has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

  5. Clinicopathological profile, airway management, and outcome in huge multinodular goiters: an institutional experience from an endemic goiter region.

    Science.gov (United States)

    Agarwal, Amit; Agarwal, Sudhi; Tewari, Prabhat; Gupta, Sushil; Chand, Gyan; Mishra, Anjali; Agarwal, Gaurav; Verma, A K; Mishra, S K

    2012-04-01

    Huge goiters are common in iodine-deficient endemic regions. They are of concern to the surgeons because of the anticipated risk of difficult dissection and increased chances of surgical complications. Similarly, they are of concern to the anesthesiologists because of anticipated intubation-related difficulties and post-thyroidectomy tracheomalacia. In the present study we aimed to present our experience of managing goiters based on their gross weight, highlighting their clinicopathological profile, perioperative airway-related difficulties, and management of surgical morbidity. Retrospective analysis of patients who underwent total thyroidectomy in the primary setting at our institute from 1995 to 2009 was carried out based on the gross gland weight. The patients were thus grouped into group A: ≤200 g; group B: 201 to ≤400 g; group C: 401 to ≤600 g; group D: >600 g. Group A (660 cases); group B (108 cases); group C (36 cases); and group D (9 cases) were included. As the goiter size increased, the mean duration of goiter, compressive symptoms, retrosternal extension (RSE), airway deformity, intubation difficulty, and tracheomalacia increased. The rate of tracheostomy, sternotomy, hemorrhage, visceral injury, and hospital stay was high with huge goiters. These features were more marked in malignant goiters compared to benign goiters. However, the postoperative complications were comparable in both of those groups. Long-standing huge goiters are common in iodine-deficient endemic areas. The majority of patients have symptomatic or clinicoradiological evidence of airway involvement. The incidence of RSE, airway deformity, intubation difficulty, and tracheomalacia is high with huge goiters. The surgery is technically demanding with greater associated chances of injury to native structures. Malignancy influences the presentation and outcome in smaller goiters. In centers with experienced endocrine surgeons and dedicated anesthetists, huge goiters can be

  6. Epidemiologic Assessment of the Protective Effects of Smallpox Vaccination

    Directory of Open Access Journals (Sweden)

    Hiroshi Nishiura

    2006-01-01

    Full Text Available Despite smallpox eradication, the widely discussed possibility of a bioterrorist attack using a variola virus makes it necessary to review the epidemiology of smallpox and the effects of various vaccination schemes. This paper provides a literature review concerning the epidemiologic assessment of the protective effects of smallpox vaccination, with particular emphasis on the statistical and theoretical points of view. Although smallpox vaccination has the longest history of all vaccinations, we lack precise epidemiologic estimates of its effectiveness. Vaccination practice continually evolved and many places experienced vaccinations with various strains over time. Despite the weak statistical evidence, it can be stated with certainty that smallpox vaccines prevented infection for a few decades after primary vaccination and that vaccinated individuals had the benefit of a longer lasting partial protection when they contracted the disease. Confronted with the huge uncertainties and with the necessity to rely on laboratory evidence, appropriate preparedness plans for countermeasures using vaccination must be based on the best available evidence.

  7. Epidemiology of visceral leishmaniasis in Algeria: an update.

    Science.gov (United States)

    Adel, Amel; Boughoufalah, Amel; Saegerman, Claude; De Deken, Redgi; Bouchene, Zahida; Soukehal, Abdelkrim; Berkvens, Dirk; Boelaert, Marleen

    2014-01-01

    Visceral leishmaniasis (VL), a zoonotic disease caused by Leishmania infantum, is endemic in Algeria. This report describes a retrospective epidemiological study conducted on human VL to document the epidemiological profile at national level. All human VL cases notified by the National Institute of Public Health between 1998 and 2008 were investigated. In parallel all VL cases admitted to the university hospitals of Algiers were surveyed to estimate the underreporting ratio. Fifteen hundred and sixty-two human VL cases were reported in Algeria between 1998-2008 with an average annual reported incidence rate of 0.45 cases per 100,000 inhabitants, of which 81.42% were in the age range of 0-4 years. Cases were detected year-round, with a peak notification in May and June. One hundred and seventy patients were admitted to the university hospitals in Algiers in the same period, of which less than one in ten had been officially notified. Splenomegaly, fever, pallor and pancytopenia were the main clinical and laboratory features. Meglumine antimoniate was the first-line therapy for paediatric VL whereas the conventional amphotericin B was used for adult patients. Visceral leishmaniasis in Algeria shows the epidemiological profile of a paediatric disease with a decrease of the annual reported incidence rate. However, vigilance is required because of huge underreporting and an apparent propagation towards the south.

  8. The role of epigenetics in genetic and environmental epidemiology.

    Science.gov (United States)

    Ladd-Acosta, Christine; Fallin, M Daniele

    2016-02-01

    Epidemiology is the branch of science that investigates the causes and distribution of disease in populations in order to provide preventative measures and promote human health. The fields of genetic and environmental epidemiology primarily seek to identify genetic and environmental risk factors for disease, respectively. Epigenetics is emerging as an important piece of molecular data to include in these studies because it can provide mechanistic insights into genetic and environmental risk factors for disease, identify potential intervention targets, provide biomarkers of exposure, illuminate gene-environment interactions and help localize disease-relevant genomic regions. Here, we describe the importance of including epigenetics in genetic and environmental epidemiology studies, provide a conceptual framework when considering epigenetic data in population-based studies and touch upon the many challenges that lie ahead.

  9. Epidemiology of bovine viral diarrhea virus.

    Science.gov (United States)

    Houe, H

    1995-11-01

    give good indication of presence of PI animals in herds not using BVDV vaccines. In herds using killed vaccine, determination of antibody titers among few young stock can show the presence of PI animals. The high incidence of infection combined with all the different damages that are seen after BVDV infection cause huge economical losses, which on a national level in the UK and Denmark (i.e., areas with widespread occurrence of infection) has been calculated as between 7 and 27 million pounds (between $11 and $42 million) per million calvings. Epidemiologic studies are important as a basis for selection of control strategy. Because of the variation in epidemiology between geographic areas, evaluation of a control strategy in an area preferentially should be based on epidemiologic studies in the same area.

  10. Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility

    NARCIS (Netherlands)

    van Vliet, Arnoud H M; Kusters, Johannes G.

    2015-01-01

    Whole-genome sequencing is becoming a leading technology in the typing and epidemiology of microbial pathogens, but the increase in genomic information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneo

  11. Epidemiological Approaches to Metal Toxicology

    DEFF Research Database (Denmark)

    Grandjean, Philippe; Budtz-Jørgensen, Esben

    2014-01-01

    to their propensity to cause chronic or delayed toxicity, epidemiological studies of metal toxicity have focused on a wide variety of organ systems, subtle effects as well as mortality, and differences in susceptibility. Toxic metals often serve as paradigms of environmental and occupational toxicity....... For these reasons, this chapter highlights the fields within epidemiology that are most relevant to toxic metals and discusses where these substances serve to illustrate important epidemiological concepts. Chapter sections include subjects such as epidemiological terms, study design, study population, exposure......Epidemiological methods are crucial to extract as much valid information as possible from human metal exposures. Thus, modern epidemiological approaches have elucidated human health effects that were not apparent in the past. At the same time, metal toxicology has served as a useful arena...

  12. Is this the real time for genomics?

    Science.gov (United States)

    Guarnaccia, Maria; Gentile, Giulia; Alessi, Enrico; Schneider, Claudio; Petralia, Salvatore; Cavallaro, Sebastiano

    2014-01-01

    In the last decades, molecular biology has moved from gene-by-gene analysis to more complex studies using a genome-wide scale. Thanks to high-throughput genomic technologies, such as microarrays and next-generation sequencing, a huge amount of information has been generated, expanding our knowledge on the genetic basis of various diseases. Although some of this information could be transferred to clinical diagnostics, the technologies available are not suitable for this purpose. In this review, we will discuss the drawbacks associated with the use of traditional DNA microarrays in diagnostics, pointing out emerging platforms that could overcome these obstacles and offer a more reproducible, qualitative and quantitative multigenic analysis. New miniaturized and automated devices, called Lab-on-Chip, begin to integrate PCR and microarray on the same platform, offering integrated sample-to-result systems. The introduction of this kind of innovative devices may facilitate the transition of genome-based tests into clinical routine.

  13. Field protocols for the genomic era

    Directory of Open Access Journals (Sweden)

    N Bulatova

    2009-08-01

    Full Text Available For many decades karyotype was the only source of overall genomic information obtained from species of mammal. However, approaches have been developed in recent years to obtain molecular and ultimately genomic information directly from the extracted DNA of an organism. Molecular data have accumulated hugely for mammalian taxa. The growing volume of studies should motivate field researchers to collect suitable samples for molecular analysis from various species across all their ranges. This is the reason why we here include a molecular sampling procedure within a field work protocol, which also includes more traditional (including cytogenetic techniques. In this way we hope to foster the development of molecular and genomic studies in non-standard wild mammals.

  14. Trichinosis: Epidemiology in Thailand

    Institute of Scientific and Technical Information of China (English)

    Natthawut Kaewpitoon; Soraya Jatesadapattaya Kaewpitoon; Chutikan Philasri; Ratana Leksomboon; Chanvit Maneenin; Samaporn Sirilaph; Prasit Pengsaa

    2006-01-01

    Trichinosis is one of the most common food-borne parasitic zoonoses in Thailand and many outbreaks are reported each year. This paper reviews the history, species,and epidemiology of the disease and food habits of the people with an emphasis on the north, northeast, central and south regions of Thailand. The earliest record of trichinosis in Thailand was in 1962 in the Mae Sariang District, Mae Hong Son Province. Since then, about 130 outbreaks have been reported involving 7392 patients and 97 deaths (1962-2005). The highest number of cases, 557, was recorded in 1983. The annual epidemiological surveillance reports of the Bureau of Epidemiology,Department of Disease Control, Ministry of Public Health,Thailand, show that trichinosis cases increased from 61 in 1997 to 351 in 1998.In contrast to these figures, the number of reported cases decreased to 16 in 1999 and 128 cases in 2000. There was no record of trichinosis in 2001, but then the figures for 2002, 2003 and 2004 were 289, 126 and 212 respectively. The infected patients were mostly in the 35-44 years age group and the disease occurred more frequently in men than women at a ratio of 1.7-2.0:1. There were 84 reported cases of trichinosis in Chiang Rai, Nan, Chiang Mai, Si Sa ket,Nakhon Phanom, Kalasin, Nakhon Ratchasima, Nakhon Nayok, Nakhon Pathom and Surat Thani, provinces located in different parts of Thailand in 2005. The outbreaks were more common in the northern areas, especially in rural areas where people ate raw or under-cooked pork and/or wild animals. This indicates the need for health education programs to prevent and control trichinosis as soon as possible in the high-risk areas.

  15. Epidemiology of tuberculosis immunology.

    Science.gov (United States)

    Fox, G J; Menzies, D

    2013-01-01

    Immunological impairment plays a major role in the epidemiology of TB. Globally, the most common causes of immunological impairment are malnutrition, diabetes, HIV/AIDS, aging, and smoking. With the notable exception of HIV, each factor leads to relatively mild immunological impairment in individuals. However, as these conditions affect a significant proportion of the population, they contribute substantially to the incidence of TB at a global scale. Understanding immunological impairment is central to understanding the global TB pandemic, and vital to the development of effective disease control strategies.

  16. Epidemiology of Brain Tumors.

    Science.gov (United States)

    McNeill, Katharine A

    2016-11-01

    Brain tumors are the commonest solid tumor in children, leading to significant cancer-related mortality. Several hereditary syndromes associated with brain tumors are nonfamilial. Ionizing radiation is a well-recognized risk factor for brain tumors. Several industrial exposures have been evaluated for a causal association with brain tumor formation but the results are inconclusive. A casual association between the common mutagens of tobacco, alcohol, or dietary factors has not yet been established. There is no clear evidence that the incidence of brain tumors has changed over time. This article presents the descriptive epidemiology of the commonest brain tumors of children and adults.

  17. Worldwide epidemiology of fibromyalgia.

    Science.gov (United States)

    Queiroz, Luiz Paulo

    2013-08-01

    Studying the epidemiology of fibromyalgia (FM) is very important to understand the impact of this disorder on persons, families and society. The recent modified 2010 classification criteria of the American College of Rheumatology (ACR), without the need of tender points palpation, allows that larger and nationwide surveys may be done, worldwide. This article reviews the prevalence and incidence studies done in the general population, in several countries/continents, the prevalence of FM in special groups/settings, the association of FM with some sociodemographic characteristics of the population, and the comorbidity of FM with others disorders, especially with headaches.

  18. Epidemiologia social Social epidemiology

    Directory of Open Access Journals (Sweden)

    Rita Barradas Barata

    2005-03-01

    Full Text Available Este artigo trata da emergência da epidemiologia social concomitantemente ao surgimento da epidemiologia como disciplina científica, destacando as condições teóricas e epistemológicas desse aparecimento. Em seguida são enfocadas as razões para o declínio dessa abordagem, assim como para seu ressurgimento na década de 60, no século XX. São apresentadas as diferentes correntes teóricas atualmente vigentes na epidemiologia social, destacando as características gerais e as limitações de cada uma delas. Especial atenção é dada às seguintes formulações: a eco-epidemiologia proposta por Mervin Susser, a teoria do capital social, a perspectiva do curso de vida, a teoria da produção social da doença e a teoria ecosocial elaborada por Nancy Krieger. O panorama traçado pretende demonstrar a vitalidade dessa abordagem, bem como indicar a diversidade de aspectos em seu interior. Para finalizar são apontados alguns dilemas e desafios.This paper reviews the latest trends in social epidemiology. It analyzes the emergence of epidemiology as a scientific discipline in the nineteenth century focusing on the main characteristics of the episteme of the period. This paper also analyzes the decline of the social approach in the beginning of the twentieth century and the resurgence of social interest in the sixties. The multiple approaches of social epidemiology currently adopted are commented. The study also emphasizes Susser's proposal of ecoepidemiology, describing its characteristics and pointing out limitations. Next, there is a discussion of the social capital theory and its potentialities for epidemiological studies. The life course perspective is also analyzed, mentioning its psychological and material versions. Latin America's social production of the health and disease process is presented along with an overview of Nancy Krieger's social ecoepidemiology. Finally, some dilemmas and challenges for the future are presented.

  19. Enabling Graph Appliance for Genome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Rina [ORNL; Graves, Jeffrey A [ORNL; Lee, Sangkeun (Matt) [ORNL; Sukumar, Sreenivas R [ORNL; Shankar, Mallikarjun [ORNL

    2015-01-01

    In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

  20. Climate change adaptation accounting for huge uncertainties in future projections - the case of urban drainage

    Science.gov (United States)

    Willems, Patrick

    2015-04-01

    Hydrological design parameters, which are currently used in the guidelines for the design of urban drainage systems (Willems et al., 2013) have been revised, taking the Flanders region of Belgium as case study. The revision involved extrapolation of the design rainfall statistics, taking into account the current knowledge on future climate change trends till 2100. Uncertainties in these trend projections have been assessed after statistically analysing and downscaling by a quantile perturbation tool based on a broad ensemble set of climate model simulation results (44 regional + 69 global control-scenario climate model run combinations for different greenhouse gas scenarios). The impact results of the climate scenarios were investigated as changes to rainfall intensity-duration-frequency (IDF) curves. Thereafter, the climate scenarios and related changes in rainfall statistics were transferred to changes in flood frequencies of sewer systems and overflow frequencies of storage facilities. This has been done based on conceptual urban drainage models. Also the change in storage capacity required to exceed a given overflow return period, has been calculated for a range of return periods and infiltration or throughflow rates. These results were used on the basis of the revision of the hydraulic design rules of urban drainage systems. One of the major challenges while formulating these policy guidelines was the consideration of the huge uncertainties in the future climate change projections and impact assessments; see also the difficulties and pitfalls reported by the IWA/IAHR Joint Committee on Urban Drainage - Working group on urban rainfall (Willems et al., 2012). We made use of the risk concept, and found it a very useful approach to deal with the high uncertainties. It involves an impact study of the different climate projections, or - for practical reasons - a reduced set of climate scenarios tailored for the specific type of impact considered (urban floods in our

  1. Huge Congenital Segmental Dilatation of the Sigmoid Colon in a Neonate: A "Rarity to Meet" and a "Challenge to Treat".

    Science.gov (United States)

    Kaiser, Margarita; Castellani, Christoph; Singer, Georg; Marterer, Robert; Ratschek, Manfred; Till, Holger

    2016-01-01

    Only ten cases of neonatal congenital segmental dilatation (CSD) of the colon have been described so far. We present a full-term female newborn with trisomy 21, ventricular septal defect, and gross abdominal distension. Plain abdominal radiographs revealed a huge cystic lesion occupying the left hemiabdomen. Upon laparotomy on day 4 a CSD of the distal sigmoid and proximal rectum was confirmed and resected. The proximal colon was exteriorized and the distal part closed as a Hartmann pouch. Histology confirmed a huge segmental dilatation of the sigmoid without dysganglionosis or pseudodiverticula, but normal intestinal architecture. After correction of the ventricular septal defect a low rectal end-to-end anastomosis could be performed at an age of 5 months. The postoperative course was uneventful. CSD of the sigmoid colon is extremely "rare to meet" and a "challenge to treat" in the newborn period, but clinical awareness of this entity prompts pediatric surgical success.

  2. Surgical technique for single-port laparoscopy in huge ovarian tumors: SW Kim's technique and comparison to laparotomy.

    Science.gov (United States)

    Kim, Jeong Sook; Lee, In Ok; Eoh, Kyung Jin; Chung, Young Shin; Lee, Inha; Lee, Jung-Yun; Nam, Eun Ji; Kim, Sunghoon; Kim, Young Tae; Kim, Sang Wun

    2017-03-01

    This study aimed to introduce a method to remove huge ovarian tumors (≥15 cm) intact with single-port laparoscopic surgery (SPLS) using SW Kim's technique and to compare the surgical outcomes with those of laparotomy. Medical records were retrospectively reviewed for patients who underwent either SPLS (n=21) with SW Kim's technique using a specially designed 30×30-cm(2)-sized 3XL LapBag or laparotomy (n=22) for a huge ovarian tumor from December 2008 to May 2016. Perioperative surgical outcomes were compared. In 19/21 (90.5%) patients, SPLS was successfully performed without any tumor spillage or conversion to multi-port laparoscopy or laparotomy. There was no significant difference in patient characteristics, including tumor diameter and total operation time, between both groups. The postoperative hospital stay was significantly shorter for the SPLS group than for the laparotomy group (median, 2 [1 to 5] vs. 4 [3 to 17] days; Phuge ovarian tumors.

  3. Concordance and discordance of sequence survey methods for molecular epidemiology.

    Science.gov (United States)

    Castro-Nallar, Eduardo; Hasan, Nur A; Cebula, Thomas A; Colwell, Rita R; Robison, Richard A; Johnson, W Evan; Crandall, Keith A

    2015-01-01

    The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.

  4. Concordance and discordance of sequence survey methods for molecular epidemiology

    Directory of Open Access Journals (Sweden)

    Eduardo Castro-Nallar

    2015-02-01

    Full Text Available The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes, and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.

  5. Global epidemiology of sporotrichosis.

    Science.gov (United States)

    Chakrabarti, Arunaloke; Bonifaz, Alexandro; Gutierrez-Galhardo, Maria Clara; Mochizuki, Takashi; Li, Shanshan

    2015-01-01

    Sporotrichosis is an endemic mycosis caused by the dimorphic fungus Sporothrix schenckii sensu lato. It has gained importance in recent years due to its worldwide prevalence, recognition of multiple cryptic species within the originally described species, and its distinctive ecology, distribution, and epidemiology across the globe. In this review, we describe the current knowledge of the taxonomy, ecology, prevalence, molecular epidemiology, and outbreaks due to S. schenckii sensu lato. Despite its omnipresence in the environment, this fungus has remarkably diverse modes of infection and distribution patterns across the world. We have delved into the nuances of how sporotrichosis is intimately linked to different forms of human activities, habitats, lifestyles, and environmental and zoonotic interactions. The purpose of this review is to stimulate discussion about the peculiarities of this unique fungal pathogen and increase the awareness of clinicians and microbiologists, especially in regions of high endemicity, to its emergence and evolving presentations and to kindle further research into understanding the unorthodox mechanisms by which this fungus afflicts different human populations.

  6. The Epidemiology of Sarcopenia.

    Science.gov (United States)

    Dodds, Richard Matthew; Roberts, Helen Clare; Cooper, Cyrus; Sayer, Avan Aihie

    2015-01-01

    The aim of this review is to describe the epidemiology of sarcopenia, specifically prevalence, health outcomes, and factors across the life course that have been linked to its development. Sarcopenia definitions involve a range of measures (muscle mass, strength, and physical performance), which tend to decline with age, and hence sarcopenia becomes increasingly prevalent with age. Less is known about prevalence in older people in hospital and care homes, although it is likely to be higher than in community settings. The range of measures used, and the cutpoints suggested for each, presents a challenge for comparing prevalence estimates between studies. The importance of sarcopenia is highlighted by the range of adverse health outcomes that strength and physical performance (and to a lesser extent, muscle mass) have been linked to. This is shown most strikingly by the finding of increased all-cause mortality rates among those with weaker grip strength and slower gait speed. A life course approach broadens the window for our understanding of the etiology of sarcopenia and hence the potential intervention. An example is physical activity, with increased levels across midadulthood appearing to increase muscle mass and strength in early old age. Epidemiologic studies will continue to make an important contribution to our understanding of sarcopenia and possible avenues for intervention and prevention.

  7. Plague in the genomic area.

    Science.gov (United States)

    Drancourt, M

    2012-03-01

    With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries. © 2012 The Author. Clinical Microbiology and Infection © 2012 European Society of

  8. Using tiltmeters for early warning of tsunamis, generated by huge submarine landslides. A case study for Spitsbergen.

    OpenAIRE

    Sascha Brune; Andrey Babeyko; Stephan V. Sobolev

    2007-01-01

    A submarine landslide west of Spitsbergen could induce a destructive tsunami in the North Atlantic. Here we suggest an effective tool for early warning of tsunamis generated by huge underwater landslides. The method is based on the fact that a displacement of ~1000 km3 of sediment produces a permanent and detectable deformation of earth's lithosphere. We numerically model the ground tilting imposed by the hypothetical Spitsbergen landslide. Virtual inclinometers, positioned at the three dist...

  9. Isolated huge aneurysm of the left main coronary artery in a 22-year-old patient with type 1 neurofibromatosis.

    Science.gov (United States)

    Pontailler, Margaux; Vilarem, Didier; Paul, Jean-François; Deleuze, Philippe H

    2015-03-01

    A 22-year-old patient with neurofibromatosis type 1 presented with acute chest pain. A computed tomography scan and coronary angiography revealed a partially thrombosed huge aneurysm of the left main coronary artery. Despite medical treatment, the patient's angina recurred. The patient underwent a coronary bypass grafting operation and surgical exclusion of the aneurysm. Postoperative imaging disclosed good permeability of the 3 coronary artery bypass grafts and complete thrombosis of the excluded aneurysm.

  10. The prostatic utricle cyst with huge calculus and hypospadias: A case report and a review of the literature

    OpenAIRE

    Wang, Weigang; WANG, YUANTAO; Zhu, Dechun; Yan, Pengfei; Dong, Biao; Zhou, Honglan

    2015-01-01

    Prostatic utricle cysts with calculus and hypospadias are rare. There are a few reported cases. We present a case of a prostatic utricle cyst with huge calculus in a 25-year-old male. He had a history of left cryptorchidism and surgery for penoscrotal hypospadias in his infancy. He was referred for frequent micturition, urgency of urination, urine pain, terminal hematuria, and dysuria. A computed tomography (CT) revealed a retrovesical cystic lesion of low density, showing a 5 × 5-cm calcific...

  11. Huge Left Ventricular Thrombus and Apical Ballooning associated with Recurrent Massive Strokes in a Septic Shock Patient

    Directory of Open Access Journals (Sweden)

    Hyun-Jung Lee

    2016-02-01

    Full Text Available The most feared complication of left ventricular thrombus (LVT is the occurrence of systemic thromboembolic events, especially in the brain. Herein, we report a patient with severe sepsis who suffered recurrent devastating embolic stroke. Transthoracic echocardiography revealed apical ballooning of the left ventricle with a huge LVT, which had not been observed in chest computed tomography before the stroke. This case emphasizes the importance of serial cardiac evaluation in patients with stroke and severe medical illness.

  12. Huge saphenous vein graft aneurysm presenting as non-ST elevation myocardial infarction and compressing the heart.

    Science.gov (United States)

    Zencir, Cemil; Akpek, Mahmut; Onay, Sevil; Selvi, Mithat

    2016-09-01

    Coronary artery bypass grafting (CABG) surgery maintains an important role in the treatment of coronary artery disease. The huge saphenous vein graft aneurysm (HSVGA) is rare and occurs as a late complication after CABG. Here, we reported a case of HSVGA presenting as non-ST elevation myocardial infarction. Copyright © 2015 Cardiological Society of India. Published by Elsevier B.V. All rights reserved.

  13. Long-Term Outcome After Resection of Huge Hepatocellular Carcinoma ≥ 10 cm: Single-Institution Experience with 471 Patients.

    Science.gov (United States)

    Hwang, Shin; Lee, Young-Joo; Kim, Ki-Hun; Ahn, Chul-Soo; Moon, Deok-Bog; Ha, Tae-Yong; Song, Gi-Won; Jung, Dong-Hwan; Lee, Sung-Gyu

    2015-10-01

    Tumor recurrence is very common after resection of huge hepatocellular carcinoma (HCC). This study intended to evaluate early recurrence and long-term outcomes in patients with huge HCC ≥ 10 cm after primary resection and treatment of recurrence. Recurrence and survival outcomes were retrospectively evaluated in 471 patients with huge HCCs who underwent resection between January 2000 and April 2012. Mean tumor diameter was 13.6 ± 3.1 cm, with 93 % of patients having single tumors. Anatomic and R0 resection rates were 91.1 and 89.4 %, respectively. Perioperative mortality rate was 1.7 %. Tumor recurrence and patient survival rates were 62.2 and 69.2 % at 1 year and 76.0 and 35.5 % at 5 years, respectively. Of patients with recurrence, 92.5 % received specific treatment. Median patient survival period after initial intrahepatic recurrence was 16 months. Tumor volume did not affect recurrence or survival outcomes. Independent risk factors for tumor recurrence and patient survival were serum alpha-fetoprotein ≥ 100 ng/mL, hypermetabolic uptake on positron emission tomography, satellite nodules, and microvascular invasion. These four factors were used to develop a risk prediction model, in which 1-year HCC recurrence rates in patients with 0, 1, 2, 3, and 4 risk factors were 18.7, 30.3, 58.7, 79.0, and 92.1 %, respectively, and their 1-year patient survival rates were 100, 97.0, 75.5, 63.9, and 42.1 %, respectively. In patients with huge HCCs, hepatic resection with active recurrence treatment resulted in improved long-term survival. Our 4-factor risk prediction model appears to contribute to quantitative postoperative risk estimation for early HCC recurrence and patient survival in patients with HCC ≥ 10 cm.

  14. Imbalance in systemic inflammation and immune response following transarterial chemoembolization potentially increases metastatic risk in huge hepatocellular carcinoma.

    Science.gov (United States)

    Xue, Tong-Chun; Jia, Qing-An; Ge, Ning-Ling; Chen, Yi; Zhang, Bo-Heng; Ye, Sheng-Long

    2015-11-01

    Inflammation plays a critical role in tumor metastasis. However, few inflammation-related biomarkers are currently available to predict the risk of metastasis for advanced hepatocellular carcinoma (HCC). Using huge tumors (diameter >10 cm) as a model, we evaluated the potential risk of pre- and post-treatment inflammatory responses in the development of metastasis of HCC patients undergoing transarterial chemoembolization (TACE). A logistic regression model was used to analyze the risk factors. One hundred and sixty-five patients with huge HCC were enrolled in the study. Metastases were identified in 25.5% (42/165) patients by imaging evaluation post-TACE. Neutrophils increased, whereas lymphocytes decreased significantly post-TACE. Univariate analysis showed that high post-treatment neutrophil-to-lymphocyte ratio (NLR; p = 0.003), low post-treatment lymphocyte count (p = 0.047), and high baseline NLR (p = 0.100) were potential risk factors for metastasis. Further, multivariate analysis showed that high post-treatment NLR, but not pre-treatment NLR, was an independent risk factor for metastasis; this was confirmed by receiver operating characteristic curve analysis. Post-treatment NLR, however, had no correlation to tumor response and overall survival of patients. In conclusion, post-treatment NLR but not pre-treatment NLR independently increases the risk of metastasis in huge HCC. Our findings suggest the potential contribution of treatment-related inflammation to metastasis in advanced HCC.

  15. Totally inverted cervix due to a huge prolapsed cervical myoma simulating chronic non-puerperal uterine inversion.

    Science.gov (United States)

    Turhan, Nilgun; Simavli, Serap; Kaygusuz, Ikbal; Kasap, Burcu

    2014-01-01

    Inversion of the uterus is an extremely rare complication of the non-puerperal period and is commonly caused by benign submucous, especially fundal, leiomyomas. A case of a totally inverted cervix due to a prolapsed huge cervical leiomyoma mimicking chronic non-puerperal uterine inversion in a perimenopausal woman is presented. A 52-year-old perimenopausal woman was admitted to our clinic with an ulcerated, necrotic, infected and swollen prolapsed mass. Gynecologic history revealed that she was advised myomectomy because of her cervical myoma 2 years ago but she refused to have an operation as she believed that her positive thoughts would shrink the myoma. Presumed diagnosis before surgery was chronic non-puerperal uterine inversion. An intraoperative diagnosis was totally inverted cervix due to a huge cervical leiomyoma. Vaginal hysterectomy without adnexectomy, was performed. This is the first case in the literature which a totally inverted cervix due to a prolapsed huge cervical leiomyoma. Cervical fibroids can grow in perimenopausal period and in extremely rare cases can cause total cervical inversion. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. [Analysis of efficacy and prognostic factors of transarterial chemoembolization combined with multimodality therapy for huge hepatocellular carcinoma].

    Science.gov (United States)

    Chang, Zhongfei; Wang, Maoqiang; Liu, Fengyong; Duan, Feng; Wang, Zhijun; Song, Peng

    2014-01-01

    The aim of this study was to evaluate the efficacy, survival and prognosis of transarterial chemoembolization (TACE) alone and TACE in combination with multimodality therapy for huge hepatocellular carcinoma. A retrospective analysis was conducted in 115 patients with huge hepatocellular carcinoma treated in our hospital from August 2008 to January 2012. Among them, 72 patients were treated by TACE alone (TACE group) and 43 patients by TACE plus multimodality therapy (TACE-combined treatment group). Their clinicopathological data and survival were analyzed. The median follow-up of the 115 cases was 24 months (range 1-40 months). The 1-, 2-, and 3-year overall survival (OS) rates for the TACE group were 60.4,% 23.3% and 9.8%, respectively, and 39 months, 78.1%, 43.3% and 36.8%, respectively, for the combined treatment group (P 0.05 for all), while multimodality therapy, Child's grading, ECOG scores, distant metastasis, and portal vein tumor thrombus were significantly related to the overall survival. Moreover, the Cox multivariate survival analysis revealed that therapy and ECOG scores were independent prognostic indicators (P huge hepatocellular carcinoma. Multimodality therapy and ECOG scores are independent prognostic indicators for the patients.

  17. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  18. Planning for the Future of Epidemiology in the Era of Big Data and Precision Medicine.

    Science.gov (United States)

    Khoury, Muin J

    2015-12-15

    We live in the era of genomics and big data. Evaluating the impact on health of large-scale biological, social, and environmental data is an emerging challenge in the field of epidemiology. In the past 3 years, major discussions and plans for the future of epidemiology, including with several recommendations for actions to transform the field, have been launched by 2 institutes within the National Institutes of Health. In the present commentary, I briefly explore the themes of these recommendations and their effects on leadership, resources, cohort infrastructure, and training. Ongoing engagement within the epidemiology community is needed to determine how to shape the evolution of the field and what truly matters for changing population health. We also need to assess how to leverage existing epidemiology resources and develop new studies to improve human health. Readers are invited to examine these recommendations, consider others that might be important, and join in the conversation about the future of epidemiology.

  19. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  20. CEDR: Comprehensive Epidemiologic Data Resource

    Energy Technology Data Exchange (ETDEWEB)

    1993-08-01

    The Department of Energy (DOE) and its predecessor agencies have a long history of epidemiologic research programs. The main focus of these programs has been the Health and Mortality Study of the DOE work force. This epidemiologic study began in 1964 with a feasibility study of workers at the Hanford facility. Studies of other populations exposed to radiation have also been supported, including the classic epidemiologic study of radium dial painters and studies of atomic bomb survivors. From a scientific perspective, these epidemiologic research program have been productive, highly credible, and formed the bases for many radiological protection standards. Recently, there has been concern that, although research results were available, the data on which these results were based were not easily obtained by interested investigators outside DOE. Therefore, as part of an effort to integrate and broaden access to its epidemiologic information, the DOE has developed the Comprehensive Epidemiologic Data Resource (CEDR) Program. Included in this effort is the development of a computer information system for accessing the collection of CEDR data and its related descriptive information. The epidemiologic data currently available through the CEDAR Program consist of analytic data sets, working data sets, and their associated documentation files. In general, data sets are the result of epidemiologic studies that have been conducted on various groups of workers at different DOE facilities during the past 30 years.

  1. The new epidemiology of nephrolithiasis.

    Science.gov (United States)

    Shoag, Jonathan; Tasian, Greg E; Goldfarb, David S; Eisner, Brian H

    2015-07-01

    Historically nephrolithiasis was considered a disease of dehydration and abnormal urine composition. However, over the past several decades, much has been learned about the epidemiology of this disease and its relation to patient demographic characteristics and common systemic diseases. Here we review the latest epidemiologic studies in the field.

  2. Epidemiology of infections in women.

    Science.gov (United States)

    Risser, Jan M H; Risser, William L; Risser, Amanda L

    2008-12-01

    This article describes the epidemiologic profiles of sexually transmitted infections seen in US women. We present a brief description of the infectious agent, describe the epidemiology of the infection among women in terms of race/ethnicity and age (if those data are available), and present what is known about the behavioral risk factors associated with acquisition.

  3. Applying molecular epidemiology in pediatric leukemia.

    Science.gov (United States)

    Schiffman, Joshua D

    2016-02-01

    Molecular epidemiology is the study of genetic and environmental risk for disease, with much effort centered on cancer. Childhood leukemia occurs in nearly a third of all patients newly diagnosed with pediatric cancer. only a small percentage of these new cases of childhood leukemia are associated with high penetrant hereditary cancer syndromes. Childhood leukemia, especially acute lymphoblastic leukemia, has been associated with a dysregulated immune system due to delayed infectious exposure at a young age. Identical twins with childhood leukemia suggest that acute lymphoblastic leukemia begins in utero and that the concordant presentation is due to a shared preleukemia subclone via placental transfer. Investigation of single nucleotide polymorphisms within candidate genes find that leukemia risk may be attributed to population-based polymorphisms affecting folate metabolism, xenobiotic metabolism, DNA repair, immunity, and B-cell development. More recently, genome-wide association studies for leukemia risk has led investigators to genes associated with B-cell development. When describing leukemia predisposition due to hereditary cancer syndromes, the following 6 categories become apparent on the basis of biology and clinical presentation: (1) genetic instability/DNA repair syndromes, (2) cell cycle/differentiation syndromes, (3) bone marrow failure syndromes, (4) telomere maintenance syndromes, (5) immunodeficiency syndromes, and (6) transcription factor syndromes and pure familial leukemia. understanding the molecular epidemiology of childhood leukemia can affect the treatment and tumor surveillance strategies for these high risk patients and their family members.

  4. Psoriasis: epidemiology, natural history, and differential diagnosis

    Directory of Open Access Journals (Sweden)

    Basko-Plluska JL

    2012-09-01

    Full Text Available Juliana L Basko-Plluska, Vesna Petronic-RosicDepartment of Medicine, Section of Dermatology, University of Chicago, Chicago, IL, USAAbstract: Psoriasis is a chronic, immune-mediated, inflammatory disease which affects primarily the skin and joints. It occurs worldwide, but its prevalence varies considerably between different regions of the world. Genetic susceptibility as well as environmental factors play an important role in determining the development and prognosis of psoriasis. Genome-wide association studies have identified many genetic loci as potential psoriasis susceptibility regions, including PSORS1 through PSORS7. Histocompatibility antigen (HLA studies have also identified several HLA antigens, with HLA-Cw6 being the most frequently associated antigen. Epidemiological studies identified several modifiable risk factors that may predispose individuals to developing psoriasis or exacerbate pre-existing disease. These include smoking, obesity, alcohol consumption, diet, infections, medications and stressful life events. The exact mechanism by which they trigger psoriasis remains to be elucidated; however, existing data suggest that they are linked through Th1-mediated immunological pathways. The natural history of psoriasis varies depending on the clinical subtype as well as special circumstances, including pregnancy and HIV infection. In general, psoriasis is a chronic disease with intermittent remissions and exacerbations. The differential diagnosis is vast and includes many other immune-mediated, inflammatory disorders.Keywords: psoriasis, epidemiology, natural history, differential diagnosis

  5. Epidemiological evidence in forensic pharmacovigilance.

    Science.gov (United States)

    Persaud, Nav; Healy, David

    2012-01-01

    Until recently epidemiological evidence was not regarded as helpful in determining cause and effect. It generated associations that then had to be explained in terms of bio-mechanisms and applied to individual patients. A series of legal cases surrounding possible birth defects triggered by doxylamine (Bendectin) and connective tissue disorders linked to breast implants made it clear that in some instances epidemiological evidence might have a more important role, but the pendulum swung too far so that epidemiological evidence has in recent decades been given an unwarranted primacy, partly perhaps because it suits the interests of certain stakeholders. Older and more recent epidemiological studies on doxylamine and other antihistamines are reviewed to bring out the ambiguities and pitfalls of an undue reliance on epidemiological studies.

  6. [Epidemiology of urinary lithiasis].

    Science.gov (United States)

    Joual, A; Rais, H; Rabii, R; el Mrini, M; Benjelloun, S

    1997-01-01

    The objective of this study was to analyse the epidemiological profile of urinary stones based on one thousand cases observed in our institution over a 10-year period. The mean age of the patients was 45 years and two-thirds of patients were males. The kidney was the commonest site of stones, in 57.8% of cases. The stone was radiopaque in 86.4% of cases and was a staghorn calculus in 12.2% of cases. An associated renal malformation was observed in 10.4% of cases. Urinary stones is therefore a common disease, essentially observed in a young population and characterized by recurrence. It therefore constitutes a public health problem and prevention consists of detecting recurrences and treating stone-inducing factors.

  7. Epidemiology of Lyme Disease

    Directory of Open Access Journals (Sweden)

    Dennis J White

    1991-01-01

    Full Text Available Investigation of the epidemiology of Lyme disease depends upon information generated from several sources. Human disease surveillance can be conducted by both passive and active means involving physicians, public health agencies and laboratories. Passive and active tick surveillance programs can document the extent of tick-borne activity, identify the geographic range of potential vector species, and determine the relative risk of exposure to Lyme disease in specific areas. Standardized laboratory services can play an important role in providing data. Epidemiologists can gain a better understanding of Lyme disease through the collection of data from such programs. The interpretation of data and provision of information to the medical and general communities are important functions of public health agencies.

  8. [Epidemiology of tuberculosis].

    Science.gov (United States)

    Mjid, M; Cherif, J; Ben Salah, N; Toujani, S; Ouahchi, Y; Zakhama, H; Louzir, B; Mehiri-Ben Rhouma, N; Beji, M

    2015-01-01

    Tuberculosis is a contagious disease caused by Mycobacterium tuberculosis. It represents, according to World Health Organization (WHO), one of the most leading causes of death worldwide. With nearly 8 million new cases each year and more than 1 million deaths per year, tuberculosis is still a public health problem. Despite of the decrease in incidence, morbidity and mortality remain important partially due to co-infection with human immunodeficiency virus and emergence of resistant bacilli. All WHO regions are not uniformly affected by TB. Africa's region has the highest rates of morbidity and mortality. The epidemiological situation is also worrying in Eastern European countries where the proportion of drug-resistant tuberculosis is increasing. These regional disparities emphasize to develop screening, diagnosis and monitoring to the most vulnerable populations. In this context, the Stop TB program, developed by the WHO and its partner's, aims to reduce the burden of disease in accordance with the global targets set for 2015.

  9. Cancer epidemiology of woodworking.

    Science.gov (United States)

    Mohtashamipur, E; Norpoth, K; Lühmann, F

    1989-01-01

    The literature published between 1965 and 1989 on the cancer epidemiology of woodworking in furniture industries and carpentry shops in 17 countries is reviewed. Included are some unpublished data obtained through personal communication with epidemiologists or collected from doctoral dissertations. Of 5,785 cases with sino-nasal cancers, about 23% were found to be woodworkers. Dusty jobs, especially wood processing using high-speed machines, are mainly associated with the enhanced incidence of nasal adenocarcinomas. The latency periods of the latter tumors ranged from 7 to 69 years in five European countries. A variety of neoplasias of the respiratory, digestive, and urinary tracts as well as the hemopoietic and lymphatic systems, including Hodgkin's disease are reported to be significantly associated with occupational exposure to wood dust. These data suggest that the exposure to some types of wood dust might cause a systemic rather than local neoplastic disorder.

  10. The Epidemiology of Sarcoma

    Directory of Open Access Journals (Sweden)

    Burningham Zachary

    2012-10-01

    Full Text Available Abstract Sarcomas account for over 20% of all pediatric solid malignant cancers and less than 1% of all adult solid malignant cancers. The vast majority of diagnosed sarcomas will be soft tissue sarcomas, while malignant bone tumors make up just over 10% of sarcomas. The risks for sarcoma are not well-understood. We evaluated the existing literature on the epidemiology and etiology of sarcoma. Risks for sarcoma development can be divided into environmental exposures, genetic susceptibility, and an interaction between the two. HIV-positive individuals are at an increased risk for Kaposi’s sarcoma, even though HHV8 is the causative virus. Radiation exposure from radiotherapy has been strongly associated with secondary sarcoma development in certain cancer patients. In fact, the risk of malignant bone tumors increases as the cumulative dose of radiation to the bone increases (p for trend

  11. Epidemiology of acne vulgaris.

    Science.gov (United States)

    Bhate, K; Williams, H C

    2013-03-01

    Despite acne being an almost universal condition in younger people, relatively little is known about its epidemiology. We sought to review what is known about the distribution and causes of acne by conducting a systematic review of relevant epidemiological studies. We searched Medline and Embase to the end of November 2011. The role of Propionibacterium acnes in pathogenesis is unclear: antibiotics have a direct antimicrobial as well as an anti-inflammatory effect. Moderate-to-severe acne affects around 20% of young people and severity correlates with pubertal maturity. Acne may be presenting at a younger age because of earlier puberty. It is unclear if ethnicity is truly associated with acne. Black individuals are more prone to postinflammatory hyperpigmentation and specific subtypes such as 'pomade acne'. Acne persists into the 20s and 30s in around 64% and 43% of individuals, respectively. The heritability of acne is almost 80% in first-degree relatives. Acne occurs earlier and is more severe in those with a positive family history. Suicidal ideation is more common in those with severe compared with mild acne. In the U.S.A., the cost of acne is over 3 billion dollars per year in terms of treatment and loss of productivity. A systematic review in 2005 found no clear evidence of dietary components increasing acne risk. One small randomized controlled trial showed that low glycaemic index (GI) diets can lower acne severity. A possible association between dairy food intake and acne requires closer scrutiny. Natural sunlight or poor hygiene are not associated. The association between smoking and acne is probably due to confounding. Validated core outcomes in future studies will help in combining future evidence.

  12. Genomic Epidemiology of a Major Mycobacterium tuberculosis Outbreak

    DEFF Research Database (Denmark)

    Folkvardsen, Dorte Bek; Norman, Anders; Andersen, Åse Bengård

    2017-01-01

    Since 1992, Denmark has documented the largest outbreak of tuberculosis in Scandinavia ascribed to a single genotype, termed C2/1112-15. As of spring 2017, the International Reference Laboratory of Mycobacteriology in Copenhagen has collected and identified isolates from more than a thousand cases...

  13. Genomics of human longevity.

    Science.gov (United States)

    Slagboom, P E; Beekman, M; Passtoors, W M; Deelen, J; Vaarhorst, A A M; Boer, J M; van den Akker, E B; van Heemst, D; de Craen, A J M; Maier, A B; Rozing, M; Mooijaart, S P; Heijmans, B T; Westendorp, R G J

    2011-01-12

    In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences on human longevity are expected to be much more complex. Strikingly however, beneficial metabolic and cellular features of long-lived families resemble those in animals for whom the lifespan is extended by applying genetic manipulation and, especially, dietary restriction. Candidate gene studies in humans support the notion that human orthologues from longevity genes identified in lower species do contribute to longevity but that the influence of the genetic variants involved is small. Here we discuss how an integration of novel study designs, labour-intensive biobanking, deep phenotyping and genomic research may provide insights into the mechanisms that drive human longevity and healthy ageing, beyond the associations usually provided by molecular and genetic epidemiology. Although prospective studies of humans from the cradle to the grave have never been performed, it is feasible to extract life histories from different cohorts jointly covering the molecular changes that occur with age from early development all the way up to the age at death. By the integration of research in different study cohorts, and with research in animal models, biological research into human longevity is thus making considerable progress.

  14. Parsing of genomic graffiti

    Energy Technology Data Exchange (ETDEWEB)

    Tibbetts, C.; Golden, J. III; Torgersen, D. [Vanderbilt Univ. School of Engineering, Nashville, TN (United States)

    1996-12-31

    A focal point of modern biology is investigation of wide varieties of phenomena at the level of molecular genetics. The nucleotide sequences of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) define the ultimate resolution of this reductionist approach to understand the determinants of heritable traits. The structure and function of genes, their composite genomic organization, and their regulated expression have been studied in systems representing every class of organism. Many human diseases or pathogenic syndromes can be directly attributed to inherited defects in either the regulated expression, or the quality of the products of specific genes. Genetic determinants of susceptibility to infectious agents or environmental hazards are amply documented. Mapping and sequencing of the DNA molecules encoding human genes have provided powerful technology for pharmaceutical bioengineering and forensic investigations. From an alternative perspective, we may anticipate that voluminous archives of singular DNA sequences alone will not suffice to define and understand the functional determinants of genome organization, allelic diversity and evolutionary plasticity of living organisms. New insights will accumulate pertaining to human evolutionary origins and relationships of human biology to models based on other mammals. Investigators of population genetics and epidemiology now exploit the technology of molecular genetics to more powerfully probe variation within the human gene pool at the level of DNA sequences. 40 refs., 7 figs., 2 tabs.

  15. Genotyping, evolution and epidemiological findings of Rickettsia species.

    Science.gov (United States)

    Merhej, Vicky; Angelakis, Emmanouil; Socolovschi, Cristina; Raoult, Didier

    2014-07-01

    Rickettsiae are obligate intracellular bacteria that can cause mild to life-threatening diseases, including epidemic typhus, one of the oldest pernicious diseases of mankind. Clinical awareness of rickettsial diseases and molecular diagnosis have shown that rickettsioses should be viewed as new emerging and reemerging diseases. Rickettsia has been shown to be a large genus with a worldwide distribution, a very diverse host range, including hosts that have no relationship with vertebrate. Genomic studies have demonstrated genome reduction due to gene loss associated with increased pathogenicity and horizontal DNA acquisition according to a sympatric mode of evolution in hosts that contain several organisms. This article presents a review of genotyping techniques and examines the principle of genotype determination in terms of taxonomic strategies and detection methods. This article summarizes the epidemiological and pathological features of Rickettsia and discusses the genomic findings that help the understanding of the evolution of pathogenicity including the deleterious mutations of repair systems and the toxin-antitoxin systems.

  16. Genomic evolution of 11 type strains within family Planctomycetaceae.

    Directory of Open Access Journals (Sweden)

    Min Guo

    Full Text Available The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes orthology system. Subsequently, we identified genomic islands (GIs and structural variations (SVs among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

  17. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  18. Stereotactic body radiotherapy combined with transarterial chemoembolization for huge (≥10 cm) hepatocellular carcinomas: A clinical study.

    Science.gov (United States)

    Zhong, Nan Bao; Lv, Guang Ming; Chen, Zhong Hua

    2014-09-01

    This study was conducted to evaluate the safety and efficacy of stereotactic body radiotherapy (SBRT) combined with transarterial chemoembolization (TACE) for huge (≥10 cm) hepatocellular carcinomas (HCCs). Between May, 2006 and December, 2012, 72 patients with huge HCCs were treated by SBRT following incomplete TACE. The median total dose of 35.6 Gy was delivered over 12-14 days with a fractional dose of 2.6-3.0 Gy and 6 fractions per week. The patients were classified into those with tumor encapsulation (group A, n=33) and those without tumor encapsulation (group B, n=39). The clinical outcomes of tumor response, overall cumulative survival and toxicities/complications were retrospectively analyzed. Among the 72 patients, CR, PR, SD and PD were achieved in 6 (8.3%), 51 (70.8%), 9 (12.5%) and 6 patients (8.3%), respectively, within a median follow-up of 18 months. The objective response rate was 79.1%. The overall cumulative 1-, 3- and 5-year survival rates and the median survival time were 38, 12 and 3% and 12.2 months, respectively. In group A, the overall cumulative 1-, 3- and 5-year survival rates were 56, 21 and 6%, respectively, with a median survival of 19 months; in group B, the overall cumulative 1-, 3- and 5-year survival rates were 23, 4 and 0%, respectively, with a median survival of 10.8 months (P=0.023). The treatment was well tolerated, with no severe radiation-induced liver disease and no reported > grade 3 toxicity. Tumor encapsulation was found to be a significant prognostic factor for survival. In conclusion, the combination of SBRT and TACE was shown to be a safe and effective treatment option for patients with unresectable huge HCC.

  19. Case of huge neurofibroma expanding extra- and intracranially through the enlarged jugular foramen. CT scan findings and surgical approach

    Energy Technology Data Exchange (ETDEWEB)

    Hanakita, Junya; Imataka, Kiyoharu; Handa, Hajime (Kyoto Univ. (Japan). Faculty of Medicine)

    1984-01-01

    The surgical approach to the jugular foramen has been considered to be very difficult and troublesome, because of the location in which important structures, such as the internal jugular vein, internal carotid artery and lower cranial nerves, converge in the narrow deep space. A case of huge neurofibroma, which extended from the tentorium cerebelli through the dilated jugular foramen to the level of the vertebral body of C/sub 3/ was presented. A 12-year-old girl was admitted with complaints of visual disturbance and palsy of the V-XII cranial nerves of the left side. Plain skull film showed prominent widening of the cranial sutures and enlargement of the sella turcica. Horizontal CT scan with contrast showed symmetrical ventricular dilatation and a heterogeneously enhanced mass, which was situated mainly in the left CP angle. Coronal CT scan with contrast revealed a huge mass and enlarged jugular foramen, through which the tumor extended to the level of the vertebral body of C/sub 3/. Occlusion of the sigmoid sinus and the internal jugular vein of the left side was noticed in the vertebral angiography. Two-stage approach, the first one for removal of the intracranial tumor and the second one for extracranial tumor, was performed for its huge tumor. Several authors have reported excellent surgical approaches for the tumors situated in the jugular foramen. By our approach, modifying Gardner's original one, a wide operative field was obtained to remove the tumor around the jugular foramen with success. Our approach for the jugular foramen was described with illustrations.

  20. Huge pelvi-abdominal malignant inflammatory myofibroblastic tumor with rapid recurrence in a 14-year-old boy

    Institute of Scientific and Technical Information of China (English)

    Chia-Hsun; Lu; Hsuan-Ying; Huang; Han-Koo; Chen; Jiin-Haur; Chuang; Shu-Hang; Ng; Sheung-Fat; Ko

    2010-01-01

    Inflammatory myofibroblastic tumor(IMT) is an uncommon benign neoplasm with locally aggressive behavior but malignant change is rare.We report an unusual case of pelvic-abdominal inflammatory myofibroblastic tumor with malignant transformation in a 14-year-old boy presenting with abdominal pain and 9 kg body weight loss in one month.Computed tomography revealed a huge pelvi-abdominal mass(30 cm),possibly originating from the pelvic extraperitoneal space,protruding into the abdomen leading to upward displace...

  1. Huge Varicose Inferior Mesenteric Vein: an Unanticipated {sup 99m}Tc-labeled Red Blood Cell Scintigraphy Finding

    Energy Technology Data Exchange (ETDEWEB)

    Hoseinzadeh, Samaneh; Shafiei, Babak; Salehian, Mohamadtaghi; Neshandar Asli, Isa; Ghodoosi, Iraj [Shaheed Beheshti Medical University, Tehran (Iran, Islamic Republic of)

    2010-09-15

    Ectopic varices (EcV) are enlarged portosystemic venous collaterals, which usually develop secondary to portal hypertension (PHT). Mesocaval collateral vessels are unusual pathways to decompress the portal system. Here we report the case of a huge varicose inferior mesenteric vein (IMV) that drained into peri rectal collateral veins, demonstrated by {sup 99m}Tc-labeled red blood cell (RBC) scintigraphy performed for lower gastrointestinal (GI) bleeding in a 14-year-old girl. This case illustrates the crucial role of {sup 99m}Tc-labeled RBC scintigraphy for the diagnosis of rare ectopic lower GI varices.

  2. The waste crisis in Campania, South Italy: a historical perspective on an epidemiological controversy.

    Science.gov (United States)

    Cantoni, Roberto

    2016-06-01

    Between 2001 and 2009, the area of Naples, South Italy, repeatedly hit the headlines of national and international media due to the waste management crisis that on many occasions filled up the streets of the region with huge piles of waste. What soon emerged as the main bone of contention concerned the connections between the population's health and the presence of dumps on the territory. What the risks for health actually were, who was entitled to assess them, and whether pollution from proximity to dumps caused health problems were all topics that came to the fore during a debate that took place within the Italian epidemiological community, alongside the political and governance crisis.

  3. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  4. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  5. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  6. Identification of Nucleotide Variation in Genomes Using Next-Generation Sequencing

    NARCIS (Netherlands)

    Megens, H.J.W.C.; Groenen, M.A.M.

    2012-01-01

    Discovery of genome-wide variation has taken a huge leap forward with the introduction of next-generation sequencing (NGS) technology. Variant discovery requires sampling of a number of haplotypes. This can be either the two haplotypes of a diploid organism or multiple haplotypes in a population. Va

  7. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  8. Epidemiology of gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Katherine D Crew; Alfred I Neugut

    2006-01-01

    The incidence and mortality of gastric cancer have fallen dramatically in US and elsewhere over the past several decades. Nonetheless, gastric cancer remains a major public health issue as the fourth most common cancer and the second leading cause of cancer death worldwide. Demographic trends differ by tumor location and histology. While there has been a marked decline in distal, intestinal type gastric cancers, the incidence of proximal, diffuse type adenocarcinomas of the gastric cardia has been increasing, particularly in the Western countries. Incidence by tumor sub-site also varies widely based on geographic location, race, and socioeconomic status. Distal gastric cancer predominates in developing countries, among blacks, and in lower socioeconomic groups, whereas proximal tumors are more common in developed countries, among whites, and in higher socio-economic classes. Diverging trends in the incidence of gastric cancer by tumor location suggest that they may represent two diseases with different etiologies. The main risk factors for distal gastric cancer include Helicobacter pylori (H pylori) infection and dietary factors, whereas gastroesophageal reflux disease and obesity play important roles in the development of proximal stomach cancer. The purpose of this review is to examine the epidemiology and risk factors of gastric cancer, and to discuss strategies for primary prevention.

  9. Epidemiology of delayed ejaculation.

    Science.gov (United States)

    Di Sante, Stefania; Mollaioli, Daniele; Gravina, Giovanni Luca; Ciocca, Giacomo; Limoncin, Erika; Carosa, Eleonora; Lenzi, Andrea; Jannini, Emmanuele A

    2016-08-01

    A large body of literature on diminished ejaculatory disorders has been generated without the use of a clear diagnostic definition. Many studies have not distinguished between the orgasm and ejaculation disorders leading to doubtful results. Delayed ejaculation (DE) is one of the diminished ejaculatory disorders, which range from varying delays in ejaculatory latency to a complete inability to ejaculate. The present review is aimed at providing a comprehensive overview of the current knowledge on the definition and epidemiology of diminished ejaculatory disorders. We focus on the acquired diseases, such as benign prostatic hyperplasia (BPH) and specific drug regimens that may cause an iatrogenic form of ejaculatory disorder. In addition, the impact of aging is discussed since the prevalence of DE appears to be moderately but positively related to age. Finally, we also focus on the importance of the hormonal milieu on male ejaculation. To date, evidence on the endocrine control of ejaculation is derived from small clinical trials, but the evidence suggests that hormones modulate the ejaculatory process by altering its overall latency.

  10. Radiobiology and Epidemiology

    Energy Technology Data Exchange (ETDEWEB)

    Desaintes, C; Holmstock, L

    2001-04-01

    The main objectives of research in the field of radiobiology and epidemiology performed at the Belgian Nuclear Research Centre SCK-CEN are: (1) to study cancer mortality in nuclear workers in Belgium and to co-ordinate the Belgian contribution to the 'International Collaborative Study of Cancer Risk among Radiation Workers in the Nuclear Industry'; (2) to elucidate the molecular basis of individual susceptibility to ionizing radiation in mammalian embryo during the early phases of its development; (3) to assess the genetic risk of maternal exposure to ionizing radiation; (4) to elucidate the cellular mechanisms leading to brain damage after prenatal irradiation; (5) to monitor the early variations of gene expression induced by ionising radiation and cytokines; (6) to evaluate the use of cytokines and natural substances for improving radiotherapy protocols; (6) to advise authorities and to provide the general population with adequate information concerning the health risk arising from radiation exposure. Progress and major achievements in these topical areas in 2000 are reported.

  11. Epidemiology of severe trauma.

    Science.gov (United States)

    Alberdi, F; García, I; Atutxa, L; Zabarte, M

    2014-12-01

    Major injury is the sixth leading cause of death worldwide. Among those under 35 years of age, it is the leading cause of death and disability. Traffic accidents alone are the main cause, fundamentally in low- and middle-income countries. Patients over 65 years of age are an increasingly affected group. For similar levels of injury, these patients have twice the mortality rate of young individuals, due to the existence of important comorbidities and associated treatments, and are more likely to die of medical complications late during hospital admission. No worldwide, standardized definitions exist for documenting, reporting and comparing data on severely injured trauma patients. The most common trauma scores are the Abbreviated Injury Scale (AIS), the Injury Severity Score (ISS) and the Trauma and Injury severity Score (TRISS). Documenting the burden of injury also requires evaluation of the impact of post-trauma impairments, disabilities and handicaps. Trauma epidemiology helps define health service and research priorities, contributes to identify disadvantaged groups, and also facilitates the elaboration of comparable measures for outcome predictions.

  12. Molecular epidemiology of giardiasis.

    Science.gov (United States)

    Cacciò, Simone M; Ryan, Una

    2008-08-01

    Giardia duodenalis is a widespread parasite of mammalian species, including humans. Due to its invariant morphology, investigation on aspects such as host specificity and transmission patterns requires a direct genetic characterization of cysts/trophozoites from host samples. A number of molecular assays have been developed to help unravel the complex epidemiology of this infection. A coherent picture has emerged from those studies, indicating the existence of seven genetic groups (or assemblages), two of which (A and B) are found in both humans and animals, whereas the remaining five (C-G) are host-specific. Sequence-based surveys have identified a number of genotypes within assemblages A and B in animal species, some of which may have zoonotic potential. Recently, however, molecular approaches have been complicated by the recognition of intra-isolate sequence heterogeneity (i.e., "mixed templates", that affects identification of subtypes within each assemblage), and by the unreliable assignment of isolates to G. duodenalis assemblages generated by different genetic markers. This raises concerns about previous interpretation of genotyping data, especially when single genetic markers have been used. The mechanisms that may be responsible for these findings, including allelic sequence heterozygosity and meiotic recombination, are discussed.

  13. Microtia: epidemiology and genetics.

    Science.gov (United States)

    Luquetti, Daniela V; Heike, Carrie L; Hing, Anne V; Cunningham, Michael L; Cox, Timothy C

    2012-01-01

    Microtia is a congenital anomaly of the ear that ranges in severity from mild structural abnormalities to complete absence of the ear, and can occur as an isolated birth defect or as part of a spectrum of anomalies or a syndrome. Microtia is often associated with hearing loss and patients typically require treatment for hearing impairment and surgical ear reconstruction. The reported prevalence varies among regions, from 0.83 to 17.4 per 10,000 births, and the prevalence is considered to be higher in Hispanics, Asians, Native Americans, and Andeans. The etiology of microtia and the cause of this wide variability in prevalence are poorly understood. Strong evidence supports the role of environmental and genetic causes for microtia. Although some studies have identified candidate genetic variants for microtia, no causal genetic mutation has been confirmed. The application of novel strategies in developmental biology and genetics has facilitated elucidation of mechanisms controlling craniofacial development. In this paper we review current knowledge of the epidemiology and genetics of microtia, including potential candidate genes supported by evidence from human syndromes and animal models. We also discuss the possible etiopathogenesis in light of the hypotheses formulated to date: Neural crest cells disturbance, vascular disruption, and altitude.

  14. Modeling Corporate Epidemiology

    CERN Document Server

    Waber, Benjamin; Cebrian, Manuel; Crane, Riley; Danon, Leon; Pentland, Alex

    2010-01-01

    Corporate responses to illness is currently an ad-hoc, subjective process that has little basis in data on how disease actually spreads at the workplace. Additionally, many studies have shown that productivity is not an individual factor but a social one: in any study on epidemic responses this social factor has to be taken into account. The barrier to addressing this problem has been the lack of data on the interaction and mobility patterns of people in the workplace. We have created a wearable Sociometric Badge that senses interactions between individuals using an infra-red (IR) transceiver and proximity using a radio transmitter. Using the data from the Sociometric Badges, we are able to simulate diseases spreading through face-to-face interactions with realistic epidemiological parameters. In this paper we construct a curve trading off productivity with epidemic potential. We are able to take into account impacts on productivity that arise from social factors, such as interaction diversity and density, wh...

  15. TUBERCULOSIS: EPIDEMIOLOGY AND CONTROL

    Directory of Open Access Journals (Sweden)

    Giorgia Sulis

    2014-10-01

    Full Text Available Tuberculosis (TB is a major public health concern worldwide: despite a regular, although slow, decline in incidence over the last decade, as many as 8.6 million new cases and 1.3 million deaths were estimated to have occurred in 2012. TB is by all means a poverty-related disease, mainly affecting the most vulnerable populations in the poorest countries. The presence of multidrug-resistant strains of M. tuberculosis in most countries, with some where prevalence is high, is among the major challenges for TB control, which may hinder recent achievements especially in some settings. Early TB case detection especially in resource-constrained settings and in marginalized groups remains a challenge, and about 3 million people are estimated to remain undiagnosed or not notified and untreated. The World Health Organization (WHO has recently launched the new global TB strategy for the “post-2015 era” aimed at “ending the global TB epidemic” by 2035, based on the three pillars that emphasize patient-centred TB care and prevention, bold policies and supportive systems, and intensified research and innovation. This paper aims to provide an overview of the global TB epidemiology as well as of the main challenges that must be faced to eliminate the disease as a public health problem everywhere.

  16. Pemphigus: Epidemiology and Pathogenesis

    Directory of Open Access Journals (Sweden)

    Yelda Karıncaoğlu

    2008-08-01

    Full Text Available Pemphigus, a group of bullous diseases affecting the oral mucosa and the skin, is caused by antibody-mediated autoimmune reaction to desmogleins (Dsg, desmosomal transmembrane glycoproteins, leading to acantholysis. Pemphigus has a worldwide distribution but the incidence in patients of Jewish origin is higher. The disease has a peak incidence of occurrence between the 4th and 6th decades. While various environmental factors have been implicated as triggering agents, HLA association is probably the most important predisposing factor. Pemphigus, is caused by antibody-mediated autoimmune reaction to desmosomal cadherins, Dsg1, and Dsg3. Recent molecular studies have shown that acantholysis can occur also in the presence of antibodies against 9a nicotinic acetylcholine receptor. Pemphigus is currently divided into three distinct varieties, i.e., pemphigus vulgaris (PV, pemphigus foliaceus (PF and other variants of pemphigus, depending on clinical features, the level of separation in the epidermis, and immunologic characteristics of auto-antigens. Blistering pathogenesis differ for each of the types of pemphigus. PV is characterized by IgG autoantibodies against Dsg 3, whereas the target of PF is Dsg1, although about 50% of PV patients also have Dsg1 autoantibodies. Lesion distribution is related to the location of the antigen (Dgs 3 and/or Dgs 1 in the epithelium and specific autoantibody production. This article reviews the epidemiology and pathogenesis of pemphigus.

  17. Genomics of clostridial pathogens: implication of extrachromosomal elements in pathogenicity.

    Science.gov (United States)

    Brüggemann, Holger

    2005-10-01

    The recently decoded genomes of the major clostridial toxin-producing pathogens Clostridium perfringens, Clostridium tetani, Clostridium botulinum and Clostridium difficile have provided a huge amount of new sequence data. Recent studies have focused on the identification and investigation of pathogenic determinants and the regulatory events governing their expression. The sequence data revealed also the genomic background of virulence genes, as well as the contribution of extrachromosomal elements to a pathogenic phenotype. This has generated new insights in clostridial pathogenesis - and will continue to do so in the future - and has deepened our understanding of the anaerobic lifestyle of clostridial species.

  18. Metabolomics and Epidemiology Working Group

    Science.gov (United States)

    The Metabolomics and Epidemiology (MetEpi) Working Group promotes metabolomics analyses in population-based studies, as well as advancement in the field of metabolomics for broader biomedical and public health research.

  19. Rosacea: current state of epidemiology.

    Science.gov (United States)

    Tan, Jerry; Berg, Mats

    2013-12-01

    Case definitions are critical in epidemiologic research. However, modern disease indicators must now consider complex data from gene-based research along with traditional clinical parameters. Rosacea is a skin disorder with multiple signs and symptoms. In individuals, these features may be multiple or one may predominate. While studies on the epidemiology of rosacea have previously been sparse, there has been a recent increase in research activity. A broader body of epidemiological information that includes a greater variety of countries beyond Northern Europe and general population-based demographics is needed. As there are operational issues in current case definitions of rosacea subtypes--rationalization and standardization--universal consistent applications in future research is also imperative. Further improvement in disease definition combining new research information along with clinical pragmatism should increase the accuracy of rosacea case ascertainment and facilitate further epidemiological research.

  20. Sociocultural epidemiology: an essential approach.

    Directory of Open Access Journals (Sweden)

    Paul Hersch-Martínez

    2013-09-01

    Full Text Available The necessity of an inclusive epidemiological approach, capable to attend the diverse dimensions involved in health damage as a reflective phenomenon of society is analyzed. The range of perspectives involved requires an inclusive methodological scope and applicative channels, in order to deal with sanitary realities systematically related to culture and social organization. Some constitutive elements of sociocultural epidemiology are underlined, shaping an operative proposal that can enhance the relationship between disciplines and sectors regarding specific outstanding public health problems.

  1. Research on fast Fourier transforms algorithm of huge remote sensing image technology with GPU and partitioning technology.

    Science.gov (United States)

    Yang, Xue; Li, Xue-You; Li, Jia-Guo; Ma, Jun; Zhang, Li; Yang, Jan; Du, Quan-Ye

    2014-02-01

    Fast Fourier transforms (FFT) is a basic approach to remote sensing image processing. With the improvement of capacity of remote sensing image capture with the features of hyperspectrum, high spatial resolution and high temporal resolution, how to use FFT technology to efficiently process huge remote sensing image becomes the critical step and research hot spot of current image processing technology. FFT algorithm, one of the basic algorithms of image processing, can be used for stripe noise removal, image compression, image registration, etc. in processing remote sensing image. CUFFT function library is the FFT algorithm library based on CPU and FFTW. FFTW is a FFT algorithm developed based on CPU in PC platform, and is currently the fastest CPU based FFT algorithm function library. However there is a common problem that once the available memory or memory is less than the capacity of image, there will be out of memory or memory overflow when using the above two methods to realize image FFT arithmetic. To address this problem, a CPU and partitioning technology based Huge Remote Fast Fourier Transform (HRFFT) algorithm is proposed in this paper. By improving the FFT algorithm in CUFFT function library, the problem of out of memory and memory overflow is solved. Moreover, this method is proved rational by experiment combined with the CCD image of HJ-1A satellite. When applied to practical image processing, it improves effect of the image processing, speeds up the processing, which saves the time of computation and achieves sound result.

  2. Free perforating branch flap for primary repairing the huge soft-tissue defects on the scalp and face.

    Science.gov (United States)

    Wang, Hong-Yuan; Wang, Ming-Gang; Yu, Gang; Chu, Yan-Jun; Wang, Kai; Wei, Xiang-Pin; Sun, Jing-Wu

    2016-11-01

    This study aimed to explore the effect of free perforating branch flap on the reconstruction of huge soft-tissue defects on the scalp and face. Sixteen cases of huge soft-tissue defects on the scalp and face were reconstructed by nine latissimus dorsi-free perforator flaps and seven anterolateral thigh-free perforator flaps. The defects area was from 12 cm× 7 cm to 20 cm × 11 cm, while the flaps area was from 14 cm × 8 cm to 23 cm × 12 cm. The survival, planeness, chromatic aberration, radiotherapy toleration of flap and the function, scar of donor site were observed postoperatively. All of the flaps were survived completely, and 15 cases presented for primary reconstruction; one underwent secondary reconstruction. One of the patients died one-year postoperatively due to intracranial tumor recurrence and the others had no recurrence. All of the flaps showed perfect shape and appropriate thickness. No roentgen ulcer was observed except for some extent of chromatic aberration. The donor-site scar was larvaceous and the function was good. This study indicated that the latissimus dorsi-free perforator flap or anterolateral thigh-free perforator flap was an ideal choice for the reconstruction of defects on the scalp and face.

  3. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  4. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  5. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  6. The false-positive to false-negative ratio in epidemiologic studies.

    Science.gov (United States)

    Ioannidis, John P A; Tarone, Robert; McLaughlin, Joseph K

    2011-07-01

    The ratio of false-positive to false-negative findings (FP:FN ratio) is an informative metric that warrants further evaluation. The FP:FN ratio varies greatly across different epidemiologic areas. In genetic epidemiology, it has varied from very high values (possibly even >100:1) for associations reported in candidate-gene studies to very low values (1:100 or lower) for associations with genome-wide significance. The substantial reduction over time in the FP:FN ratio in human genome epidemiology has corresponded to the routine adoption of stringent inferential criteria and comprehensive, agnostic reporting of all analyses. Most traditional fields of epidemiologic research more closely follow the practices of past candidate gene epidemiology, and thus have high FP:FN ratios. Further, FP and FN results do not necessarily entail the same consequences, and their relative importance may vary in different settings. This ultimately has implications for what is the acceptable FP:FN ratio and for how the results of published epidemiologic studies should be presented and interpreted.

  7. Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission

    NARCIS (Netherlands)

    Zarrabi, N.; Prosperi, M.; Belleman, R.G.; Colafigli, M.; De Luca, A.; Sloot, P.M.A.

    2012-01-01

    Inferring disease transmission networks is important in epidemiology in order to understand and prevent the spread of infectious diseases. Reconstruction of the infection transmission networks requires insight into viral genome data as well as social interactions. For the HIV-1 epidemic, current res

  8. Relevance of the Human Genome Project to inherited metabolic disease.

    Science.gov (United States)

    Burn, J

    1994-01-01

    The Human Genome Project is an international effort to identify the complete structure of the human genome. HUGO, the Human Genome Organization, facilitates international cooperation and exchange of information while the Genome Data Base will act as the on-line information retrieval and storage system for the huge amount of information being accumulated. The clinical register MIM (Mendelian Inheritance in Man) established by Victor McKusick is now an on-line resource that will allow biochemists working with inborn errors of metabolism to access the rapidly expanding body of knowledge. Biochemical and molecular genetics are complementary and should draw together to find solutions to the academic and clinical problems posed by inborn errors of metabolism.

  9. Mendelian randomization: genetic anchors for causal inference in epidemiological studies

    Science.gov (United States)

    Davey Smith, George; Hemani, Gibran

    2014-01-01

    Observational epidemiological studies are prone to confounding, reverse causation and various biases and have generated findings that have proved to be unreliable indicators of the causal effects of modifiable exposures on disease outcomes. Mendelian randomization (MR) is a method that utilizes genetic variants that are robustly associated with such modifiable exposures to generate more reliable evidence regarding which interventions should produce health benefits. The approach is being widely applied, and various ways to strengthen inference given the known potential limitations of MR are now available. Developments of MR, including two-sample MR, bidirectional MR, network MR, two-step MR, factorial MR and multiphenotype MR, are outlined in this review. The integration of genetic information into population-based epidemiological studies presents translational opportunities, which capitalize on the investment in genomic discovery research. PMID:25064373

  10. Epidemiology and ionizing radiations; Epidemiologie et rayonnements ionisants

    Energy Technology Data Exchange (ETDEWEB)

    Bourguignon, M. [Direction generale de la surete nucleaire et de la radioprotection (DGSNR), 75 - Paris (France); Masse, R. [Academie des technologies, 75 - Paris (France); Slama, R.; Spira, A. [Inserm et Ined U569, Epidemiologie, Demographie et Sciences Sociales: Sante Reproductive, Sexualite et Infection a VIH, 94 - Le Kremlin-Bicetre (France); Timarche, M.; Laurier, D.; Billon, S.; Rogel, A.; Telle Lamberton, M.; Catelinois, O.; Thierry, I. [Institut de Radioprotection et de Surete Nucleaire (IRSN), 92 - Clamart (France); Grosche, B. [Bundesamt fuer Strahlenschutz, Neuherberg (Germany). Inst. fuer Strahlenhygiene; Hall, P. [Karolinska Inst., Dept. d' Epidemiologie Medicale, Stockholm (Sweden); Ron, E. [Institut national du cancer, Div. Epidemiologie du Cancer et Genetique (United States); Vathaire, F. de [INSERM XR 521, Institut Gustave Roussy, 94 - Villejuif (France); Cherie Challine, L.; Donadieu, J.; Pirard, Ph. [Institut de veille sanitaire (InVs), 94415 - Saint-Maurice (France); Bloch, J. [Direction generale de la sante, 75 - Paris (France); Setbon, M. [Centre National de la Recherche Scientifique (CNRS), 75 - Paris (France)

    2004-01-01

    The ionizing radiations have effects on living being. The determinist effects appear since a threshold of absorbed dose of radiation is reached. In return, the stochastic effects of ionizing radiations are these ones whom apparition cannot be described except in terms of probabilities. They are in one hand, cancers and leukemia, on the other hand, lesions of the genome potentially transmissible to the descendants. That is why epidemiology, defined by specialists as the science that studies the frequency and distribution of illness in time and space, the contribution of factors that determine this frequency and this distribution among human populations. This issue gathers and synthesizes the knowledge and examines the difficulties of methodologies. It allows to give its true place to epidemiology. (N.C.)

  11. CLINICAL, EPIDEMIOLOGICAL AND MYCOLOGICA

    Directory of Open Access Journals (Sweden)

    Ratheesh T

    2014-09-01

    Full Text Available BACKGROUND: Tinea versicolor is a chronic, mild, usually asymptomatic infection of the stratum corneum. The lesions are discrete or confluent and appear as discolored or hypo pigmented areas of the skin. The affected areas are located principally on the chest, abdomen, upper extremities and back. The etiologic agent is the lipophilic yeast Pityrosporum orbiculare, part of the normal flora of the human skin. This study is undertaken to know “clinical, patterns of the disease with respect to morphology and distribution, associated conditions and epidemiological factors like age, sex distribution and seasonal variation of the disease”. METHODS: Two hundred patients of tinea versicolor were selected. Patients belonging to the age group of above 10 years and below 60 years belonging to both sexes were selected and included in the study group after taking consent. A detailed history was taken with particular reference to onset, duration, symptoms and treatment taken and were recorded. Factors like – seasonal variation, family history and presence of any associated illnesses was also noted. A thorough clinical examination was done with reference to the location, the color, the extent of the lesions, the margins, the type of lesions and the details were recorded. Potassium hydroxide (KOH examination and Wood’s lamp examination were done in all the patients before therapy. RESULTS: Out of 200 patients, majority of them belong to 2nd and 3rd decade of life (72%. The Male: Female ratio was 1.5:1. There was a family history of 16%. The trunk was the most common site involved. Majority of the patients had exacerbation in summer. The most common associated dermatoses were acne vulgaris, immunosuppression and infections. INTERPRETATION AND CONCLUSION: Tinea versicolor is a disease of worldwide distribution, although it is significantly more common in humid and tropical climates. The true incidence cannot be estimated precisely because the disease is

  12. The Association Between the Peroxisome Proliferator-Activated Receptor-γ2 (PPARG2) Pro12Ala Gene Variant and Type 2 Diabetes Mellitus: A HuGE Review and Meta-Analysis

    Science.gov (United States)

    Gouda, Hebe N.; Sagoo, Gurdeep S.; Harding, Anne-Helen; Yates, Jan; Sandhu, Manjinder S.; Higgins, Julian P. T.

    2010-01-01

    The peroxisome proliferator-activated receptor-γ gene (PPARG) has been implicated in the etiology of type 2 diabetes mellitus and has been investigated in numerous epidemiologic studies. In this Human Genome Epidemiology review, the authors assessed this relation in an updated meta-analysis of 60 association studies. Electronic literature searches were conducted on September 14, 2009. Population-based cohort, case-control, cross-sectional, or genome-wide association studies reporting associations between the PPARG Pro12Ala gene variant (rs1801282) and type 2 diabetes were included. An updated literature-based meta-analysis involving 32,849 type 2 diabetes cases and 47,456 controls in relation to the PPARG Pro12Ala variant was conducted. The combined overall odds ratio, calculated by per-allele genetic model random-effects meta-analysis for type 2 diabetes and the Pro12Ala polymorphism, was 0.86 (95% confidence interval: 0.81, 0.90). The analysis indicated a moderate level of heterogeneity attributable to genuine variation in gene effect size (I2 = 37%). This may reflect the variation observed between ethnic populations and/or differences in body mass index. Work on PPARG Pro12Ala should now focus on the observed heterogeneity in the magnitude of the association between populations. Further investigations into gene-gene and gene-environment interactions may prove enlightening. PMID:20179158

  13. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  14. Hydrogen-terminated mesoporous silicon monoliths with huge surface area as alternative Si-based visible light-active photocatalysts

    KAUST Repository

    Li, Ting

    2016-07-21

    Silicon-based nanostructures and their related composites have drawn tremendous research interest in solar energy storage and conversion. Mesoporous silicon with a huge surface area of 400-900 m2 g-1 developed by electrochemical etching exhibits excellent photocatalytic ability and stability after 10 cycles in degrading methyl orange under visible light irradiation, owing to its unique mesoporous network, abundant surface hydrides and efficient light harvesting. This work showcases the profound effects of surface area, crystallinity, pore topology on charge migration/recombination and mass transportation. Therein the ordered 1D channel array has outperformed the interconnected 3D porous network by greatly accelerating the mass diffusion and enhancing the accessibility of the active sites on the extensive surfaces. © 2016 The Royal Society of Chemistry.

  15. The prostatic utricle cyst with huge calculus and hypospadias: A case report and a review of the literature.

    Science.gov (United States)

    Wang, Weigang; Wang, Yuantao; Zhu, Dechun; Yan, Pengfei; Dong, Biao; Zhou, Honglan

    2015-01-01

    Prostatic utricle cysts with calculus and hypospadias are rare. There are a few reported cases. We present a case of a prostatic utricle cyst with huge calculus in a 25-year-old male. He had a history of left cryptorchidism and surgery for penoscrotal hypospadias in his infancy. He was referred for frequent micturition, urgency of urination, urine pain, terminal hematuria, and dysuria. A computed tomography (CT) revealed a retrovesical cystic lesion of low density, showing a 5 × 5-cm calcification. Retrograde urethrocystography showed a 5 × 5-cm high-density shadow in the posterior urethra. The cyst was incised by transperineal approach and the stone was clearly observed and removed. Urethral stricture repair was performed simultaneously. The patient recovered smoothly after surgery.

  16. L-Tree Match: A New Data Extraction Model and Algorithm for Huge Text Stream with Noises

    Institute of Scientific and Technical Information of China (English)

    Xu-Bin Deng; Yang-Yong Zhu

    2005-01-01

    In this paper, a new method, named as L-tree match, is presented for extracting data from complex data sources. Firstly, based on data extraction logic presented in this work, a new data extraction model is constructed in which model components are structurally correlated via a generalized template. Secondly, a database-populating mechanism is built, along with some object-manipulating operations needed for flexible database design, to support data extraction from huge text stream. Thirdly, top-down and bottom-up strategies are combined to design a new extraction algorithm that can extract data from data sources with optional, unordered, nested, and/or noisy components. Lastly, this method is applied to extract accurate data from biological documents amounting to 100GB for the first online integrated biological data warehouse of China.

  17. Playing games with a thrombus: a dangerous match. Paradoxical embolism from a huge central venous cathether thrombus: a case report

    Directory of Open Access Journals (Sweden)

    Mariana Sylvie

    2010-03-01

    Full Text Available Abstract Thromboembolism is a major cause of death in cancer patients. The association between paraneoplastic hypercoagulability of oncological patients and long-term central venous catheters (CVC may result in CVC associated thrombosis. Patent Foramen Ovale (PFO, especially when associated with atrial septal aneurysm (ASA is a risk factor for paradoxical embolism. We report a case of paradoxical embolism with stroke in an oncological patient with a huge CVC thrombus playing "ping-pong" with an hypermobile ASA with a PFO. We review the management of hypercoagulability in oncologic patients and discuss the potential role of routine transthoracic echocardiography before the implantation of long term central venous catheters to identify predisposing conditions to paradoxical embolism and select patients for anticoagulant therapy.

  18. False positives in cancer epidemiology.

    Science.gov (United States)

    McLaughlin, Joseph K; Tarone, Robert E

    2013-01-01

    A recent attempt to estimate the false-positive rate for cancer epidemiology studies is based on agents in International Agency for Research on Cancer (IARC) category 3 (agent not classifiable as to its carcinogenicity to humans) in the IARC Monographs Program. The estimation method is critiqued regarding biases caused by its reliance on the IARC classification criteria for assessing carcinogenic potential. The privileged position given to epidemiologic studies by the IARC criteria ensures that the percentage of positive epidemiologic studies for an agent will depend strongly on the IARC category to which the agent is assigned. Because IARC category 3 is composed of agents with the lowest-assessed carcinogenic potential to which the estimation approach in question could be applied, a spuriously low estimated false-positive rate was necessarily the outcome of this approach. Tendentious estimation approaches like that employed will by necessity produce spuriously low and misleading false positive rates. The recently reported estimates of the false-positive rate in cancer epidemiology are seriously biased and contribute nothing substantive to the literature on the very real problems related to false-positive findings in epidemiology.

  19. Draft Genome Sequence of White Spot Syndrome Virus Isolated from Cultured Litopenaeus vannamei in Mexico

    Science.gov (United States)

    Rodriguez-Anaya, Libia Zulema; Gonzalez-Galaviz, Jose Reyes; Casillas-Hernandez, Ramón; Lares-Villa, Fernando; Estrada, Karel

    2016-01-01

    The first genome sequence of a Mexican white spot syndrome virus is presented here. White spot syndrome is a shrimp pandemic virus that has devastated production in Mexico for more than 10 years. The availability of this genome will greatly aid epidemiological studies worldwide, contributing to the molecular diagnostic and disease prevention in shrimp farming. PMID:26966222

  20. Genome organization of epidemic Acinetobacter baumannii strains

    Directory of Open Access Journals (Sweden)

    Triassi Maria

    2011-10-01

    Full Text Available Abstract Background Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of epidemics caused by multi-drug resistant strains assigned to novel genotypes have been reported over the last few years. Results In the present study, we compared whole genome sequences of three A. baumannii strains assigned to genotypes ST2, ST25 and ST78, representative of the most frequent genotypes responsible for epidemics in several Mediterranean hospitals, and four complete genome sequences of A. baumannii strains assigned to genotypes ST1, ST2 and ST77. Comparative genome analysis showed extensive synteny and identified 3068 coding regions which are conserved, at the same chromosomal position, in all A. baumannii genomes. Genome alignments also identified 63 DNA regions, ranging in size from 4 o 126 kb, all defined as genomic islands, which were present in some genomes, but were either missing or replaced by non-homologous DNA sequences in others. Some islands are involved in resistance to drugs and metals, others carry genes encoding surface proteins or enzymes involved in specific metabolic pathways, and others correspond to prophage-like elements. Accessory DNA regions encode 12 to 19% of the potential gene products of the analyzed strains. The analysis of a collection of epidemic A. baumannii strains showed that some islands were restricted to specific genotypes. Conclusion The definition of the genome components of A. baumannii provides a scaffold to rapidly evaluate the genomic organization of novel clinical A. baumannii isolates. Changes in island profiling will be useful in genomic epidemiology of A. baumannii population.

  1. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  2. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  3. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends

    Science.gov (United States)

    Ramos-Castañeda, José; Barreto dos Santos, Flavia; Martínez-Vega, Ruth; Galvão de Araujo, Josélio Maria; Joint, Graham; Sarti, Elsa

    2017-01-01

    Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity. PMID:28068335

  4. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends.

    Science.gov (United States)

    Ramos-Castañeda, José; Barreto Dos Santos, Flavia; Martínez-Vega, Ruth; Galvão de Araujo, Josélio Maria; Joint, Graham; Sarti, Elsa

    2017-01-01

    Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity.

  5. Epidemiología de campo y epidemiología social Field epidemiology and social epidemiology

    Directory of Open Access Journals (Sweden)

    Javier Segura del Pozo

    2006-03-01

    Full Text Available Mediante la comparación de la epidemiología de campo y la epidemiología social, se pretende reflexionar sobre los imaginarios no explícitos que operan en ambos ámbitos, necesariamente convergentes, sobre los obstáculos de la práctica epidemiológica actual para alcanzar su función social y sobre la necesidad de cambiar las bases epistemológicas, metodológicas y prácticas que operan en la epidemiología, empezando por la formación del epidemiólogo de campo. La epidemiología de campo tiende a la acción sin marco teórico. La epidemiología social, por el contrario, tiende a los desarrollos teóricos (reflexión e investigación sobre los determinantes sociales alejados de la acción, debido a los limitantes para cambiar las políticas públicas. Otras diferencias se sitúan en el nivel de intervención (micro/macroespacios, el objeto de intervención (control del brote frente a control de las desigualdades y en la forma de articular la comunicación con la sociedad. Se asemejan en la preocupación por el método, la predominancia de una orientación positivista y condicionada por la estadística, aunque en proceso de cierta apertura epistemológica, la tensión experimentada entre relacionarse con un mundo virtual de bases de datos o con la sociedad real, su situación en la periferia del sistema político-social-institucional-profesional y por estar abocadas a la frustración profesional. Finalmente, se formulan 10 interrogantes a los epidemiólogos de campo sobre su práctica actual, a través de los cuales se podría evaluar si están realizando una epidemiología social, y se sugieren cambios para introducir en la formación y práctica del epidemiólogo.Comparing field epidemiology and social epidemiology, we pretend to think about the no explicit images and meanings operating in both necessary convergent fields, about the obstacles present in epidemiological practice to fulfil its social function and about the necessity of

  6. Epidemiology of idiopathic pulmonary fibrosis

    Directory of Open Access Journals (Sweden)

    Ley B

    2013-11-01

    Full Text Available Brett Ley, Harold R Collard Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, California, USA Abstract: Idiopathic pulmonary fibrosis is a chronic fibrotic lung disease of unknown cause that occurs in adults and has a poor prognosis. Its epidemiology has been difficult to study because of its rarity and evolution in diagnostic and coding practices. Though uncommon, it is likely underappreciated both in terms of its occurrence (ie, incidence, prevalence and public health impact (ie, health care costs and resource utilization. Incidence and mortality appear to be on the rise, and prevalence is expected to increase with the aging population. Potential risk factors include occupational and environmental exposures, tobacco smoking, gastroesophageal reflux, and genetic factors. An accurate understanding of its epidemiology is important, especially as novel therapies are emerging. Keywords: idiopathic pulmonary fibrosis, epidemiology, incidence, prevalence, mortality, risk factors

  7. Viral marketing as epidemiological model

    CERN Document Server

    Rodrigues, Helena Sofia

    2015-01-01

    In epidemiology, an epidemic is defined as the spread of an infectious disease to a large number of people in a given population within a short period of time. In the marketing context, a message is viral when it is broadly sent and received by the target market through person-to-person transmission. This specific marketing communication strategy is commonly referred as viral marketing. Due to this similarity between an epidemic and the viral marketing process and because the understanding of the critical factors to this communications strategy effectiveness remain largely unknown, the mathematical models in epidemiology are presented in this marketing specific field. In this paper, an epidemiological model SIR (Susceptible- Infected-Recovered) to study the effects of a viral marketing strategy is presented. It is made a comparison between the disease parameters and the marketing application, and simulations using the Matlab software are performed. Finally, some conclusions are given and their marketing impli...

  8. Molecular Epidemiology of Koi Herpesvirus

    NARCIS (Netherlands)

    Kurita, J.; Yuasa, K.; Ito, T.; Sano, M.; Hedrick, R.P.; Engelsma, M.Y.; Haenen, O.L.M.; Sunarto, A.; Kholidin, E.B.; Chou, H.Y.; Tung, M.C.; Pena, de la L.; Lio-Po, G.; Tu, C.; Way, K.; Iida, T.

    2009-01-01

    Three regions of koi herpesvirus (KHV) genomic DNA were compared for 34 samples from Japan, six from Indonesia, two from Taiwan, one from the Philippines, 13 from the Netherlands, one from the UK, one from the USA and one from Israel. The analyzed genomic regions included known PCR-detection targets

  9. snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund;

    2012-01-01

    Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differe......Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis...... from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script. The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evalution results for the first three...

  10. High-resolution genomic fingerprinting of Campylobacter jejuni and Campylobacter coli by analysis of amplified fragment length polymorphisms

    DEFF Research Database (Denmark)

    Kokotovic, Branko; On, Stephen L.W.

    1999-01-01

    A method for high-resolution genomic fingerprinting of the enteric pathogens Campylobacter jejuni and Campylobacter coli, based on the determination of amplified fragment length polymorphism, is described. The potential of this method for molecular epidemiological studies of these species...

  11. Nephrogenic systemic fibrosis: epidemiology update

    DEFF Research Database (Denmark)

    Marckmann, P.

    2008-01-01

    Purpose of review The aim of this article is to outline the history of nephrogenic systemic fibrosis, a new and serious disease of patients with renal failure, and to give an update on its aetiology and prevalence. Recent findings Epidemiological and histochemical studies demonstrated that gadoli......Purpose of review The aim of this article is to outline the history of nephrogenic systemic fibrosis, a new and serious disease of patients with renal failure, and to give an update on its aetiology and prevalence. Recent findings Epidemiological and histochemical studies demonstrated...

  12. Huge Investment Needed

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    China needs a massive investment to maintain its rampant economic boom-at least a 20 percent annual growth rate, according to Fan Gang, Deputy Director of the National Economic Research Institute and a member of the central bank's Monetary Policy Committee.

  13. Molecular epidemiology of heteroresistant vancomycin-intermediate Staphylococcus aureus in Brazil

    Directory of Open Access Journals (Sweden)

    Alessandro Conrado de Oliveira Silveira

    2015-10-01

    Full Text Available ABSTRACTTo determine the epidemiological and molecular characteristics of 12 Staphylococcus aureus isolates presenting heteroresistance to vancomycin in laboratories of two cities in Santa Catarina, southern Brazil. Epidemiological data, including the city of isolation, health institution, and date of isolation were considered, as well as the associated clinical specimen. For molecular characterization, we analyzed the staphylococcal cassette chromosome types, the erm gene presence, and the genomic diversity of isolates using pulsed-field gel electrophoresis. The 12 isolates of S. aureus were previously confirmed as heteroresistance to vancomycin using the population analysis profile-area under curve. Regarding genetic variability, two clones were detected: the main one (clone A composed of four isolates and the clones B, with two isolates. For clone A, two isolates presented identical band patterns and were related to the same hospital, with an interval of 57 days between their isolation. The other isolates of this clone showed no epidemiological link between them because they were isolated in different hospitals and had no temporal relationship. The other clone showed no detectable epidemiological relationship. The heteroresistance to vancomycin recovered in Santa Catarina State from 2009 to 2012 had, in general, heterogeneous genomic patterns based on pulsed-field gel electrophoresis results, which is in accordance with the fact that these isolates had little or no epidemiological relationship among them. Due to the characteristic phenotypic instability and often prolonged vancomycin therapy for selection, clonal spread is not as common as for other resistance mechanisms disseminated through horizontal gene transfer.

  14. Genomic Epidemiology: Whole-Genome-Sequencing–Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens

    DEFF Research Database (Denmark)

    Deng, Xiangyu; den Bakker, Henk C.; Hendriksen, Rene S.

    2016-01-01

    As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-cal...

  15. Candida infections : detection and epidemiology

    NARCIS (Netherlands)

    Borst, A. (Annemarie)

    2002-01-01

    Despite the fact that the yeast Candida is the number 4 cause of bloodstream infections in the United States and ranks number 8 in Europe, adequate detection methods are lacking. Furthermore, relatively little is known about the epidemiology of Candida. Our aim was to improve the detection and ident

  16. Brain Tumor Epidemiology Consortium (BTEC)

    Science.gov (United States)

    The Brain Tumor Epidemiology Consortium is an open scientific forum organized to foster the development of multi-center, international and inter-disciplinary collaborations that will lead to a better understanding of the etiology, outcomes, and prevention of brain tumors.

  17. Glossary for econometrics and epidemiology.

    Science.gov (United States)

    Gunasekara, F Imlach; Carter, K; Blakely, T

    2008-10-01

    Epidemiologists and econometricians are often interested in similar topics-socioeconomic position and health outcomes-but the different languages that epidemiologists and economists use to interpret and discuss their results can create a barrier to mutual communication. This glossary defines key terms used in econometrics and epidemiology to assist in bridging this gap.

  18. Implementation epidemiology: The study of the frequency ...

    African Journals Online (AJOL)

    Campus, Kuala Lumpur, Malaysia .... of new epidemiological findings into policy action the American College of Epidemiology ..... The underlying contexts of seat belt wearing rates in a community relate to the economic, social, political and.

  19. Why does epidemiology need better questionnaires?

    DEFF Research Database (Denmark)

    Tong, S.; Ring, I.; Olsen, Jørn

    2003-01-01

    The authors argue for the use of validated questionnaires whenever possible to improve the quality of epidemiological research.......The authors argue for the use of validated questionnaires whenever possible to improve the quality of epidemiological research....

  20. Mitochondrial DNA and Cancer Epidemiology Workshop

    Science.gov (United States)

    A workshop to review the state-of-the science in the mitochondrial DNA field and its use in cancer epidemiology, and to develop a concept for a research initiative on mitochondrial DNA and cancer epidemiology.