WorldWideScience

Sample records for genome epidemiology huge

  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. Development and application of Human Genome Epidemiology

    Science.gov (United States)

    Xu, Jingwen

    2017-12-01

    Epidemiology is a science that studies distribution of diseases and health in population and its influencing factors, it also studies how to prevent and cure disease and promote health strategies and measures. Epidemiology has developed rapidly in recent years and it is an intercross subject with various other disciplines to form a series of branch disciplines such as Genetic epidemiology, molecular epidemiology, drug epidemiology and tumor epidemiology. With the implementation and completion of Human Genome Project (HGP), Human Genome Epidemiology (HuGE) has emerged at this historic moment. In this review, the development of Human Genome Epidemiology, research content, the construction and structure of relevant network, research standards, as well as the existing results and problems are briefly outlined.

  3. Epidemiology & Genomics Research Program

    Science.gov (United States)

    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. 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.

  5. 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. © 2013 Wiley Periodicals, Inc.

  6. 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.

  7. About the Epidemiology and Genomics Research Program

    Science.gov (United States)

    Epidemiology is the scientific study of the causes and distribution of disease in populations. NCI-funded epidemiology research is conducted through research at institutions in the United States and internationally.

  8. Whole Genome Epidemiological Typing of Salmonella

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas

    available Salmonella enterica genomes (accessed in April 2011). A consensus tree based on variation of the core genes gives better resolution than 16S rRNA and MLST that rarely provide separation between closely related strains. The performance of the pan-genome tree which is based on the presence....../absence of all genes across genomes, is similar to the consensus tree but with higher branching confidence value. 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. These core genes are useful for investigating molecular...... 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...

  9. Whole Genome Epidemiological Typing of Escherichia coli

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer

    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...

  10. Molecular Epidemiology and Genomics of Group A Streptococcus

    Science.gov (United States)

    Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

    2014-01-01

    Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818

  11. Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing

    Science.gov (United States)

    Fu, Songzhe; Octavia, Sophie; Tanaka, Mark M.; Sintchenko, Vitali

    2015-01-01

    Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium. PMID:26019201

  12. Leptospira species molecular epidemiology in the genomic era.

    Science.gov (United States)

    Caimi, K; Repetto, S A; Varni, V; Ruybal, P

    2017-10-01

    Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

    Science.gov (United States)

    Argimón, Silvia; Abudahab, Khalil; Goater, Richard J E; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J; Holden, Matthew T G; Yeats, Corin A; Grundmann, Hajo; Spratt, Brian G; Aanensen, David M

    2016-11-01

    Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.

  14. A huge cystic craniopharyngioma

    International Nuclear Information System (INIS)

    Takamura, Seishi; Fukumura, Akinobu; Ito, Yoshihiro; Itoyama, Yoichi; Matsukado, Yasuhiko.

    1986-01-01

    The findings of computed tomography (CT) of a huge cystic craniopharyngioma in a 57-year-old woman are described. Cyst density varied from low to high levels in a short duration. Follow-up CT scans were regarded as important to diagnose craniopharyngioma. The mechanism of increment of cyst density was discussed. (author)

  15. Safety of huge systems

    International Nuclear Information System (INIS)

    Kondo, Jiro.

    1995-01-01

    Recently accompanying the development of engineering technology, huge systems tend to be constructed. The disaster countermeasures of huge cities become large problems as the concentration of population into cities is conspicuous. To make the expected value of loss small, the knowledge of reliability engineering is applied. In reliability engineering, even if a part of structures fails, the safety as a whole system must be ensured, therefore, the design having margin is carried out. The degree of margin is called redundancy. However, such design concept makes the structure of a system complex, and as the structure is complex, the possibility of causing human errors becomes high. At the time of huge system design, the concept of fail-safe is effective, but simple design must be kept in mind. The accident in Mihama No. 2 plant of Kansai Electric Power Co. and the accident in Chernobyl nuclear power station, and the accident of Boeing B737 airliner and the fatigue breakdown are described. The importance of safety culture was emphasized as the method of preventing human errors. Man-system interface and management system are discussed. (K.I.)

  16. 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...

  17. The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis.

    Science.gov (United States)

    Mirabello, Lisa; Clarke, Megan A; Nelson, Chase W; Dean, Michael; Wentzensen, Nicolas; Yeager, Meredith; Cullen, Michael; Boland, Joseph F; Schiffman, Mark; Burk, Robert D

    2018-02-13

    Of the ~60 human papillomavirus (HPV) genotypes that infect the cervicovaginal epithelium, only 12-13 "high-risk" types are well-established as causing cervical cancer, with HPV16 accounting for over half of all cases worldwide. While HPV16 is the most important carcinogenic type, variants of HPV16 can differ in their carcinogenicity by 10-fold or more in epidemiologic studies. Strong genotype-phenotype associations embedded in the small 8-kb HPV16 genome motivate molecular studies to understand the underlying molecular mechanisms. Understanding the mechanisms of HPV genomic findings is complicated by the linkage of HPV genome variants. A panel of experts in various disciplines gathered on 21 November 2016 to discuss the interdisciplinary science of HPV oncogenesis. Here, we summarize the discussion of the complexity of the viral-host interaction and highlight important next steps for selected applied basic laboratory studies guided by epidemiological genomic findings.

  18. The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis

    Directory of Open Access Journals (Sweden)

    Lisa Mirabello

    2018-02-01

    Full Text Available Of the ~60 human papillomavirus (HPV genotypes that infect the cervicovaginal epithelium, only 12–13 “high-risk” types are well-established as causing cervical cancer, with HPV16 accounting for over half of all cases worldwide. While HPV16 is the most important carcinogenic type, variants of HPV16 can differ in their carcinogenicity by 10-fold or more in epidemiologic studies. Strong genotype-phenotype associations embedded in the small 8-kb HPV16 genome motivate molecular studies to understand the underlying molecular mechanisms. Understanding the mechanisms of HPV genomic findings is complicated by the linkage of HPV genome variants. A panel of experts in various disciplines gathered on 21 November 2016 to discuss the interdisciplinary science of HPV oncogenesis. Here, we summarize the discussion of the complexity of the viral–host interaction and highlight important next steps for selected applied basic laboratory studies guided by epidemiological genomic findings.

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

    Science.gov (United States)

    Mustapha, Mustapha M; Marsh, Jane W; Krauland, Mary G; Fernandez, Jorge O; de Lemos, Ana Paula S; Dunning Hotopp, Julie C; Wang, Xin; Mayer, Leonard W; Lawrence, Jeffrey G; Hiller, N Luisa; Harrison, Lee H

    2015-10-01

    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.

  20. Genomic epidemiology of global VIM-producing Enterobacteriaceae.

    Science.gov (United States)

    Matsumura, Yasufumi; Peirano, Gisele; Devinney, Rebekah; Bradford, Patricia A; Motyl, Mary R; Adams, Mark D; Chen, Liang; Kreiswirth, Barry; Pitout, Johann D D

    2017-08-01

    International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited. We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14). VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 ). Klebsiella pneumoniae was the most common species ( n  = 45); CC147 from Greece was the most prevalent clone and contained In 590 -like integrons with four different bla VIM s. Enterobacter cloacae complex was the second most common species and mainly consisted of Enterobacter hormaechei ( Enterobacter xiangfangensis , subsp. steigerwaltii and Hoffmann cluster III). CC200 (from Croatia and Turkey), CC114 (Croatia, Greece, Italy and the USA) and CC78 (from Greece, Italy and Spain) containing bla VIM-1 were the most common clones among the E. cloacae complex. This study highlights the importance of surveillance programmes using the latest molecular techniques in providing insight into the characteristics and global distribution of Enterobacteriaceae with bla VIM s. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Using whole genome sequencing to study American foulbrood epidemiology in honeybees.

    Directory of Open Access Journals (Sweden)

    Joakim Ågren

    Full Text Available American foulbrood (AFB, caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily transmitted via the movement of hive equipment or bees. Molecular epidemiology of AFB currently largely relies on placing isolates in one of four ERIC-genotypes. However, a more powerful alternative is multi-locus sequence typing (MLST using whole-genome sequencing (WGS, which allows for high-resolution studies of disease outbreaks. To evaluate WGS as a tool for AFB-epidemiology, we applied core genome MLST (cgMLST on isolates from a recent outbreak of AFB in Sweden. The high resolution of the cgMLST allowed different bacterial clones involved in the disease outbreak to be identified and to trace the source of infection. The source was found to be a beekeeper who had sold bees to two other beekeepers, proving the epidemiological link between them. No such conclusion could have been made using conventional MLST or ERIC-typing. This is the first time that WGS has been used to study the epidemiology of AFB. The results show that the technique is very powerful for high-resolution tracing of AFB-outbreaks.

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

    Directory of Open Access Journals (Sweden)

    João Perdigão

    2015-01-01

    Full Text Available Multidrug- (MDR and extensively drug-resistant (XDR tuberculosis (TB present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidencerate and unusual and successful XDR-TB strains that have been found in circulation foralmost 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

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

    KAUST Repository

    Perdigã o, Joã o; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; McNerney, Ruth; Pain, Arnab; Clark, Taane G.; Viveiros, Miguel; Portugal, Isabel

    2015-01-01

    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

  4. 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

  5. Supersize me: how whole-genome sequencing and big data are transforming epidemiology.

    Science.gov (United States)

    Kao, Rowland R; Haydon, Daniel T; Lycett, Samantha J; Murcia, Pablo R

    2014-05-01

    In epidemiology, the identification of 'who infected whom' allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Epidemiological analysis of Salmonella clusters identified by whole genome sequencing, England and Wales 2014.

    Science.gov (United States)

    Waldram, Alison; Dolan, Gayle; Ashton, Philip M; Jenkins, Claire; Dallman, Timothy J

    2018-05-01

    The unprecedented level of bacterial strain discrimination provided by whole genome sequencing (WGS) presents new challenges with respect to the utility and interpretation of the data. Whole genome sequences from 1445 isolates of Salmonella belonging to the most commonly identified serotypes in England and Wales isolated between April and August 2014 were analysed. Single linkage single nucleotide polymorphism thresholds at the 10, 5 and 0 level were explored for evidence of epidemiological links between clustered cases. Analysis of the WGS data organised 566 of the 1445 isolates into 32 clusters of five or more. A statistically significant epidemiological link was identified for 17 clusters. The clusters were associated with foreign travel (n = 8), consumption of Chinese takeaways (n = 4), chicken eaten at home (n = 2), and one each of the following; eating out, contact with another case in the home and contact with reptiles. In the same time frame, one cluster was detected using traditional outbreak detection methods. WGS can be used for the highly specific and highly sensitive detection of biologically related isolates when epidemiological links are obscured. Improvements in the collection of detailed, standardised exposure information would enhance cluster investigations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. 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.

  8. 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

  9. Huge interparietal posterior fontanel meningohydroencephalocele

    Directory of Open Access Journals (Sweden)

    Jorge Félix Companioni Rosildo

    2015-03-01

    Full Text Available Congenital encephalocele is a neural tube defect characterized by a sac-like protrusion of the brain, meninges, and other intracranial structures through the skull, which is caused by an embryonic development abnormality. The most common location is at the occipital bone, and its incidence varies according to different world regions. We report a case of an 1-month and 7-day-old male child with a huge interparietal-posterior fontanel meningohydroencephalocele, a rare occurrence. Physical examination and volumetric computed tomography were diagnostic. The encephalocele was surgically resected. Intradural and extradural approaches were performed; the bone defect was not primarily closed. Two days after surgery, the patient developed hydrocephaly requiring ventriculoperitoneal shunting. The surgical treatment of the meningohydroencephalocele of the interparietal-posterior fontanel may be accompanied by technical challenges and followed by complications due to the presence of large blood vessels under the overlying skin. In these cases, huge sacs herniate through large bone defects including meninges, brain, and blood vessels. The latter present communication with the superior sagittal sinus and ventricular system. A favorable surgical outcome generally follows an accurate strategy taking into account individual features of the lesion.

  10. Racial and Ethnic Differences in the Epidemiology and Genomics of Lung Cancer.

    Science.gov (United States)

    Schabath, Matthew B; Cress, Douglas; Munoz-Antonia, Teresita

    2016-10-01

    Lung cancer is the most common cancer in the world. In addition to the geographical and sex-specific differences in the incidence, mortality, and survival rates of lung cancer, growing evidence suggests that racial and ethnic differences exist. We reviewed published data related to racial and ethnic differences in lung cancer. Current knowledge and substantive findings related to racial and ethnic differences in lung cancer were summarized, focusing on incidence, mortality, survival, cigarette smoking, prevention and early detection, and genomics. Systems-level and health care professional-related issues likely to contribute to specific racial and ethnic health disparities were also reviewed to provide possible suggestions for future strategies to reduce the disproportionate burden of lung cancer. Although lung carcinogenesis is a multifactorial process driven by exogenous exposures, genetic variations, and an accumulation of somatic genetic events, it appears to have racial and ethnic differences that in turn impact the observed epidemiological differences in rates of incidence, mortality, and survival.

  11. 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

    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...

  12. Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital.

    Science.gov (United States)

    Lesho, Emil P; Bronstein, Melissa Z; McGann, Patrick; Stam, Jason; Kwak, Yoon; Maybank, Rosslyn; McNamara, Jodi; Callahan, Megan; Campbell, Jean; Hinkle, Mary K; Walsh, Edward E

    2018-01-01

    OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure. DESIGN Quasi-experimental observation. SETTING A 528-bed teaching hospital. PATIENTS The index case patient and 17 collocated ward mates. INTERVENTION Immediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology. RESULTS Candida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4-8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later. CONCLUSION Compared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations. Infect Control Hosp Epidemiol 2018;39:53-57.

  13. 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

  14. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit.

    Directory of Open Access Journals (Sweden)

    Taj Azarian

    Full Text Available Despite infection prevention efforts, neonatal intensive care unit (NICU patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA infection. Modes of transmission for healthcare-associated (HA and community-associated (CA MRSA remain poorly understood and may vary by genotype, hindering the development of effective prevention and control strategies. From 2008-2010, all patients admitted to a level III NICU were screened for MRSA colonization, and all available isolates were spa-typed. Spa-type t008, the most prevalent CA- genotype in the United States, spa-type t045, a HA- related genotype, and a convenience sample of strains isolated from 2003-2011, underwent whole-genome sequencing and phylodynamic analysis. Patient risk factors were compared between colonized and noncolonized infants, and virulence and resistance genes compared between spa-type t008 and non-t008 strains. Epidemiological and genomic data were used to estimate MRSA importations and acquisitions through transmission reconstruction. MRSA colonization was identified in 9.1% (177/1940 of hospitalized infants and associated with low gestational age and birth weight. Among colonized infants, low gestational age was more common among those colonized with t008 strains. Our data suggest that approximately 70% of colonizations were the result of transmission events within the NICU, with the remainder likely to reflect importations of "outside" strains. While risk of transmission within the NICU was not affected by spa-type, patterns of acquisition and importation differed between t008 and t045 strains. Phylodynamic analysis showed the effective population size of spa-type t008 has been exponentially increasing in both community and hospital, with spa-type t008 strains possessed virulence genes not found among t045 strains; t045 strains, in contrast, appeared to be of more recent origin, with a possible hospital source. Our data highlight the importance of both intra

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

    Science.gov (United States)

    Fitzpatrick, Margaret A.; Hauser, Alan R.

    2015-01-01

    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. PMID:26699703

  16. 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

  17. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    NARCIS (Netherlands)

    Belkum, van A.; Struelens, M.; Visser, de J.A.G.M.; Verburgh, H.; Tibayrenc., M.

    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

  18. Population Genomics of Francisella tularensis subsp. holarctica and its Implication on the Eco-Epidemiology of Tularemia in Switzerland.

    Science.gov (United States)

    Wittwer, Matthias; Altpeter, Ekkehard; Pilo, Paola; Gygli, Sebastian M; Beuret, Christian; Foucault, Frederic; Ackermann-Gäumann, Rahel; Karrer, Urs; Jacob, Daniela; Grunow, Roland; Schürch, Nadia

    2018-01-01

    Whole genome sequencing (WGS) methods provide new possibilities in the field of molecular epidemiology. This is particularly true for monomorphic organisms where the discriminatory power of traditional methods (e.g., restriction enzyme length polymorphism typing, multi locus sequence typing etc.) is inadequate to elucidate complex disease transmission patterns, as well as resolving the phylogeny at high resolution on a micro-geographic scale. In this study, we present insights into the population structure of Francisella tularensis subsp. holarctica , the causative agent of tularemia in Switzerland. A total of 59 Fth isolates were obtained from castor bean ticks ( Ixodes ricinus) , animals and humans and a high resolution phylogeny was inferred using WGS methods. The majority of the Fth population in Switzerland belongs to the west European B.11 clade and shows an extraordinary genetic diversity underlining the old evolutionary history of the pathogen in the alpine region. Moreover, a new B.11 subclade was identified which was not described so far. The combined analysis of the epidemiological data of human tularemia cases with the whole genome sequences of the 59 isolates provide evidence that ticks play a pivotal role in transmitting Fth to humans and other vertebrates in Switzerland. This is further underlined by the correlation of disease risk estimates with climatic and ecological factors influencing the survival of ticks.

  19. Gene Set Analyses of Genome-Wide Association Studies on 49 Quantitative Traits Measured in a Single Genetic Epidemiology Dataset

    Directory of Open Access Journals (Sweden)

    Jihye Kim

    2013-09-01

    Full Text Available 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 < 0.05. Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  20. Population Genomics of Francisella tularensis subsp. holarctica and its Implication on the Eco-Epidemiology of Tularemia in Switzerland

    Science.gov (United States)

    Wittwer, Matthias; Altpeter, Ekkehard; Pilo, Paola; Gygli, Sebastian M.; Beuret, Christian; Foucault, Frederic; Ackermann-Gäumann, Rahel; Karrer, Urs; Jacob, Daniela; Grunow, Roland; Schürch, Nadia

    2018-01-01

    Whole genome sequencing (WGS) methods provide new possibilities in the field of molecular epidemiology. This is particularly true for monomorphic organisms where the discriminatory power of traditional methods (e.g., restriction enzyme length polymorphism typing, multi locus sequence typing etc.) is inadequate to elucidate complex disease transmission patterns, as well as resolving the phylogeny at high resolution on a micro-geographic scale. In this study, we present insights into the population structure of Francisella tularensis subsp. holarctica, the causative agent of tularemia in Switzerland. A total of 59 Fth isolates were obtained from castor bean ticks (Ixodes ricinus), animals and humans and a high resolution phylogeny was inferred using WGS methods. The majority of the Fth population in Switzerland belongs to the west European B.11 clade and shows an extraordinary genetic diversity underlining the old evolutionary history of the pathogen in the alpine region. Moreover, a new B.11 subclade was identified which was not described so far. The combined analysis of the epidemiological data of human tularemia cases with the whole genome sequences of the 59 isolates provide evidence that ticks play a pivotal role in transmitting Fth to humans and other vertebrates in Switzerland. This is further underlined by the correlation of disease risk estimates with climatic and ecological factors influencing the survival of ticks. PMID:29623260

  1. 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. Copyright © 2016, American Association for the Advancement of Science.

  2. Huge cystic craniopharyngioma with unusual extensions

    Energy Technology Data Exchange (ETDEWEB)

    Kitano, I.; Yoneda, K.; Yamakawa, Y.; Fukui, M.; Kinoshita, K.

    1981-09-01

    The findings on computed tomography (CT) of a huge cystic craniopharyngioma in a 3-year-old girl are described. The cyst occupied both anterior cranial fossae and a part of it extended to the region of the third ventricle which was displaced posteriorly. The tumor showed no contrast enhancement after the intravenous administration of contrast medium.

  3. Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington.

    Science.gov (United States)

    Austin, Melissa A

    2002-04-01

    Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.

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

    OpenAIRE

    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. ...

  5. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    OpenAIRE

    Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.

    2001-01-01

    textabstractCurrently, 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 microbiologi...

  6. Huge Thornwaldt's Cyst: A Case Report

    Directory of Open Access Journals (Sweden)

    Jia-Hau Lin

    2006-10-01

    Full Text Available Thornwaldt's bursa, also known as nasopharyngeal bursa, is a recess in the midline of the nasopharynx that is produced by persistent notochord remnants. If its opening becomes obstructed, possibly due to infection or a complication from adenoidectomy, a Thornwaldt's cyst might develop. Here, we present a 53-year-old man who complained of nasal obstruction that had progressed for 1 year. Nasopharyngoscopy showed a huge nasopharyngeal mass. Thornwaldt's cyst was suspected. Magnetic resonance imaging showed a lesion measuring 3.6 × 3.4 cm, intermediate on T1-weighted and high signal intensity on T2-weighted imaging, neither bony destruction nor connection to the brain. The patient underwent endoscopic surgery for this huge mass. Afterwards, his symptoms improved significantly. We present the treatment and differential diagnosis of a nasopharyngeal cyst.

  7. 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

  8. Connecting slow earthquakes to huge earthquakes

    OpenAIRE

    Obara, Kazushige; Kato, Aitaro

    2016-01-01

    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 th...

  9. 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...

  10. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

    Science.gov (United States)

    Schürch, A C; Arredondo-Alonso, S; Willems, R J L; Goering, R V

    2018-04-01

    Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Personal collection of relevant publications. When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. 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.

  12. Epidemiology of Danish Aeromonas salmonicida subsp salmonicida in Fish Farms Using Whole Genome Sequencing

    DEFF Research Database (Denmark)

    Bartkova, Simona; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller

    2017-01-01

    transmission of the bacterium could have been from seawater to freshwater or vice versa, and most minor clades include a mixture of strains from different fresh- and seawater farms. Genomic variation of A. salmonicida subsp. salmonicida mostly appeared to be associated with their plasmids and plasmid encoded...

  13. 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

    serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains...

  14. 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...

  15. Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

    Science.gov (United States)

    Ou, Hong-Yu; Kuang, Shan N.; He, Xinyi; Molgora, Brenda M.; Ewing, Peter J.; Deng, Zixin; Osby, Melanie; Chen, Wangxue; Xu, H. Howard

    2015-01-01

    Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii. PMID:25728466

  16. [Genomic DNA fingerprints of Legionella pneumophila serogroup 2 strains as an epidemiologic marker].

    Science.gov (United States)

    Bender-Beck, L; Mühlenberg, W; Lück, P C; Ott, M; Horbach, I; Fehrenbach, F J; Wewalka, G; Hacker, J

    1995-08-01

    Using pulsed-field gel electrophoresis, DNA fingerprints of eleven Legionella pneumophila isolates of serogroup 2 were generated. It was shown that two strains from a patient suffering from pneumonia as well as three environmental strains isolated from the shower in the hotel where the patient stayed 5 days before his illness were identical. Six strains of the same serogroup isolated from other sources were clearly separated. Thus, DNA fingerprints by pulsed-field gel electrophoresis are excellent epidemiological markers for the rarely occurring serogroup 2 of Legionella pneumophila.

  17. 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.

  18. 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

    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. PMID:24378019

  19. 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.

  20. Genomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection.

    Science.gov (United States)

    Grinberg, Alex; Biggs, Patrick J; Zhang, Ji; Ritchie, Stephen; Oneroa, Zachary; O'Neill, Charlotte; Karkaba, Ali; Velathanthiri, Niluka S; Coombs, Geoffrey W

    2017-10-01

    Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains. We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets. Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%). In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk. Copyright © 2017 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  1. 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. Copyright © 2016 David et al.

  2. The Genomic Architecture of Novel Simulium damnosum Wolbachia Prophage Sequence Elements and Implications for Onchocerciasis Epidemiology

    Directory of Open Access Journals (Sweden)

    James L. Crainey

    2017-05-01

    Full Text Available Research interest in Wolbachia is growing as new discoveries and technical advancements reveal the public health importance of both naturally occurring and artificial infections. Improved understanding of the Wolbachia bacteriophages (WOs WOcauB2 and WOcauB3 [belonging to a sub-group of four WOs encoding serine recombinases group 1 (sr1WOs], has enhanced the prospect of novel tools for the genetic manipulation of Wolbachia. The basic biology of sr1WOs, including host range and mode of genomic integration is, however, still poorly understood. Very few sr1WOs have been described, with two such elements putatively resulting from integrations at the same Wolbachia genome loci, about 2 kb downstream from the FtsZ cell-division gene. Here, we characterize the DNA sequence flanking the FtsZ gene of wDam, a genetically distinct line of Wolbachia isolated from the West African onchocerciasis vector Simulium squamosum E. Using Roche 454 shot-gun and Sanger sequencing, we have resolved >32 kb of WO prophage sequence into three contigs representing three distinct prophage elements. Spanning ≥36 distinct WO open reading frame gene sequences, these prophage elements correspond roughly to three different WO modules: a serine recombinase and replication module (sr1RRM, a head and base-plate module and a tail module. The sr1RRM module contains replication genes and a Holliday junction recombinase and is unique to the sr1 group WOs. In the extreme terminal of the tail module there is a SpvB protein homolog—believed to have insecticidal properties and proposed to have a role in how Wolbachia parasitize their insect hosts. We propose that these wDam prophage modules all derive from a single WO genome, which we have named here sr1WOdamA1. The best-match database sequence for all of our sr1WOdamA1-predicted gene sequences was annotated as of Wolbachia or Wolbachia phage sourced from an arthropod. Clear evidence of exchange between sr1WOdamA1 and other Wolbachia

  3. 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...... organization enables an attractive new class of applications for managing ever-increasing music databases. For these types of applications, extraction of music features as well as subsequent feature processing and music classification have to be performed. However, these are computationally intensive tasks...... 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...

  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. Nanocellulose, a tiny fiber with huge applications.

    Science.gov (United States)

    Abitbol, Tiffany; Rivkin, Amit; Cao, Yifeng; Nevo, Yuval; Abraham, Eldho; Ben-Shalom, Tal; Lapidot, Shaul; Shoseyov, Oded

    2016-06-01

    Nanocellulose is of increasing interest for a range of applications relevant to the fields of material science and biomedical engineering due to its renewable nature, anisotropic shape, excellent mechanical properties, good biocompatibility, tailorable surface chemistry, and interesting optical properties. We discuss the main areas of nanocellulose research: photonics, films and foams, surface modifications, nanocomposites, and medical devices. These tiny nanocellulose fibers have huge potential in many applications, from flexible optoelectronics to scaffolds for tissue regeneration. We hope to impart the readers with some of the excitement that currently surrounds nanocellulose research, which arises from the green nature of the particles, their fascinating physical and chemical properties, and the diversity of applications that can be impacted by this material. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. 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.

  7. 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 ...... that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak....... remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse...... French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck...

  8. 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.

  9. 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

  10. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis.

    Science.gov (United States)

    Wyrsch, Ethan R; Roy Chowdhury, Piklu; Chapman, Toni A; Charles, Ian G; Hammond, Jeffrey M; Djordjevic, Steven P

    2016-01-01

    Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

  11. Epidemiological and Genome-Wide Association Study of Gastritis or Gastric Ulcer in Korean Populations

    Directory of Open Access Journals (Sweden)

    Sumin Oh

    2014-09-01

    Full Text Available Gastritis is a major disease that has the potential to grow as gastric cancer. Gastric cancer is a very common cancer, and it is related to a very high mortality rate in Korea. This disease is known to have various reasons, including infection with Helicobacter pylori, dietary habits, tobacco, and alcohol. The incidence rate of gastritis has reported to differ between age, population, and gender. However, unlike other factors, there has been no analysis based on gender. So, we examined the high risk factors of gastritis in each gender in the Korean population by focusing on sex. We performed an analysis of 120 clinical characteristics and genome-wide association studies (GWAS using 349,184 single-nucleotide polymorphisms from the results of Anseong and Ansan cohort study in the Korea Association Resource (KARE project. As the result, we could not prove a strong relation with these factors and gastritis or gastric ulcer in the GWAS. However, we confirmed several already-known risk factors and also found some differences of clinical characteristics in each gender using logistic regression. As a result of the logistic regression, a relation with hyperlipidemia, coronary artery disease, myocardial infarction, hyperlipidemia therapy, hypotensive or antihypotensive drug, diastolic blood pressure, and gastritis was seen in males; the results of this study suggest that vascular disease has a potential association with gastritis in males.

  12. 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.

  13. Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study.

    Science.gov (United States)

    Jajou, Rana; de Neeling, Albert; van Hunen, Rianne; de Vries, Gerard; Schimmel, Henrieke; Mulder, Arnout; Anthony, Richard; van der Hoek, Wim; van Soolingen, Dick

    2018-01-01

    Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping. VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated. In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%). When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.

  14. Huge hydrocephalus: definition, management, and complications.

    Science.gov (United States)

    Faghih Jouibari, Morteza; Baradaran, Nazanin; Shams Amiri, Rouzbeh; Nejat, Farideh; El Khashab, Mostafa

    2011-01-01

    Lack of comprehensive knowledge and numerous socioeconomic problems may make the parents leave hydrocephalic children untreated, leading to progressive hydrocephalus and eventual unordinary big head. Management of huge hydrocephalus (HH) differs from common hydrocephalus. We present our experience in the management of these children. HH is defined as head circumference larger than the height of the infant. Nine infants with HH have been shunted in Children's Hospital Medical Center and followed up for 0.5 to 7 years. The most common cause of hydrocephalus was aqueductal stenosis. The mean age of patients during shunting was 3 months. The head circumference ranged from 56 to 94 cm with the average of 67 cm. Cognitive statuses were appropriate based on their age in five patients. Motor development was normal only in one patient. Complications were found in most cases which included subdural effusion (six patients), shunt infection (four patients), skin injury (three patients), proximal catheter coming out of ventricle to the subdural space (two patients), and shunt exposure (one patient). Three patients died due to shunt infection and sepsis. Numerous complications may occur in patients with HH after shunt operation such as subdural effusion, ventricular collapse, electrolyte disturbance, skull deformity, scalp injury, and shunt infection. Mental and motor disabilities are very common in patients with HH. Many of these complications can be related to overdrainage; therefore, drainage control using programmable shunts is advisable.

  15. Process control upgrades yield huge operational improvements

    International Nuclear Information System (INIS)

    Fitzgerald, W.V.

    2001-01-01

    Most nuclear plants in North America were designed and built in the late 60 and 70. The regulatory nature of this industry over the years has made design changes at the plant level difficult, if not impossible, to implement. As a result, many plants in this world region have been getting by on technology that is over 40 years behind the times. What this translates into is that the plants have not been able to take advantage of the huge technology gains that have been made in process control during this period. As a result, most of these plants are much less efficient and productive than they could be. One particular area of the plant that is receiving a lot of attention is the feedwater heaters. These systems were put in place to improve efficiency, but most are not operating correctly. This paper will present a case study where one progressive mid-western utility decided that enough was enough and implemented a process control audit of their heater systems. The audit clearly pointed out the existing problems with the current process control system. It resulted in a proposal for the implementation of a state of the art, digital distributed process control system for the heaters along with a complete upgrade of the level controls and field devices that will stabilize heater levels, resulting in significant efficiency gains and lower maintenance bills. Overall the payback period for this investment should be less than 6 months and the plant is now looking for more opportunities that can provide even bigger gains. (author)

  16. 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

  17. Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses.

    Science.gov (United States)

    Lockhart, Shawn R; Etienne, Kizee A; Vallabhaneni, Snigdha; Farooqi, Joveria; Chowdhary, Anuradha; Govender, Nelesh P; Colombo, Arnaldo Lopes; Calvo, Belinda; Cuomo, Christina A; Desjardins, Christopher A; Berkow, Elizabeth L; Castanheira, Mariana; Magobo, Rindidzani E; Jabeen, Kauser; Asghar, Rana J; Meis, Jacques F; Jackson, Brendan; Chiller, Tom; Litvintseva, Anastasia P

    2017-01-15

    Candida auris, a multidrug-resistant yeast that causes invasive infections, was first described in 2009 in Japan and has since been reported from several countries. To understand the global emergence and epidemiology of C. auris, we obtained isolates from 54 patients with C. auris infection from Pakistan, India, South Africa, and Venezuela during 2012-2015 and the type specimen from Japan. Patient information was available for 41 of the isolates. We conducted antifungal susceptibility testing and whole-genome sequencing (WGS). Available clinical information revealed that 41% of patients had diabetes mellitus, 51% had undergone recent surgery, 73% had a central venous catheter, and 41% were receiving systemic antifungal therapy when C. auris was isolated. The median time from admission to infection was 19 days (interquartile range, 9-36 days), 61% of patients had bloodstream infection, and 59% died. Using stringent break points, 93% of isolates were resistant to fluconazole, 35% to amphotericin B, and 7% to echinocandins; 41% were resistant to 2 antifungal classes and 4% were resistant to 3 classes. WGS demonstrated that isolates were grouped into unique clades by geographic region. Clades were separated by thousands of single-nucleotide polymorphisms, but within each clade isolates were clonal. Different mutations in ERG11 were associated with azole resistance in each geographic clade. C. auris is an emerging healthcare-associated pathogen associated with high mortality. Treatment options are limited, due to antifungal resistance. WGS analysis suggests nearly simultaneous, and recent, independent emergence of different clonal populations on 3 continents. Risk factors and transmission mechanisms need to be elucidated to guide control measures. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  18. Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India.

    Science.gov (United States)

    Qumar, Shamsul; Majid, Mohammad; Kumar, Narender; Tiwari, Sumeet K; Semmler, Torsten; Devi, Savita; Baddam, Ramani; Hussain, Arif; Shaik, Sabiha; Ahmed, Niyaz

    2017-01-01

    Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken isolates

  19. Calculation of evolutionary correlation between individual genes and full-length genome: a method useful for choosing phylogenetic markers for molecular epidemiology.

    Directory of Open Access Journals (Sweden)

    Shuai Wang

    Full Text Available Individual genes or regions are still commonly used to estimate the phylogenetic relationships among viral isolates. The genomic regions that can faithfully provide assessments consistent with those predicted with full-length genome sequences would be preferable to serve as good candidates of the phylogenetic markers for molecular epidemiological studies of many viruses. Here we employed a statistical method to evaluate the evolutionary relationships between individual viral genes and full-length genomes without tree construction as a way to determine which gene can match the genome well in phylogenetic analyses. This method was performed by calculation of linear correlations between the genetic distance matrices of aligned individual gene sequences and aligned genome sequences. We applied this method to the phylogenetic analyses of porcine circovirus 2 (PCV2, measles virus (MV, hepatitis E virus (HEV and Japanese encephalitis virus (JEV. Phylogenetic trees were constructed for comparisons and the possible factors affecting the method accuracy were also discussed in the calculations. The results revealed that this method could produce results consistent with those of previous studies about the proper consensus sequences that could be successfully used as phylogenetic markers. And our results also suggested that these evolutionary correlations could provide useful information for identifying genes that could be used effectively to infer the genetic relationships.

  20. Molecular epidemiology of HIV type 1 infection in Iran: genomic evidence of CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use.

    Science.gov (United States)

    Jahanbakhsh, Fatemeh; Ibe, Shiro; Hattori, Junko; Monavari, Seyed Hamid Reza; Matsuda, Masakazu; Maejima, Masami; Iwatani, Yasumasa; Memarnejadian, Arash; Keyvani, Hossein; Azadmanesh, Kayhan; Sugiura, Wataru

    2013-01-01

    To understand the molecular epidemiology of HIV-1 infection in Iran, we conducted the first study to analyze the genome sequence of Iranian HIV-1 isolates. For this cross-sectional study, we enrolled 10 HIV-1-infected individuals associated with injection drug use from Tehran, Shiraz, and Kermanshah. Near full-length genome sequences obtained from their plasma samples were used for phylogenetic tree and similarity plotting analyses. Among 10 isolates, nine were clearly identified as CRF35_AD and the remaining one as CRF01_AE. Interestingly, five of our Iranian CRF35_AD isolates made two clusters with 10 Afghan CRF35_AD isolates in a phylogenetic tree, indicating epidemiological connections among injection drug users in Iran and Afghanistan. In contrast, our CRF01_AE isolate had no genetic relationship with any other CRF01_AE isolates worldwide, even from Afghanistan. This study provides the first genomic evidence of HIV-1 CRF35_AD predominance and CRF01_AE infection among individuals associated with injection drug use in Iran.

  1. 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

  2. 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

  3. Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.

    Science.gov (United States)

    Woksepp, Hanna; Ryberg, Anna; Berglind, Linda; Schön, Thomas; Söderman, Jan

    2017-12-01

    Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  4. 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.

    Directory of Open Access Journals (Sweden)

    Kyung-Hwa Park

    Full Text Available 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.

  5. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  6. Huge maternal hydronephrosis: a rare complication in pregnancy.

    Science.gov (United States)

    Peng, Hsiu-Huei; Wang, Chin-Jung; Yen, Chih-Feng; Chou, Chien-Chung; Lee, Chyi-Long

    2003-06-10

    A huge maternal hydronephrosis is uncommon in pregnancy and might be mistaken as a pelvic mass. A 21-year-old primigravida was noted at 25th week of gestation to have a visible bulging mass on her left flank. The mass was originally mistaken as a large ovarian cyst but later proved to be a huge hydronephrosis. Retrograde insertion of ureteroscope and a ureteric stent failed, so we performed repeated ultrasound-guided needle aspiration to decompress the huge hydronephrosis, which enabled the patient to proceed to a successful term vaginal delivery. Nephrectomy was performed after delivery and proved the diagnosis of congenital ureteropelvic junction obstruction.

  7. Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015.

    Science.gov (United States)

    Thompson, C K; Wang, Q; Bag, S K; Franklin, N; Shadbolt, C T; Howard, P; Fearnley, E J; Quinn, H E; Sintchenko, V; Hope, K G

    2017-07-01

    During May 2015, an increase in Salmonella Agona cases was reported from western Sydney, Australia. We examine the public health actions used to investigate and control this increase. A descriptive case-series investigation was conducted. Six outbreak cases were identified; all had consumed cooked tuna sushi rolls purchased within a western Sydney shopping complex. Onset of illness for outbreak cases occurred between 7 April and 24 May 2015. Salmonella was isolated from food samples collected from the implicated premise and a prohibition order issued. No further cases were identified following this action. Whole genome sequence (WGS) analysis was performed on isolates recovered during this investigation, with additional S. Agona isolates from sporadic-clinical cases and routine food sampling in New South Wales, January to July 2015. Clinical isolates of outbreak cases were indistinguishable from food isolates collected from the implicated sushi outlet. Five additional clinical isolates not originally considered to be linked to the outbreak were genomically similar to outbreak isolates, indicating the point-source contamination may have started before routine surveillance identified an increase. This investigation demonstrated the value of genomics-guided public health action, where near real-time WGS enhanced the resolution of the epidemiological investigation.

  8. Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses

    NARCIS (Netherlands)

    Lockhart, S.R.; Etienne, K.A.; Vallabhaneni, S.; Farooqi, J.; Chowdhary, A.; Govender, N.P.; Colombo, A.L.; Calvo, B.; Cuomo, C.A.; Desjardins, C.A.; Berkow, E.L.; Castanheira, M.; Magobo, R.E.; Jabeen, K.; Asghar, R.J.; Meis, J.F.G.M.; Jackson, B.; Chiller, T.; Litvintseva, A.P.

    2017-01-01

    BACKGROUND: Candida auris, a multidrug-resistant yeast that causes invasive infections, was first described in 2009 in Japan and has since been reported from several countries. METHODS: To understand the global emergence and epidemiology of C. auris, we obtained isolates from 54 patients with C.

  9. Aggressive angiomyxoma presenting with huge abdominal lump: A case report

    Science.gov (United States)

    Kumar, Sanjeev; Agrawal, Nikhil; Khanna, Rahul; Khanna, AK

    2008-01-01

    Agressive angiomyxoma is a rare mesenchymal neoplasm. It mainly presents in females. We here present a case of angiomyxoma presenting as huge abdominal lump along with gluteal swelling. Case note is described along with brief review of literature. PMID:18755035

  10. Huge magnetoresistance effect of highly oriented pyrolytic graphite

    International Nuclear Information System (INIS)

    Du Youwei; Wang Zhiming; Ni Gang; Xing Dingyu; Xu Qingyu

    2004-01-01

    Graphite is a quasi-two-dimensional semimetal. However, for usual graphite the magnetoresistance is not so high due to its small crystal size and no preferred orientation. Huge positive magnetoresistance up to 85300% at 4.2 K and 4950% at 300 K under 8.15 T magnetic field was found in highly oriented pyrolytic graphite. The mechanism of huge positive magnetoresistance is not only due to ordinary magnetoresistance but also due to magnetic-field-driven semimetal-insulator transition

  11. Taxonomic and epidemiological aspects of the bovine viral diarrhoea virus 2 species through the observation of the secondary structures in the 5' genomic untranslated region

    Directory of Open Access Journals (Sweden)

    Massimo Giangaspero

    2008-06-01

    Full Text Available Bovine viral diarrhoea virus 2 (BVDV-2 strains demonstrated in cattle, sheep and adventitious contaminants of biological products were evaluated by the palindromic nucleotide substitutions (PNS method at the three variable loci (V1, V2 and V3 in the 5’ untranslated region (UTR, to determine their taxonomic status. Variation in conserved genomic sequences was used as a parameter for the epidemiological evaluation of the species in relation to geographic distribution, animal host and virulence. Four genotypes were identified within the species. Taxonomic segregation corresponded to geographic distribution of genotype variants. Genotype 2a was distributed worldwide and was also the only genotype that was circulating in sheep and cattle. Genotypes 2b, 2c and 2d were restricted to South America. Genotypes 2a and 2d were related to the contamination of biological products. Genetic variation could be related to the spread of BVDV-2 species variants in different geographic areas. Chronologically, the species emerged in North America in 1978 and spread to the United Kingdom and Japan, continental Europe, South America and New Zealand. Correlation between clinical features related with isolation of BVDV-2 strains and genetic variation indicated that subgenotype 1, variant 4 of genotype 2a, was related to a haemorrhagic syndrome. These observations suggest that the evaluation of genomic secondary structures, by identifying markers for expression of virus biological activities and species evolutionary history, may be a useful tool for the epidemiological evaluation of BVDV-2 species and possibly of other species of the genus Pestivirus.

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

    Science.gov (United States)

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    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. 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 ViroSeq™ HIV-1 Genotyping System. 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 ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. 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.

  13. 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

  14. Application of whole genome sequence data in analyzing the molecular epidemiology of Shiga toxin-producing Escherichia coli O157:H7/H.

    Science.gov (United States)

    Yokoyama, Eiji; Hirai, Shinichiro; Ishige, Taichiro; Murakami, Satoshi

    2018-01-02

    Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs). Among both SNPs, those that were detected in genes with a gap were excluded to remove ambiguous SNPs from further analysis. The effectiveness of both SNPs was investigated among all the concatenated SNPs that were detected (whole SNP set); SNPs were divided into three categories based on the genes in which they were located (i.e., backbone SNP set, O-island SNP set, and mobile element SNP set); and SNPs in non-coding regions (intergenic region SNP set). When SNPs from strains isolated from the nine single source derived outbreaks were analyzed using an unweighted pair group method with arithmetic mean tree (UPGMA) and a minimum spanning tree (MST), the maximum pair-wise distances of the backbone SNP set of the mapping derived SNPs were significantly smaller than those of the whole and intergenic region SNP set on both UPGMAs and MSTs. This significant difference was also observed when the backbone SNP set of the common SNPs were examined (Steel-Dwass test, P≤0.01). When the maximum pair-wise distances were compared between the mapping derived and common SNPs, significant differences were observed in those of the whole, mobile element, and intergenic region SNP set (Wilcoxon signed rank test, P≤0.01). When all

  15. Hospital Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Tertiary Care Hospital in Moshi, Tanzania, as Determined by Whole Genome Sequencing

    DEFF Research Database (Denmark)

    Kumburu, Happiness H.; Sonda, Tolbert; Leekitcharoenphon, Pimlapas

    2018-01-01

    Objective. To determine molecular epidemiology of methicillin-resistant S. aureus in Tanzania using whole genome sequencing. Methods. DNA from 33 Staphylococcus species was recovered from subcultured archived Staphylococcus isolates. Whole genome sequencing was performed on IlluminaMiseq using...... among the 30 S. aureus isolates, with ST-8 (n = seven, 23%) being the most common. Gene detection in S. aureus stains were as follows: mecA, 10 (33.3%); pvl, 5 (16.7%); tst, 2 (6.7%). The SNP difference among the six Tanzanian ST-8MRSA isolates ranged from 24 to 196 SNPs and from 16 to 446 SNPs when...... using the USA300_FPR3757 or the USA500 2395 as a reference, respectively. The mutation rate was 1.38 x 10(-11) SNPs/site/year or 1.4 x 10(-6) SNPs/site/year as estimated by USA300 FPR3757 or the USA500 2395, respectively. Conclusion. S. aureus isolates causing infections in hospitalized patients...

  16. 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.

  17. Detection of Multiple Parallel Transmission Outbreak of Streptococcus suis Human Infection by Use of Genome Epidemiology, China, 2005.

    Science.gov (United States)

    Du, Pengcheng; Zheng, Han; Zhou, Jieping; Lan, Ruiting; Ye, Changyun; Jing, Huaiqi; Jin, Dong; Cui, Zhigang; Bai, Xuemei; Liang, Jianming; Liu, Jiantao; Xu, Lei; Zhang, Wen; Chen, Chen; Xu, Jianguo

    2017-02-01

    Streptococcus suis sequence type 7 emerged and caused 2 of the largest human infection outbreaks in China in 1998 and 2005. To determine the major risk factors and source of the infections, we analyzed whole genomes of 95 outbreak-associated isolates, identified 160 single nucleotide polymorphisms, and classified them into 6 clades. Molecular clock analysis revealed that clade 1 (responsible for the 1998 outbreak) emerged in October 1997. Clades 2-6 (responsible for the 2005 outbreak) emerged separately during February 2002-August 2004. A total of 41 lineages of S. suis emerged by the end of 2004 and rapidly expanded to 68 genome types through single base mutations when the outbreak occurred in June 2005. We identified 32 identical isolates and classified them into 8 groups, which were distributed in a large geographic area with no transmission link. These findings suggest that persons were infected in parallel in respective geographic sites.

  18. Huge Mesenteric Lymphangioma – A Rare Cause of Acute Abdomen

    African Journals Online (AJOL)

    Lymphangiomas are benign congenital masses which occur most commonly in head and neck of children and incidence of mesenteric lymphangiomas is very rare. We report such a case of huge mesenteric lymphangioma in a 20 year old male who presented to us with acute abdomen. Pre-operative diagnosis is difficult ...

  19. 61 HUGE BENIGN GRANULOSA CELL TUMOUR IN A 61 YEAR ...

    African Journals Online (AJOL)

    Dr. E. P. Gharoro

    peritoneal cavity, huge right ovarian cyst measuring 37cm/29cm as in figure 1a, weighing 8.3 kg with a thick smooth wall without excrescences on surface. ... is released in the blood during pregnancy and is produced in other conditions such as endometriosis, fibroids and diverticulitis. It is useful in monitoring therapy.

  20. Umbilicoplasty in children with huge umbilical hernia | Komlatsè ...

    African Journals Online (AJOL)

    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 fl aps umbilicoplasty is well-adapted to HUH in children. Itis simple and assures a satisfactory anatomical and cosmetic result. Key words: Children, huge umbilical hernia, Togo, umbilical ...

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

    OpenAIRE

    Uyanikoglu, Hacer; Dusak, Abdurrahim

    2017-01-01

    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.

  2. Huge cystic craniopharyngioma. Changes of cyst density on computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Takamura, Seishi; Fukumura, Akinobu; Ito, Yoshihiro; Itoyama, Yoichi; Matsukado, Yasuhiko

    1986-06-01

    The findings of computed tomography (CT) of a huge cystic craniopharyngioma in a 57-year-old woman are described. Cyst density varied from low to high levels in a short duration. Follow-up CT scans were regarded as important to diagnose craniopharyngioma. The mechanism of increment of cyst density was discussed.

  3. Huge mucinous cystadenoma of the pancreas mistaken for a ...

    African Journals Online (AJOL)

    Cystic tumors of the pancreas are rare and can be confused with pseudocysts.We present a 50 year old woman with a huge mucinous cystadenoma of the pancreas initially diagnosed and managed with a cystojejunostomy and cyst wall biopsy. She required another laparotomy and tumor excision after histological ...

  4. 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.

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

    Science.gov (United States)

    Park, Kyong; Son, Jakyung; Jang, Jiyoung; Kang, Ryungwoo; Chung, Hye-Kyung; Lee, Kyong Won; Lee, Seung-Min; Lim, Hyunjung; Shin, Min-Jeong

    2017-01-01

    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. PMID:28505126

  6. Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

    Science.gov (United States)

    Demirkan, A; Lahti, J; Direk, N; Viktorin, A; Lunetta, K L; Terracciano, A; Nalls, M A; Tanaka, T; Hek, K; Fornage, M; Wellmann, J; Cornelis, M C; Ollila, H M; Yu, L; Smith, J A; Pilling, L C; Isaacs, A; Palotie, A; Zhuang, W V; Zonderman, A; Faul, J D; Sutin, A; Meirelles, O; Mulas, A; Hofman, A; Uitterlinden, A; Rivadeneira, F; Perola, M; Zhao, W; Salomaa, V; Yaffe, K; Luik, A I; Liu, Y; Ding, J; Lichtenstein, P; Landén, M; Widen, E; Weir, D R; Llewellyn, D J; Murray, A; Kardia, S L R; Eriksson, J G; Koenen, K; Magnusson, P K E; Ferrucci, L; Mosley, T H; Cucca, F; Oostra, B A; Bennett, D A; Paunio, T; Berger, K; Harris, T B; Pedersen, N L; Murabito, J M; Tiemeier, H; van Duijn, C M; Räikkönen, K

    2016-06-01

    Major depressive disorder (MDD) is moderately heritable, however genome-wide association studies (GWAS) for MDD, as well as for related continuous outcomes, have not shown consistent results. Attempts to elucidate the genetic basis of MDD may be hindered by heterogeneity in diagnosis. The Center for Epidemiological Studies Depression (CES-D) scale provides a widely used tool for measuring depressive symptoms clustered in four different domains which can be combined together into a total score but also can be analysed as separate symptom domains. We performed a meta-analysis of GWAS of the CES-D symptom clusters. We recruited 12 cohorts with the 20- or 10-item CES-D scale (32 528 persons). One single nucleotide polymorphism (SNP), rs713224, located near the brain-expressed melatonin receptor (MTNR1A) gene, was associated with the somatic complaints domain of depression symptoms, with borderline genome-wide significance (p discovery = 3.82 × 10-8). The SNP was analysed in an additional five cohorts comprising the replication sample (6813 persons). However, the association was not consistent among the replication sample (p discovery+replication = 1.10 × 10-6) with evidence of heterogeneity. Despite the effort to harmonize the phenotypes across cohorts and participants, our study is still underpowered to detect consistent association for depression, even by means of symptom classification. On the contrary, the SNP-based heritability and co-heritability estimation results suggest that a very minor part of the variation could be captured by GWAS, explaining the reason of sparse findings.

  7. 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.

  8. It was huge! Nursing students' first experience at AORN Congress.

    Science.gov (United States)

    Byrne, Michelle; Cantrell, Kelly; Fletcher, Daphne; McRaney, David; Morris, Kelly

    2004-01-01

    AN EXPERIENTIAL KNOWLEDGE of mentoring through nursing students' perspectives may enhance AORN's ability to recruit students to perioperative nursing and aid future planning for student involvement in the Association. IN 2003, four first-year nursing students attended the AORN Congress in Chicago with their nursing instructor and mentor. The students' experiences were captured using a thematic analysis to analyze their journals. THE FIVE COMMON THEMES identified were "it was huge," "exhibits," "student program," "exploring the city," and "suggestions for future planning."

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

    Directory of Open Access Journals (Sweden)

    Linda Glaser

    Full Text Available 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.

  10. A meta-analysis of four genome-wide association studies of survival to age 90 years or older: the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.

    Science.gov (United States)

    Newman, Anne B; Walter, Stefan; Lunetta, Kathryn L; Garcia, Melissa E; Slagboom, P Eline; Christensen, Kaare; Arnold, Alice M; Aspelund, Thor; Aulchenko, Yurii S; Benjamin, Emelia J; Christiansen, Lene; D'Agostino, Ralph B; Fitzpatrick, Annette L; Franceschini, Nora; Glazer, Nicole L; Gudnason, Vilmundur; Hofman, Albert; Kaplan, Robert; Karasik, David; Kelly-Hayes, Margaret; Kiel, Douglas P; Launer, Lenore J; Marciante, Kristin D; Massaro, Joseph M; Miljkovic, Iva; Nalls, Michael A; Hernandez, Dena; Psaty, Bruce M; Rivadeneira, Fernando; Rotter, Jerome; Seshadri, Sudha; Smith, Albert V; Taylor, Kent D; Tiemeier, Henning; Uh, Hae-Won; Uitterlinden, André G; Vaupel, James W; Walston, Jeremy; Westendorp, Rudi G J; Harris, Tamara B; Lumley, Thomas; van Duijn, Cornelia M; Murabito, Joanne M

    2010-05-01

    Genome-wide association studies (GWAS) may yield insights into longevity. We performed a meta-analysis of GWAS in Caucasians from four prospective cohort studies: the Age, Gene/Environment Susceptibility-Reykjavik Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study participating in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Longevity was defined as survival to age 90 years or older (n = 1,836); the comparison group comprised cohort members who died between the ages of 55 and 80 years (n = 1,955). In a second discovery stage, additional genotyping was conducted in the Leiden Longevity Study cohort and the Danish 1905 cohort. There were 273 single-nucleotide polymorphism (SNP) associations with p < .0001, but none reached the prespecified significance level of 5 x 10(-8). Of the most significant SNPs, 24 were independent signals, and 16 of these SNPs were successfully genotyped in the second discovery stage, with one association for rs9664222, reaching 6.77 x 10(-7) for the combined meta-analysis of CHARGE and the stage 2 cohorts. The SNP lies in a region near MINPP1 (chromosome 10), a well-conserved gene involved in regulation of cellular proliferation. The minor allele was associated with lower odds of survival past age 90 (odds ratio = 0.82). Associations of interest in a homologue of the longevity assurance gene (LASS3) and PAPPA2 were not strengthened in the second stage. Survival studies of larger size or more extreme or specific phenotypes may support or refine these initial findings.

  11. Partial ureterectomy for a huge primary leiomyoma of the ureter

    International Nuclear Information System (INIS)

    Nouralizadeh, A.; Tabib, A.; Taheri, M.; Torbati, P.M.

    2010-01-01

    A case of a huge primary leiomyoma of the ureter in which only partial ureterectomy was performed is presented. The benign nature of the mass was primarily confirmed with frozen section at the time of surgery and then with immunohistochemistry (IHC). To the best of our knowledge, this case is a unique form of leiomyoma of the ureter due to its large size. There have been only ten cases of primary leiomyoma of the ureter reported since 1955 and all of them were very small in size. Our case is considered to be the eleventh. (author)

  12. 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.

  13. How a huge HEP experiment is designed course

    CERN Multimedia

    CERN. Geneva HR-FAS

    2007-01-01

    More than twenty years after the idea of building the LHC machine was discussed in a workshop in Lausanne in 1984 for the first time, it is instructive to look back on the historical process which has led the community to where we are today with four huge detectors being commissioned and eagerly awaiting first beam collisions in 2008. The main design principles, detector features and performance characteristics of the ATLAS and CMS detectors will be briefly covered in these two lectures with, as an interlude, a wonderful DVD from ATLAS outreach depicting how particles interact and are detected in the various components of the experiments.

  14. 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

  15. TRPV1 Gene Polymorphisms Are Associated with Type 2 Diabetes by Their Interaction with Fat Consumption in the Korean Genome Epidemiology Study.

    Science.gov (United States)

    Park, Sunmin; Zhang, Xin; Lee, Na Ra; Jin, Hyun-Seok

    2016-01-01

    Different transient receptor potential vanilloid 1 (TRPV1) variants may be differently activated by noxious stimuli. We investigated how TRPV1 variants modulated the prevalence of type 2 diabetes and specific gene-nutrient interactions. Among 8,842 adults aged 40-69 years in the Korean Genome Epidemiology Study, the associations between TRPV1 genotypes and the prevalence of type 2 diabetes as well as their gene-nutrient interactions were investigated after adjusting for the covariates of age, gender, residence area, body mass index, daily energy intake, and total activity. The TRPV1 rs161364 and rs8065080 minor alleles lowered HOMA-IR and the risk of type 2 diabetes after adjusting for covariates. There were gene-nutrient interactions between TRPV1 variants rs161364 and rs8065080 and preference for oily taste, intake of oily foods, and fat intake after adjusting for covariates. Among subjects with the minor alleles of TRPV1 rs161364 and rs8065080, the group with a high preference for oily foods had a lower odds ratio for type 2 diabetes. Consistent with the preference for taste, among subjects with the minor alleles, the group with high fat intake from oily foods also exhibited a lower risk of type 2 diabetes than subjects with the major alleles. People with the minor alleles of the TRPV1 single nucleotide polymorphisms rs161364 and rs8065080 have a lower risk of diabetes with a high-fat diet, but people with the major alleles are at a higher risk of type 2 diabetes when consuming high-fat diets. The majority of people should be careful about a high fat intake. © 2016 S. Karger AG, Basel.

  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. 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.

    Science.gov (United States)

    Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I; Pérez, Lester J

    2015-01-01

    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 molecular

  18. Profesi Epidemiologi

    Directory of Open Access Journals (Sweden)

    Buchari Lapau

    2011-01-01

    Full Text Available Makalah ini pertama kali menjelaskan perlu adanya profesi kesehatan masyarakat dalam rangka pembangunan kesehatan. Lalu dijelaskan apa profesi itu dan standar keberadaan profesi, atas dasar mana dapat ditetapkan bahwa pelayanan epidemiologi merupakan salah satu profesi. Dalam rangka pembinaan profesi kesehatan masyarakat, IAKMI dan APTKMI telah membentuk Majelis Kolegium Kesehatan Masyarakat Indonesia (MKKMI yang terdiri atas 8 kolegium antara lain Kolegium Epidemiologi, yang telah menyusun Standar Profesi Epidemiologi yang terdiri atas beberapa standar. Masing-masing standar dijelaskan mulai dari kurikulum, standar pelayanan epidmiologi, profil epidemiolog kesehatan, peran epidemiolog kesehatan, fungsi epidemiolog kesehatan, standar kompetensi epidemiologi, dan standar pendidikan profesi epidemiologi.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Airway management of a rare huge-size supraglottic mass

    International Nuclear Information System (INIS)

    Abou-Zeid, Haitham A.; Al-Ghamdi, Abdel Mohsin A.; Al-Qurain, Abdel-Aziz A.; Mokhazy, Khalid M.

    2006-01-01

    Laser excision of a huge-sized supraglottic mass nearly obstructing the airway passage is a real challenge to anesthesiologists. Upper airway obstruction due to neoplasm in supraglottic region, is traditionally managed by preoperative tracheostomy, however, such a common procedure can potentially have an impact on long-term outcome. A 26-year-old patient presented with dysphagia caused by left cystic vallecular synovial sarcoma. The airway was successfully secured via fiberoptic bronchoscopy, followed by excision of the supraglottic tumor with CO2 laser surgery. Tracheostomy was not required. The patient was discharged from the hospital on the 4th day of surgery. This case, highlights the possibility to secure the airway passage without performing preoperative tracheostomy resulting in good outcome and short hospital stay. (author)

  4. Huge endometrioma mimicking mucinous cystadenoma on MR : A case report

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Im Kyung; Kim, Bong Soo; Nam, Kung Sook; Kim, Heung Cheol; Yoo, Yun Sik; Lee, Mee Ran; Hwang, Woo Chul [Hallym University, Chunchon (Korea, Republic of)

    2001-12-01

    Endometriosis is a relatively common gynecologic disease affecting women during their reproductive years. For its diagnosis, magnetic resonance imaging has been shown to have greater specificity than other modalities. Although lesions may show variable signal intensity due to numerous stages of bleeding, the characteristic finding of endometrioma which distinguishes it from other ovarian cystic masses is relatively high signal intensity on T1-weighted images and heterogeneous signal intensity with prominent shading on 72-weighted images. We report an atypical case involving a huge endometrioma. Because of varying signal intensity on T1- and T2-weighted images and scanty shading on T2-weighted images, the findings were misinterpreted and mucinous cystadenoma was diagnosed.

  5. Black hole firewalls require huge energy of measurement

    Science.gov (United States)

    Hotta, Masahiro; Matsumoto, Jiro; Funo, Ken

    2014-06-01

    The unitary moving mirror model is one of the best quantum systems for checking the reasoning of the original firewall paradox of Almheiri et al. [J. High Energy Phys. 02 (2013) 062] in quantum black holes. Though the late-time part of radiations emitted from the mirror is fully entangled with the early part, no firewall exists with a deadly, huge average energy flux in this model. This is because the high-energy entanglement structure of the discretized systems in almost maximally entangled states is modified so as to yield the correct description of low-energy effective field theory. Furthermore, the strong subadditivity paradox of firewalls is resolved using nonlocality of general one-particle states and zero-point fluctuation entanglement. Due to the Reeh-Schlieder theorem in quantum field theory, another firewall paradox is inevitably raised with quantum remote measurements in the model. We resolve this paradox from the viewpoint of the energy cost of measurements. No firewall appears, as long as the energy for the measurement is much smaller than the ultraviolet cutoff scale.

  6. Progressive skin necrosis of a huge occipital encephalocele

    Science.gov (United States)

    Andarabi, Yasir; Nejat, Farideh; El-Khashab, Mostafa

    2008-01-01

    Objects: Progressive skin necrosis of giant occipital encephalocoele is an extremely rare complication found in neonates. Infection and ulceration of the necrosed skin may lead to meningitis or sepsis. We present here a neonate with giant occipital encephalocoele showing progressive necrosis during the first day of his life. Methods: A newborn baby was found to have a huge mass in the occipital region, which was covered by normal pink-purplish skin. During the last hours of the first day of his life, the sac started becoming ulcerated accompanied with a rapid color change in the skin, gradually turning darker and then black. The neonate was taken up for urgent excision and repair of the encephalocele. Two years after the operation, he appears to be well-developed without any neurological problems. Conclusion: Necrosis may have resulted from arterial or venous compromise caused by torsion of the pedicle during delivery or after birth. The high pressure inside the sac associated with the thin skin of the encephalocoele may be another predisposing factor. In view of the risk of ulceration and subsequent infection, urgent surgery of the necrotizing encephalocele is suggested. PMID:19753210

  7. Progressive skin necrosis of a huge occipital encephalocele

    Directory of Open Access Journals (Sweden)

    Andarabi Yasir

    2008-01-01

    Full Text Available Objects: Progressive skin necrosis of giant occipital encephalocoele is an extremely rare complication found in neonates. Infection and ulceration of the necrosed skin may lead to meningitis or sepsis. We present here a neonate with giant occipital encephalocoele showing progressive necrosis during the first day of his life. Methods: A newborn baby was found to have a huge mass in the occipital region, which was covered by normal pink-purplish skin. During the last hours of the first day of his life, the sac started becoming ulcerated accompanied with a rapid color change in the skin, gradually turning darker and then black. The neonate was taken up for urgent excision and repair of the encephalocele. Two years after the operation, he appears to be well-developed without any neurological problems. Conclusion: Necrosis may have resulted from arterial or venous compromise caused by torsion of the pedicle during delivery or after birth. The high pressure inside the sac associated with the thin skin of the encephalocoele may be another predisposing factor. In view of the risk of ulceration and subsequent infection, urgent surgery of the necrotizing encephalocele is suggested.

  8. [A Case of Huge Colon Cancer Accompanied with Severe Hypoproteinemia].

    Science.gov (United States)

    Hiraki, Sakurao; Kanesada, Kou; Harada, Toshio; Tada, Kousuke; Fukuda, Shintaro

    2017-11-01

    We report a case of huge colon cancer accompanied with severe hypoproteinemia. A7 4-year-old woman was referred to our hospital because of abdominal fullness. Blood examinations revealed anemia(hemoglobin 8.8 g/dL)and sever hypopro- teinemia(total protein 4.5 g/dL, albumin 1.1 g/dL). Computed tomography examination of abdomen revealed ascites and large tumor(12.5×10.5 cm)at the right side colon. By further examinations ascending colon cancer without distant metastasis was diagnosed, then we performed right hemicolectomy and primary intestinal anastomosis by open surgery. Ahuge type 1 tumor(18×12 cm)was observed in the excised specimen, which invaded to terminal ileum directly. The tumor was diagnosed moderately differentiated adenocarcinoma without lymph node metastasis(pT3N0M0, fStage II ). Postoperative course was uneventful and serum protein concentration recovered gradually to normal range. Protein leakage from the tumor cannot be proved by this case, so we can't diagnose as protein-losing enteropathy, but we strongly doubt this etiology from postoperative course in this case.

  9. A huge bladder calculus causing acute renal failure.

    Science.gov (United States)

    Komeya, Mitsuru; Sahoda, Tamami; Sugiura, Shinpei; Sawada, Takuto; Kitami, Kazuo

    2013-02-01

    A 81-year-old male was referred to our emergency outpatient unit due to acute renal failure. The level of serum creatinine was 276 μmol/l. A CT scan showed bilateral hydronephroureter, large bladder stone (7 cm × 6 cm × 6 cm) and bladder wall thickness. He was diagnosed as post renal failure due to bilateral hydronephroureter. Large bladder stone is thought to be the cause of bilateral hydronephroureter and renal failure. To improve renal failure, we performed open cystolithotomy and urethral catheterization. Three days after the surgery, the level of serum creatinine decreased to 224 μmol/l. He was discharged from our hospital with uneventful course. Bladder calculus is thought to be a rare cause of renal failure. We summarize the characteristics of bladder calculus causing renal failure. We should keep that long-term pyuria and urinary symptom, and repeated urinary tract infection can cause huge bladder calculus and renal failure in mind.

  10. 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. © The Author 2015. 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.

  11. Epidemiología genómica y paraparesia espástica tropical asociada a la infección por el virus linfotrópico humano de células T tipo 1 Genome epidemiology and tropical spastic paraparesis associated with human T-cell lymphotropic virus type 1

    Directory of Open Access Journals (Sweden)

    Mercedes Salcedo-Cifuentes

    2011-11-01

    of genes and LINE type repetitions, and DNA transposons which, overall, would form the genomic environments targeted for integration. This new scenario will promote substantial changes in the field of public health and in epidemiological management of infectious diseases. It will also foster the development of powerful tools for increasing the efficiency of epidemiological surveillance

  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

    2016-04-01

    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. 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. 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.

  13. 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

  14. 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.

  15. Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC Lineages

    Directory of Open Access Journals (Sweden)

    Sabiha Shaik

    2017-10-01

    Full Text Available Escherichia coli sequence type 131 (ST131, a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12, ST405 (n = 10, and ST648 (n = 18, and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.

  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. Genomic epidemiology of a major Mycobacterium tuberculosis outbreak: Retrospective cohort study in a low incidence setting using sparse time-series sampling

    DEFF Research Database (Denmark)

    Folkvardsen, Dorte Bek; Norman, Anders; Andersen, Åse Bengård

    2017-01-01

    cases belonging to this outbreak via routine MIRU-VNTR typing. Here, we present a retrospective analysis of the C2/1112-15 dataset, based on whole-genome data from a sparse time-series consisting of five randomly selected isolates from each of the 23 years. Even if these data are derived from only 12...

  18. From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen

    NARCIS (Netherlands)

    Guo, Weina; Jelocnik, Martina; Li, Jing; Sachse, Konrad; Polkinghorne, Adam; Pannekoek, Yvonne; Kaltenboeck, Bernhard; Gong, Jiansen; You, Jinfeng; Wang, Chengming

    2017-01-01

    Chlamydia (C.) gallinacea is a recently identified bacterium that mainly infects domestic chickens. Demonstration of C. gallinacea in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of C. psittaci, but genetic and genomic research on C. gallinacea is

  19. Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013.

    Science.gov (United States)

    Adedokun, Babatunde O; Olopade, Christopher O; Olopade, Olufunmilayo I

    2016-01-01

    The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA. SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis. The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions. Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

  20. 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

    Czech Academy of Sciences Publication Activity Database

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D. T. J.

    2015-01-01

    Roč. 8, JUN 19 2015 (2015), s. 336 ISSN 1756-3305 R&D Projects: GA MŠk(CZ) EE2.3.30.0032; GA ČR(CZ) GA15-14198S Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:60077344 Keywords : Diplostomum (Platyhelminthes: Trematoda) * fish pathogens * mitochondrial genome * ribosomal RNA * illumina next-generation sequencing * phylogeny Subject RIV: EG - Zoology Impact factor: 3.234, year: 2015

  1. 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.

  2. 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.

  3. 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.

  4. Epidemiology and ionizing radiations

    International Nuclear Information System (INIS)

    Bourguignon, M.; Masse, R.; Slama, R.; Spira, A.; Timarche, M.; Laurier, D.; Billon, S.; Rogel, A.; Telle Lamberton, M.; Catelinois, O.; Thierry, I.; Grosche, B.; Ron, E.; Vathaire, F. de; Cherie Challine, L.; Donadieu, J.; Pirard, Ph.; Bloch, J.; Setbon, M.

    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.)

  5. Pulsed-field gel electrophoresis of Staphylococcus hyicus and Staphylococcus chromogenes genomic DNA and its taxonomic, epidemiologic and ecologic applications in veterinary medicine.

    Science.gov (United States)

    Shimizu, A; Kloos, W E; Berkhoff, H A; George, C G; Ballard, D N

    1997-06-01

    One hundred and thirty-eight strains of Staphylococcus hyicus and 21 strains of S. chromogenes isolated from animals were analyzed by pulsed-field gel electrophoresis (PFGE) after restriction endonuclease Smal digestion of chromosomal DNA. Eighty-eight strains of S. hyicus from pigs with or without exudative epidermitis (EE) generated 16 to 26 fragments in the size range of chromogenes from pigs and cows generated 17 to 24 fragments ranging from chromogenes strains were more highly conserved than those of S. hyicus. S. chromogenes strains could be distinguished from S. hyicus strains by fragments within the range of 305 to 545 kb. The results indicate that PFGE analysis could be used to distinguish between S. hyicus and S. chromogenes. We conclude that PFGE analysis is a useful tool not only for species or strain identification but also for epidemiologic or ecologic studies of S. hyicus and S. chromogenes.

  6. 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.

  7. 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......, Guatemala and the Philippines. Genomic DNA was extracted from each worm and a 450 base pair fragment of the mitochondrial cytochrome oxidase gene subunit 1 (COI) was PCR amplified. The products were sequenced from both strands and sequences were manually edited. Fifty different Ascaris CO1 haplotypes were...

  8. 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.

  9. Molecular epidemiology of human rhinoviruses

    OpenAIRE

    Savolainen-Kopra, Carita

    2006-01-01

    The first part of this work investigates the molecular epidemiology of a human enterovirus (HEV), echovirus 30 (E-30). This project is part of a series of studies performed in our research team analyzing the molecular epidemiology of HEV-B viruses. A total of 129 virus strains had been isolated in different parts of Europe. The sequence analysis was performed in three different genomic regions: 420 nucleotides (nt) in the VP4/VP2 capsid protein coding region, the entire VP1 capsid protein cod...

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

    Energy Technology Data Exchange (ETDEWEB)

    Nishikawa, Ryusuke; Nakao, Ken-ichi [Department of Mathematics and Physics, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan); Yoo, Chul-Moon, E-mail: ryusuke@sci.osaka-cu.ac.jp, E-mail: knakao@sci.osaka-cu.ac.jp, E-mail: yoo@gravity.phys.nagoya-u.ac.jp [Division of Particle and Astrophysical Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    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.

  11. [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.

  12. Human Germline Genome Editing

    OpenAIRE

    Ormond, Kelly E.; Mortlock, Douglas P.; Scholes, Derek T.; Bombard, Yvonne; Brody, Lawrence C.; Faucett, W. Andrew; Garrison, Nanibaa’ A.; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E.

    2017-01-01

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Gen...

  13. A case report of surgical debulking for a huge mass of elephantiasis neuromatosa

    Science.gov (United States)

    Hoshi, Manabu; Ieguchi, Makoto; Taguchi, Susumu; Yamasaki, Shinya

    2009-01-01

    Achievement of a safe outcome for an extensive mass with hypervascularity in the extremities requires a surgical team skilled in musculoskeletal oncology. We report debulking surgery for a huge mass of elephantiasis neuromatosa in the right leg of a 56-year old man using the novel Ligasure® vessel sealing system. PMID:21139882

  14. A case report of surgical debulking for a huge mass of elephantiasis neuromatosa

    Directory of Open Access Journals (Sweden)

    Shinya Yamasaki

    2009-07-01

    Full Text Available Achievement of a safe outcome for an extensive mass with hypervascularity in the extremities requires a surgical team skilled in musculoskeletal oncology. We report debulking surgery for a huge mass of elephantiasis neuromatosa in the right leg of a 56-year old man using the novel Ligasure® vessel sealing system.

  15. 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.

  16. 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.

  17. Worldwide molecular epidemiology of HIV

    Directory of Open Access Journals (Sweden)

    Henry I Z Requejo

    2006-04-01

    Full Text Available Human immunodeficiency virus (HIV is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS. HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Churn prediction on huge telecom data using hybrid firefly based classification

    Directory of Open Access Journals (Sweden)

    Ammar A.Q. Ahmed

    2017-11-01

    Full Text Available Churn prediction in telecom has become a major requirement due to the increase in the number of telecom providers. However due to the hugeness, sparsity and imbalanced nature of the data, churn prediction in telecom has always been a complex task. This paper presents a metaheuristic based churn prediction technique that performs churn prediction on huge telecom data. A hybridized form of Firefly algorithm is used as the classifier. It has been identified that the compute intensive component of the Firefly algorithm is the comparison block, where every firefly is compared with every other firefly to identify the one with the highest light intensity. This component is replaced by Simulated Annealing and the classification process is carried out. Experiments were conducted on the Orange dataset. It was observed that Firefly algorithm works best on churn data and the hybridized Firefly algorithm provides effective and faster results.

  3. The therapy for huge goiter together with hyperthyroidism through 131I case studies

    International Nuclear Information System (INIS)

    He Jianhua; Yu Wencai; Zeng Qingwen; Wu Congjun

    2001-01-01

    Objective: 214 cases of the treatment of huge goiter with hyperthyroidism are revised to collect clinic material for the improvement of therapy to hyperthyroidism indications through 131 I. Methods: In all of these cases, patients take a full dose of 131 I based on MC Garack's formula for one time. Results: Among them, 154 resolved, accounting for 72%, 139 of the cases were reduced to normal size, which accounted for 64.9% of the patients. Only 114 cases of patients had side-effect, and during one year 12.1% of them have symptoms of hypothyroidism. Conclusion: The statistics shows that 131 I is convenient, safe, well and with reduces suffering from treating huge goiter with hyperthyroidism

  4. 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.

  5. 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...

  6. EPRI epidemiology

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    A fight is brewing within the electric power community over the fate of a proposed $5 to $8 million epidemiological study of the effects of radiation on US nuclear plant workers. Several industry experts, claiming the project would merely lead to confusion by producing no clear results, are trying to prevent the Electric Power Research Institute (EPRI) from funding what would be the largest ever occupational study of this kind, covering perhaps as many as 500,000 workers. Ralph Lapp, a well-known radiation physicist, says that EPRI is facing unprecedented technical dissent from within. He claims there is already plenty of evidence that nuclear utilities are among the safest places to work, at least in terms of cancer risk, and that the proposed EPRI study would raise new concerns without yielding any answers

  7. Transcatheter Closure of Bilateral Multiple Huge Pulmonary Arteriovenous Malformations with Homemade Double-Umbrella Occluders

    International Nuclear Information System (INIS)

    Zhong Hongshan; Xu Ke; Shao Haibo

    2008-01-01

    A 28-year-old man underwent successful transcatheter occlusion of three huge pulmonary arteriovenous malformations (PAVMs) using homemade double-umbrella occluders and stainless steel coils. Thoracic CT with three-dimensional reconstruction and pulmonary angiography were used for treatment planning and follow-up. The diameters of the feeding vessels were 11 mm, 13 mm, and 14 mm, respectively. This report demonstrates the novel design and utility of the double-umbrella occluder, an alternative tool for treatment of large PAVMs.

  8. On the huge Lie superalgebra of pseudo superdifferential operators and super KP-hierarchies

    International Nuclear Information System (INIS)

    Sedra, M.B.

    1995-08-01

    Lie superalgebraic methods are used to establish a connection between the huge Lie superalgebra Ξ of super (pseudo) differential operators and various super KP-hierarchies. We show in particular that Ξ splits into 5 = 2 x 2 + 1 graded algebras expected to correspond to five classes of super KP-hierarchies generalizing the well-known Manin-Radul and Figueroa O'Farrill-Ramos supersymmetric KP-hierarchies. (author). 10 refs

  9. Propranolol in Treatment of Huge and Complicated Infantile Hemangiomas in Egyptian Children

    OpenAIRE

    Hassan, Basheir A.; Shreef, Khalid S.

    2014-01-01

    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...

  10. 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

  11. 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

  12. [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. © 2016 médecine/sciences – Inserm.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  14. A case of huge neurofibroma expanding extra- and intracranially through the enlarged jugular foramen

    International Nuclear Information System (INIS)

    Hanakita, Junya; Imataka, Kiyoharu; Handa, Hajime

    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 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 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. (author)

  15. 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.

  16. Huge residual resistivity in the quantum critical region of CeAgSb2

    International Nuclear Information System (INIS)

    Nakashima, Miho; Kirita, Shingo; Asai, Rihito; Kobayashi, Tatsuo C; Okubo, Tomoyuki; Yamada, Mineko; Thamizhavel, Arumugam; Inada, Yoshihiko; Settai, Rikio; Galatanu, Andre; Yamamoto, Etsuji; Ebihara, Takao; Onuki, Yoshichika

    2003-01-01

    We have studied the effect of pressure on the electrical resistivity of a high-quality single crystal CeAgSb 2 which has a small net ferromagnetic moment of 0.4μ B /Ce. The magnetic ordering temperature T ord = 9.7 K decreases with increasing pressure p and disappears at a critical pressure p c ≅ 3.3 GPa. The residual resistivity, which is close to zero up to 3 GPa, increases steeply above 3 GPa, reaching 55μΩ cm at p c . A huge residual resistivity is found to appear when the magnetic order disappears. (letter to the editor)

  17. Acute abdomen in early pregnancy caused by torsion of bilateral huge multiloculated ovarian cysts

    OpenAIRE

    Sathiyakala Rajendran; Suthanthira Devi

    2015-01-01

    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. ...

  18. Genomics for paediatricians: promises and pitfalls.

    Science.gov (United States)

    Hammond, Carrie Louise; Willoughby, Josh Matthew; Parker, Michael James

    2018-03-24

    In recent years, there have been significant advances in genetic technologies, evolving the field of genomics from genetics. This has huge diagnostic potential, as genomic testing increasingly becomes part of mainstream medicine. However, there are numerous potential pitfalls in the interpretation of genomic data. It is therefore essential that we educate clinicians more widely about the appropriate interpretation and utilisation of genomic testing. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  19. Clinical epidemiology.

    Science.gov (United States)

    Martin, S W; Bonnett, B

    1987-06-01

    Rational clinical practice requires deductive particularization of diagnostic findings, prognoses, and therapeutic responses from groups of animals (herds) to the individual animal (herd) under consideration This process utilizes concepts, skills, and methods of epidemiology, as they relate to the study of the distribution and determinants of health and disease in populations, and casts them in a clinical perspective.We briefly outline diagnostic strategies and introduce a measure of agreement, called kappa, between clinical diagnoses. This statistic is useful not only as a measure of diagnostic accuracy, but also as a means of quantifying and understanding disagreement between diagnosticians. It is disconcerting to many, clinicians included, that given a general deficit of data on sensitivity and specificity, the level of agreement between many clinical diagnoses is only moderate at best with kappa values of 0.3 to 0.6.Sensitivity, specificity, pretest odds, and posttest probability of disease are defined and related to the interpretation of clinical findings and ancillary diagnostic test results. An understanding of these features and how they relate to ruling-in or ruling-out a diagnosis, or minimizzing diagnostic errors will greatly enhance the diagnostic accuracy of the practitioner, and reduce the frequency of clinical disagreement. The approach of running multiple tests on every patient is not only wasteful and expensive, it is unlikely to improve the ability of the clinician to establish the correct diagnosis.We conclude with a discussion of how to decide on the best therapy, a discussion which centers on, and outlines the key features of, the well designed clinical trial. Like a diagnosis, the results from a clinical trial may not always be definitive, nonetheless it is the best available method of gleaning information about treatment efficacy.

  20. 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.

  1. Huge natural gas reserves central to capacity work, construction plans in Iran

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    Questions about oil production capacity in Iran tend to mask the country's huge potential as a producer of natural gas. Iran is second only to Russia in gas reserves, which National Iranian Gas Co. estimates at 20.7 trillion cu m. Among hurdles to Iran's making greater use of its rich endowment of natural gas are where and how to sell gas not used inside the country. The marketing logistics problem is common to other Middle East holders of gas reserves and a reason behind the recent proliferation of proposals for pipeline and liquefied natural gas schemes targeting Europe and India. But Iran's challenges are greater than most in the region. Political uncertainties and Islamic rules complicate long-term financing of transportation projects and raise questions about security of supply. As a result, Iran has remained mostly in the background of discussions about international trade of Middle Eastern gas. The country's huge gas reserves, strategic location, and existing transport infrastructure nevertheless give it the potential to be a major gas trader if the other issues can be resolved. The paper discusses oil capacity plans, gas development, gas injection for enhanced oil recovery, proposals for exports of gas, and gas pipeline plans

  2. Salmonella epidemiology: A whirlwind of change.

    Science.gov (United States)

    Besser, John M

    2018-05-01

    The field of infectious disease epidemiology for Salmonella and other enteric pathogens is undergoing some of the most profound changes since the time of Kauffman and White. Rapid advances in "big data" technologies such as genomics and metagenomics are making it possible to monitor and control salmonellosis in new and exciting ways. Epidemiological methods are becoming increasingly robust through the routine use of standardized hypothesis-generating questionnaires, iterative open-ended interviewing, informational trace-backs and new modeling techniques for describing the attribution of disease to food sources. In addition, Salmonella epidemiology is facing important challenges and new opportunities due to the rapid adoption of culture independent diagnostic test panels by clinical laboratories. Where is this unprecedented wave of change taking us? This chapter will examine emerging trends in Salmonella epidemiology, and take a peek into the not-so-distant future. Published by Elsevier Ltd.

  3. Sleeping money: investigating the huge surpluses of social health insurance in China.

    Science.gov (United States)

    Liu, JunQiang; Chen, Tao

    2013-12-01

    The spreading of social health insurance (SHI) worldwide poses challenges for fledging public administrators. Inefficiency, misuse and even corruption threaten the stewardship of those newly established health funds. This article examines a tricky situation faced by China's largest SHI program: the basic health insurance (BHI) scheme for urban employees. BHI accumulated a 406 billion yuan surplus by 2009, although the reimbursement level was still low. Using a provincial level panel database, we find that the huge BHI surpluses are related to the (temporarily) decreasing dependency ratio, the steady growth of average wages, the extension of BHI coverage, and progress in social insurance agency building. The financial situations of local governments and risk pooling level also matter. Besides, medical savings accounts result in about one third of BHI surpluses. Although these findings are not causal, lessons drawn from this study can help to improve the governance and performance of SHI programs in developing countries.

  4. Subcortical heterotopia appearing as huge midline mass in the newborn brain.

    Science.gov (United States)

    Fukumura, Shinobu; Watanabe, Toshihide; Kimura, Sachiko; Ochi, Satoko; Yoshifuji, Kazuhisa; Tsutsumi, Hiroyuki

    2016-02-01

    We report the case of a 2-year-old boy who showed a huge midline mass in the brain at prenatal assessment. After birth, magnetic resonance imaging (MRI) revealed a conglomerate mass with an infolded microgyrus at the midline, which was suspected as a midline brain-in-brain malformation. MRI also showed incomplete cleavage of his frontal cortex and thalamus, consistent with lobar holoprosencephaly. The patient underwent an incisional biopsy of the mass on the second day of life. The mass consisted of normal central nervous tissue with gray and white matter, representing a heterotopic brain. The malformation was considered to be a subcortical heterotopia. With maturity, focal signal changes and decreased cerebral perfusion became clear on brain imaging, suggesting secondary glial degeneration. Coincident with these MRI abnormalities, the child developed psychomotor retardation and severe epilepsy focused on the side of the intracranial mass.

  5. 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.

  6. 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

    2013-01-01

    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. PMID:23659350

  7. 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

  8. Hydrogen-terminated mesoporous silicon monoliths with huge surface area as alternative Si-based visible light-active photocatalysts

    KAUST Repository

    Li, Ting; Li, Jun; Zhang, Qiang; Blazeby, Emma; Shang, Congxiao; Xu, Hualong; Zhang, Xixiang; Chao, Yimin

    2016-01-01

    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

  9. Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants

    DEFF Research Database (Denmark)

    Lindow, Morten; Jacobsen, Anders; Nygaard, Sanne

    2007-01-01

    indicates that only a few of the candidates are conserved between the species. We conclude that there is a large potential for miRNA-mediated regulatory interactions encoded in the genomes of the investigated plants. We hypothesize that some of these interactions may be realized under special environmental...

  10. Epidemiology: past, present and future.

    Science.gov (United States)

    Kesteloot, H

    2004-01-01

    Epidemiology in the past was concerned essentially by the study of infectious diseases which were the cause of huge mortalities especially since urbanisation was initiated. Epidemics of pest, typhus, cholera, influenza a.o. were common. The epidemics were halted by better hygiene, vaccination and antibiotics. Since the second world war epidemiology was dominated by an "epidemic" of new chronic diseases, especially heart disease and cancer. This was due to an increase in life span and to an increase in smoking habits and in the intake of saturated fat and a too small intake of fruit and vegetables combined with a too high intake of salt (NaCl). Gradually epidemiology evolved as the study of the causes, the distribution, the risk factors and the prevention of chronic diseases, but also including accidents, suicide, depression a.o., diseases with a mass occurrence at the population level. The importance of nutrition as a determinant of health gradually became recognized, but remains undervalued by the medical profession. Mortality at the population level follows some simple mathematical laws and can be represented accurately (r2>0.99) between the ages of 35 and 84 year by either Gompertz equations (ln mortality versus age) or by a polynomial equation (ln mortality versus age, age2). This is valid for all populations and both sexes and remains valid at times of great and rapid changes in mortality. This shows that measures for prevention should be directed towards the total population. The future of epidemiology should be directed towards the slowing of the ageing process at the population level by a healthy life style consisting of: not smoking, avoiding obesity, a fair amount of physical activity and a healthy nutrition i.e little salt, little saturated fat, an adequate amount of omega-3 fatty acids and a large amount of fruit and vegetables, with an occasional glass of red wine. This contains the secret of a long and healthy life. Conceptually it will be important

  11. Epidemiology of IBD

    Science.gov (United States)

    ... IBD? Projects and Partners Data and Statistics Resources Epidemiology of the IBD Recommend on Facebook Tweet Share ... 5:1424-9. 2 Loftus EV, Jr. Clinical epidemiology of inflammatory bowel disease: Incidence, prevalence, and environmental ...

  12. 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.

  13. Evaluation of epidemiological studies

    International Nuclear Information System (INIS)

    Breckow, J.

    1995-01-01

    The publication is intended for readers with a professional background in radiation protection who are not experts in the field of epidemiology. The potentials and the limits of epidemiology are shown and concepts and terminology of radioepidemilogic studies as well as epidemiology in general are explained, in order to provide the necessary basis for understanding or performing evaluations of epidemiologic studies. (orig./VHE) [de

  14. 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.

  15. Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

    Science.gov (United States)

    Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

    2013-12-06

    Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

  16. 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.

  17. Propranolol in treatment of huge and complicated infantile hemangiomas in egyptian children.

    Science.gov (United States)

    Hassan, Basheir A; Shreef, Khalid S

    2014-01-01

    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.

  18. Huge thermal conductivity enhancement in boron nitride – ethylene glycol nanofluids

    International Nuclear Information System (INIS)

    Żyła, Gaweł; Fal, Jacek; Traciak, Julian; Gizowska, Magdalena; Perkowski, Krzysztof

    2016-01-01

    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.

  19. A rare life-threatening disease: unilateral kidney compressed by huge chronic spontaneous retroperitoneal hemorrhage

    Directory of Open Access Journals (Sweden)

    Lu HY

    2018-03-01

    Full Text Available Hao-Yuan Lu,1,* Wei Wei,2,* Qi-Wei Chen,1,* Qing-Gui Meng,1 Gao-Hua Hu,1 Xian-Lin Yi,1,3 Xian-Zhong Bai1 1Department of Urology, Tumor Hospital of Guangxi Medical University and Guangxi Cancer Research Institute, Nanning 530021, China; 2Department of Radiology, Tumor Hospital of Guangxi Medical University and Guangxi Cancer Research Institute, Nanning 530021,China; 3Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China *These authors contributed equally to this work Objectives: To study an uncommon life-threatening disease, spontaneous retroperitoneal and perirenal hemorrhage. Case descriptions: A 69-year-old male presented with pain in the left waist and back of 1 month duration. The renal abscess was suspected by magnetic resonance imaging before operation. The perirenal hematoma was cleaned by operation. In another case, the patient had a functional solitary left kidney compressed by a huge retroperitoneal mass and uropenia appeared. Results: The first patient died of adult respiratory distress syndrome after surgery. The second patient died of cardiac insufficiency and pulmonary embolism on the second day after evacuation of retroperitoneal hematoma. Conclusion: Conservative surgery, such as selective arterial embolization, is a reasonable approach in patients with chronic spontaneous retroperitoneal and perirenal space hemorrhage and with poor general condition. We strongly recommend drainage or interventional therapy, but not a major surgery, in patients with poor condition. Keywords: kidney, spontaneous, retroperitoneal, hemorrhage, surgery

  20. 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.

  1. Low dose epidemiology

    International Nuclear Information System (INIS)

    Tirmarche, M.; Hubert, P.

    1992-01-01

    Actually, epidemiological studies have to establish if the assessment of cancer risk can be verified at low chronic radiation doses. The population surveillance must be very long, the side effects and cancers of such radiation appearing much later. In France, this epidemiological study on nuclear workers have been decided recently. Before describing the experiment and french projects in epidemiology of nuclear workers, the authors present the main english and american studies

  2. Molecular Epidemiology of Heart Failure

    Directory of Open Access Journals (Sweden)

    J. Gustav Smith, MD, PhD

    2017-12-01

    Full Text Available Heart failure (HF is the end-stage of all heart disease and arguably constitutes the greatest unmet therapeutic need in cardiovascular medicine today. Classic epidemiological studies have established clinical risk factors for HF, but the cause remains poorly understood in many cases. Biochemical analyses of small case-control series and animal models have described a plethora of molecular characteristics of HF, but a single unifying pathogenic theory is lacking. Heart failure appears to result not only from cardiac overload or injury but also from a complex interplay among genetic, neurohormonal, metabolic, inflammatory, and other biochemical factors acting on the heart. Recent development of robust, high-throughput tools in molecular biology provides opportunity for deep molecular characterization of population-representative cohorts and HF cases (molecular epidemiology, including genome sequencing, profiling of myocardial gene expression and chromatin modifications, plasma composition of proteins and metabolites, and microbiomes. The integration of such detailed information holds promise for improving understanding of HF pathophysiology in humans, identification of therapeutic targets, and definition of disease subgroups beyond the current classification based on ejection fraction which may benefit from improved individual tailoring of therapy. Challenges include: 1 the need for large cohorts with deep, uniform phenotyping; 2 access to the relevant tissues, ideally with repeated sampling to capture dynamic processes; and 3 analytical issues related to integration and analysis of complex datasets. International research consortia have formed to address these challenges and combine datasets, and cohorts with up to 1 million participants are being collected. This paper describes the molecular epidemiology of HF and provides an overview of methods and tissue types and examples of published and ongoing efforts to systematically evaluate molecular

  3. The contribution of epidemiology

    NARCIS (Netherlands)

    Brandt, P. van den; Voorrips, L.; Hertz-Picciotto, I.; Shuker, D.; Boeing, H.; Speijers, G.; Guittard, C.; Kleiner, J.; Knowles, M.; Wolk, A.; Goldbohm, A.

    2002-01-01

    Epidemiologic studies directly contribute data on risk (or benefit) in humans as the investigated species, and in the full food intake range normally encountered by humans. This paper starts with introducing the epidemiologic approach, followed by a discussion of perceived differences between

  4. 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

  5. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  6. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  7. 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...

  8. 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.

  9. Biomarkers in molecular epidemiology study of oral squamous cell carcinoma in the era of precision medicine

    Directory of Open Access Journals (Sweden)

    Qing-Hao Zhu

    2017-01-01

    Full Text Available Oral cancer, which occurs in the mouth, lips, and tongue, is a multifactorial disease whose etiology involves environment, genetic, and epigenetic factors. Tobacco use and alcohol consumption are regarded as the primary risk factors for oral squamous cell carcinoma (OSCC, and betel use, other chemicals, radiation, environmental, and genetics are reported as relevant risk factors for oral carcinogenesis. The human papillomavirus infection is an independent risk factor. Traditional epidemiology studies have revealed that environmental carcinogens are risk factors for OSCC. Molecular epidemiology studies have revealed that the susceptibility to OSCC is influenced by both environmental and genetic risk factors. However, the details and mechanisms of risk factors involved in OSCC are unclear. Advanced methods and techniques used in human genome studies provide great opportunities for researchers to explore and identify (a the details of such risk factors and (b genetic susceptibility involved in OSCC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era into the era of genome-wide association study. In the era of precision medicine, molecular epidemiology studies should focus on biomarkers for cancer genomics and their potential utility in clinical practice. Here, we briefly reviewed several molecular epidemiology studies of OSCC, focusing on biomarkers as valuable utility in risk assessment, clinical screening, diagnosis, and prognosis prediction of OSCC in the era of precision medicine.

  10. WHO - IPHECA: Epidemiological aspects

    International Nuclear Information System (INIS)

    Souchkevitch, G.

    1996-01-01

    In May 1991 the World Health Assembly endorsed the establishment of the International Programme on the Health Effects of the Chernobyl Accident (IPHECA) under the auspices of WHO. Five pilot projects have been carried out within IPHECA in the study territories of Belarus, Russian Federation and Ukraine in a period from 1991 to 1994. This pilot projects dealt with the detection and treatment of leukaemia and related diseases (Haematology Project), thyroid disorders (Thyroid project), brain damage during exposure 'in-utero' (Brain Damage 'in-Utero' project) and with the development of the Chernobyl registries (Epidemiological Registry Project). A fifth pilot project on oral health was performed only in Belarus. Epidemiological investigations have been an important component of all IPHECA pilot projects. Within 'Epidemiological Registry' Project such investigations have been the principal activity. But with respect to other IPHECA projects it was carried out in addition to main objectives relating to medical monitoring, early diagnosis and treatment of specific diseases included in project protocols. To support the epidemiological investigations within IPHECA, WHO supplied 41 computers in Belarus, Russian Federation and Ukraine and provided training for specialists from these countries in internationally recognized centres. The training programmes and host countries were as follows: standardization of epidemiological investigations (United Kingdom), radiation epidemiology (Russia), development of software (United Kingdom), principles of epidemiological investigations (The Czech Republic), cohort investigations (Japan)

  11. WHO - IPHECA: Epidemiological aspects

    Energy Technology Data Exchange (ETDEWEB)

    Souchkevitch, G [World Health Organization, Geneva (Swaziland)

    1996-07-01

    In May 1991 the World Health Assembly endorsed the establishment of the International Programme on the Health Effects of the Chernobyl Accident (IPHECA) under the auspices of WHO. Five pilot projects have been carried out within IPHECA in the study territories of Belarus, Russian Federation and Ukraine in a period from 1991 to 1994. This pilot projects dealt with the detection and treatment of leukaemia and related diseases (Haematology Project), thyroid disorders (Thyroid project), brain damage during exposure 'in-utero' (Brain Damage 'in-Utero' project) and with the development of the Chernobyl registries (Epidemiological Registry Project). A fifth pilot project on oral health was performed only in Belarus. Epidemiological investigations have been an important component of all IPHECA pilot projects. Within 'Epidemiological Registry' Project such investigations have been the principal activity. But with respect to other IPHECA projects it was carried out in addition to main objectives relating to medical monitoring, early diagnosis and treatment of specific diseases included in project protocols. To support the epidemiological investigations within IPHECA, WHO supplied 41 computers in Belarus, Russian Federation and Ukraine and provided training for specialists from these countries in internationally recognized centres. The training programmes and host countries were as follows: standardization of epidemiological investigations (United Kingdom), radiation epidemiology (Russia), development of software (United Kingdom), principles of epidemiological investigations (The Czech Republic), cohort investigations (Japan)

  12. Basic concepts of epidemiology

    International Nuclear Information System (INIS)

    Savitz, D.A.

    1984-01-01

    Epidemiology can be defined simply as the science of the distribution and determinants of disease in human populations. As a descriptive tool, epidemiology can aid health care service providers, for example, in allocation of resources. In its analytic capacity, the epidemiologic approach can help identify determinants of disease through the study of human populations. Epidemiology is primarily an observational rather than experimental methodology, with corresponding strengths and limitations. Relative to other approaches for assessing disease etiology and impacts of potential health hazards, epidemiology has a rather unique role that is complementary to, but independent of, both basic biologic sciences and clinical medicine. Experimental biologic sciences such as toxicology and physiology provide critical information on biologic mechanisms of disease required for causal inference. Clinical medicine often serves as the warning system that provides etiologic clues to be pursued through systematic investigation. The advantage of the epidemiologic approach is its reliance on human field experience, that is, the real world. While laboratory experimentation is uniquely well suited to defining potential hazards, it can neither determine whether human populations have actually been affected nor quantify that effect. Building all the complexities of human behavior and external factors into a laboratory study or mathematical model is impossible. By studying the world as it exists, epidemiology examines the integrated, summarized product of the myriad factors influencing health

  13. Epidemiology and Radiation Protection

    International Nuclear Information System (INIS)

    1987-01-01

    Epidemiology aims at providing direct evidence of the long term health effects in humans due to potentially dangerous exposures to various nuisance agents, including ionising radiation. Inappropriate interpretation and use of the results of epidemiological studies may result in inaccurate assessments of the risks associated with radiation exposure. This report presents the proceedings of a Workshop organised by the NEA to create an opportunity for epidemiologists and radiation protection specialists to exchange their experiences and views on the problems of methodology in epidemiological research and on the application of its results to the assessment of radiation risks

  14. Huge increase in gas phase nanoparticle generation by pulsed direct current sputtering in a reactive gas admixture

    Science.gov (United States)

    Polonskyi, Oleksandr; Peter, Tilo; Mohammad Ahadi, Amir; Hinz, Alexander; Strunskus, Thomas; Zaporojtchenko, Vladimir; Biederman, Hynek; Faupel, Franz

    2013-07-01

    Using reactive DC sputtering in a gas aggregation cluster source, we show that pulsed discharge gives rise to a huge increase in deposition rate of nanoparticles by more than one order of magnitude compared to continuous operation. We suggest that this effect is caused by an equilibrium between slight target oxidation (during "time-off") and subsequent sputtering of Ti oxides (sub-oxides) at "time-on" with high power impulse.

  15. Reconstruction of juxta-articular huge defects of distal femur with vascularized fibular bone graft and Ilizarov's distraction osteogenesis.

    Science.gov (United States)

    Lai, Davy; Chen, Chuan-Mu; Chiu, Fang-Yao; Chang, Ming-Chau; Chen, Tain-Hsiung

    2007-01-01

    We evaluate the effect of reconstructing huge defects (mean, 15.8 cm) of the distal femur with Ilizarov's distraction osteogenesis and free twin-barreled vascularized fibular bone graft (TVFG). We retrospectively reviewed a consecutive series of five patients who had cases of distal femoral fractures with huge defects and infection that were treated by the Ilizarov's distraction osteogenesis. After radical debridement, two of the five cases had free TVFG and monolocal distraction osteogenesis, and another two cases had multilocal distraction osteogenesis with knee fusion because of loss of the joint congruity. The other case with floating knee injury had bilocal distraction osteogenesis and a preserved knee joint. The mean defect of distal femur was 15.8 cm (range, 14-18 cm) in length. The mean length of distraction osteogenesis by Ilizarov's apparatus was 8.2 cm. The mean length of TVFG was 8 cm. The average duration from application of Ilizarov's apparatus to achievement of bony union was 10.2 months (range, 8-13 months). At the end of the follow-up, ranges of motion of three knees were 0 to 45 degrees, 0 to 60 degrees, and 0 to 90 degrees. Two cases had knee arthrodesis with bony fusion because of loss of the joint congruity. There were no leg length discrepancies in all five patients. In addition, three patients had pin tract infections and one case had a 10 degree varus deformity of the femur. Juxta-articular huge defect (>10 cm) of distal femur remains a challenge to orthopedic surgeons. Ilizarov's technique provides the capability to maintain stability, eradicate infection, restore leg length, and to perform adjuvant reconstructive procedure easily. In this study, we found that combining Ilizarov's distraction osteogenesis with TVFG results in improved patient outcome for patients with injuries such as supracondylar or intercondylar infected fractures or nonunion of distal femur with huge bone defect.

  16. 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.

  17. Systematics of Short-range Correlations in Eukaryotic Genomes

    Science.gov (United States)

    Hameister, Jörn; Helm, Werner E.; Hütt, Marc-Thorsten; Dehnert, Manuel

    Attempts to identify a species on the basis of its DNA sequence on purely statistical grounds have been formulated for more than a decade. Solving this problem could have a huge impact on understanding processes of genome evolution and on the design of classification schemes for DNA sequences.

  18. Hypointensity on postcontrast MR imaging from compression of the sacral promontory in enlarged uterus with huge leiomyoma and adenomyosis

    International Nuclear Information System (INIS)

    Uotani, Kensuke; Monzawa, Shuichi; Adachi, Shuji; Takemori, Masayuki; Kaji, Yasushi; Sugimura, Kazuro

    2007-01-01

    In patients with huge leiomyoma and with adenomyosis of the uterus, a peculiar area of hypointensity was occasionally observed on postcontrast magnetic resonance (MR) imaging in the dorsal portion of the enlarged uterus near the sacral promontory. We describe the imaging characteristics of these MR findings and correlate them with histopathological findings to examine whether the areas represent specific pathological changes. Ten patients with huge leiomyomas and two with huge adenomyotic lesions whose imaging revealed the hypointensity were enrolled. All had enlarged uteri that extended beyond the sacral promontory. MR findings of the hypointense areas were evaluated and correlated with histopathological findings in 5 patients with leiomyoma and two with adenomyosis who had hysterectomy. The ten patients with leiomyoma showed flare-shaped hypointensity arising from the dorsal surface of the uterine body that extended deep into the tumor. The base of the hypointense areas was narrow in 5 patients with intramural leiomyoma and broad in five with subserosal leiomyoma. Two patients with adenomyosis showed nodular-shaped areas of hypointensity in front of the sacral promontory. Precontrast T 1 - and T 2 -weighted MR images showed no signal abnormalities in the portions corresponding to the hypointensity in any of the 12 patients. Pathological examinations showed no specific findings in the portions corresponding to the hypointensity in the 7 patients who had hysterectomy. The areas of hypointensity may represent functional changes, such as decreased localized blood flow caused by compression of the sacral promontory. (author)

  19. The causes and the nursing interventions of the complications due to repeated embolization therapy for huge cerebral arteriovenous malformations

    International Nuclear Information System (INIS)

    Sun Lingfang; Sun Ge

    2010-01-01

    Objective: To investigate the causes of the complications occurred after repeated embolization therapy for huge cerebral arteriovenous malformations and to discuss their nursing interventions. Methods: A total of 54 embolization procedures were performed in 17 patients with huge cerebral arteriovenous malformations. The clinical data were retrospectively analyzed. The causes of complications were carefully examined and the preventive measures were discussed. The prompt and necessary nursing interventions were formulated in order to prevent the complications or serious consequences. Results: Among the total 17 patients, one patient gave up the treatment because of the cerebral hemorrhage which occurred two months after receiving 3 times of embolization therapy. One patient experienced cerebral vascular spasm during the procedure, which was relieved after antispasmodic medication and no neurological deficit was left behind. Two patients developed transient dizziness and headache, which were alleviated spontaneously. One patient presented with nervousness, fear and irritability, which made him hard to cooperate with the operation and the basis intravenous anesthesia was employed. No complications occurred in the remaining cases. Conclusion: The predictive nursing interventions for the prevention of complications are very important for obtaining a successful repeated embolization therapy for huge cerebral arteriovenous malformations, which will ensure that the patients can get the best treatment and the complications can be avoided. (authors)

  20. [Radical Resection of Huge Gastrointestinal Stromal Tumor of the Stomach Following Neoadjuvant Chemotherapy with lmatinib - ACase Report].

    Science.gov (United States)

    Hiraki, Yoko; Kato, Hiroaki; Shiraishi, Osamu; Tanaka, Yumiko; Iwama, Mitsuru; Yasuda, Atsushi; Shinkai, Masayuki; Kimura, Yutaka; Imano, Motohiro; Imamoto, Haruhiko; Yasuda, Takushi

    2017-11-01

    The usefulness and safety of imatinibfor neoadjuvant chemotherapy for resectable gastrointestinal stromal tumor(GIST) has not been established. We reported a case of a huge GIST of the stomach that was safely resected following preoperative imatinibtherapy. A 69-year-old man was hospitalized with abdominal fullness which increased rapidly from a month ago. A CT scan showed a huge tumor containing solid and cystic component which was accompanied by an extra-wall nodule. The tumor was strongly suspected to be originated from the stomach and EUS-FNA revealed GIST. We diagnosed GIST of the stomach and initiated preoperative adjuvant chemotherapy with imatinib because there was a risk for the break of tumor capsule and composite resection of the other organs without prior chemotherapy. After the administration of imatinib4 00 mg/day for 6months, the solid component was decreased in size and its' activity by PET-CT had declined, but the size of the cystic component was not changed and the patient's complaint of fullness was not reduced. Then, after a week cessation of imatinib, we performed surgical removal of the tumor with partial gastrectomy without surgical complication during and after the operation. Imatinibwas resumed 2 weeks later postoperatively and 1 year and 8 months has passed since the operation without recurrence. Neoadjuvant chemotherapy with imatinibhas the potential to become an important therapeutic option for the treatment of huge GISTs.

  1. 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.

  2. 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

  3. Methodologic frontiers in environmental epidemiology.

    OpenAIRE

    Rothman, K J

    1993-01-01

    Environmental epidemiology comprises the epidemiologic study of those environmental factors that are outside the immediate control of the individual. Exposures of interest to environmental epidemiologists include air pollution, water pollution, occupational exposure to physical and chemical agents, as well as psychosocial elements of environmental concern. The main methodologic problem in environmental epidemiology is exposure assessment, a problem that extends through all of epidemiologic re...

  4. 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.

  5. Huge Varicose Inferior Mesenteric Vein: an Unanticipated 99mTc-labeled Red Blood Cell Scintigraphy Finding

    International Nuclear Information System (INIS)

    Hoseinzadeh, Samaneh; Shafiei, Babak; Salehian, Mohamadtaghi; Neshandar Asli, Isa; Ghodoosi, Iraj

    2010-01-01

    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 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 99m Tc-labeled RBC scintigraphy for the diagnosis of rare ectopic lower GI varices.

  6. 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.

  7. 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.

  8. 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.

  9. [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

  10. Against Popperized epidemiology.

    Science.gov (United States)

    Jacobsen, M

    1976-03-01

    The recommendation of Popper's philosophy of science should be adopted by epidemiologists is disputed. Reference is made to other authors who have shown that the most constructive elements in Popper's ideas have been advocated by earlier philosophers and have been used in epidemiology without abandoning inductive reasoning. It is argued that Popper's denigration of inductive methods is particularly harmful to epidemiology. Inductive reasoning and statistical inference play a key role in the science; it is suggested that unfamiliarity with these ideas contributes to widespread misunderstanding of the function of epidemiology. Attention is drawn to a common fallacy involving correlations between three random variables. The prevalence of the fallacy may be related to confusion between deductive and inductive logic.

  11. 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......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 European participants. The aim of the consortium is to promote and sustain collaboration and sharing of data and knowledge in the field of ophthalmic epidemiology in Europe, with particular focus on the harmonization of methods for future research, estimation and projection of frequency and impact...

  12. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  13. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  14. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  15. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  16. Nuclear accidents and epidemiology

    International Nuclear Information System (INIS)

    1987-01-01

    A consultation on epidemiology related to the Chernobyl accident was held in Copenhagen in May 1987 as a basis for concerted action. This was followed by a joint IAEA/WHO workshop in Vienna, which reviewed appropriate methodologies for possible long-term effects of radiation following nuclear accidents. The reports of these two meetings are included in this volume, and cover the subjects: 1) Epidemiology related to the Chernobyl nuclear accident. 2) Appropriate methodologies for studying possible long-term effects of radiation on individuals exposed in a nuclear accident. Figs and tabs

  17. Advances in radiation epidemiology

    International Nuclear Information System (INIS)

    Boice, J.

    1997-01-01

    The 1994 UNSCEAR report provides an informative review of radiation epidemiology. During the past 2 years there have been several major advances in our understanding of radiation effects based on new studies of atomic bomb survivors in Japan, of patients given diagnostic and therapeutic radiation (including iodine-131), of workers occupationally exposed, and of general populations exposed to residential radon. Laboratory approaches are also being incorporated into epidemiological investigations to learn more about the biological mechanism by which radiation causes cancer in man. (author)

  18. 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.

  19. Ubiquitous UAVs: a cloud based framework for storing, accessing and processing huge amount of video footage in an efficient way

    Science.gov (United States)

    Efstathiou, Nectarios; Skitsas, Michael; Psaroudakis, Chrysostomos; Koutras, Nikolaos

    2017-09-01

    Nowadays, video surveillance cameras are used for the protection and monitoring of a huge number of facilities worldwide. An important element in such surveillance systems is the use of aerial video streams originating from onboard sensors located on Unmanned Aerial Vehicles (UAVs). Video surveillance using UAVs represent a vast amount of video to be transmitted, stored, analyzed and visualized in a real-time way. As a result, the introduction and development of systems able to handle huge amount of data become a necessity. In this paper, a new approach for the collection, transmission and storage of aerial videos and metadata is introduced. The objective of this work is twofold. First, the integration of the appropriate equipment in order to capture and transmit real-time video including metadata (i.e. position coordinates, target) from the UAV to the ground and, second, the utilization of the ADITESS Versatile Media Content Management System (VMCMS-GE) for storing of the video stream and the appropriate metadata. Beyond the storage, VMCMS-GE provides other efficient management capabilities such as searching and processing of videos, along with video transcoding. For the evaluation and demonstration of the proposed framework we execute a use case where the surveillance of critical infrastructure and the detection of suspicious activities is performed. Collected video Transcodingis subject of this evaluation as well.

  20. 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

  1. Translational Epidemiology in Psychiatry

    Science.gov (United States)

    Weissman, Myrna M.; Brown, Alan S.; Talati, Ardesheer

    2012-01-01

    Translational research generally refers to the application of knowledge generated by advances in basic sciences research translated into new approaches for diagnosis, prevention, and treatment of disease. This direction is called bench-to-bedside. Psychiatry has similarly emphasized the basic sciences as the starting point of translational research. This article introduces the term translational epidemiology for psychiatry research as a bidirectional concept in which the knowledge generated from the bedside or the population can also be translated to the benches of laboratory science. Epidemiologic studies are primarily observational but can generate representative samples, novel designs, and hypotheses that can be translated into more tractable experimental approaches in the clinical and basic sciences. This bedside-to-bench concept has not been explicated in psychiatry, although there are an increasing number of examples in the research literature. This article describes selected epidemiologic designs, providing examples and opportunities for translational research from community surveys and prospective, birth cohort, and family-based designs. Rapid developments in informatics, emphases on large sample collection for genetic and biomarker studies, and interest in personalized medicine—which requires information on relative and absolute risk factors—make this topic timely. The approach described has implications for providing fresh metaphors to communicate complex issues in interdisciplinary collaborations and for training in epidemiology and other sciences in psychiatry. PMID:21646577

  2. 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...

  3. Human Germline Genome Editing.

    Science.gov (United States)

    Ormond, Kelly E; Mortlock, Douglas P; Scholes, Derek T; Bombard, Yvonne; Brody, Lawrence C; Faucett, W Andrew; Garrison, Nanibaa' A; Hercher, Laura; Isasi, Rosario; Middleton, Anna; Musunuru, Kiran; Shriner, Daniel; Virani, Alice; Young, Caroline E

    2017-08-03

    With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  4. Toward systems epidemiology of coffee and health.

    Science.gov (United States)

    Cornelis, Marilyn C

    2015-02-01

    Coffee is one of the most widely consumed beverages in the world and has been associated with many health conditions. This review examines the limitations of the classic epidemiological approach to studies of coffee and health, and describes the progress in systems epidemiology of coffee and its correlated constituent, caffeine. Implications and applications of this growing body of knowledge are also discussed. Population-based metabolomic studies of coffee replicate coffee-metabolite correlations observed in clinical settings but have also identified novel metabolites of coffee response, such as specific sphingomyelin derivatives and acylcarnitines. Genome-wide analyses of self-reported coffee and caffeine intake and serum levels of caffeine support an overwhelming role for caffeine in modulating the coffee consumption behavior. Interindividual variation in the physiological exposure or response to any of the many chemicals present in coffee may alter the persistence and magnitude of their effects. It is thus imperative that future studies of coffee and health account for this variation. Systems epidemiological approaches promise to inform causality, parse the constituents of coffee responsible for health effects, and identify the subgroups most likely to benefit from increasing or decreasing coffee consumption.

  5. 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.

  6. Elective hemi transurethral resection of prostate: a safe and effective method of treating huge benign prostatic hyperplasia

    International Nuclear Information System (INIS)

    Abidi, S.S.; Feroz, I.; Aslam, M.; Fawad, A.

    2012-01-01

    To evaluate the safety and efficacy of elective hemi-resection of prostate in patients with huge gland, weighing more than 120 grams. Study Design: Multi centric, analytical comparative study. Place and Duration of Study: Department of Urology, Karachi Medical and Dental College, Abbasi Shaheed Hospital and Dr. Ziauddin Hospital, Karachi, from August 2006 to July 2009. Methodology: All benign cases were included in this study and divided into two groups. In group A, patients having huge prostate (> 120 grams) were placed and hemi TURP was performed. In group B, patients having 60 to 100 grams prostate were placed and conventional Blandy's TURP was performed. Results of both groups were compared in terms of duration of surgery, amount of tissue resected, operative bleeding, postoperative complications, duration of postoperative catheterization, re-admission and re-operations. Effectiveness of procedure was assessed by a simple questionnaire filled by the patients at first month, first year and second year. Patients satisfaction in terms of their ability to void, control urination, frequency, urgency, urge incontinence, haematuria, recurrent UTI, re-admission and re-operations were also assessed. Fisher exact test was applied to compare the safety and efficacy of variables. Results: In group A and B, average age range was 72 and 69 years, average weight of prostate was 148 and 70 grams, average duration of surgery was 102 and 50 minutes respectively. Average weight of resected tissue was 84 and 54 grams and haemoglobin loss was two grams and one gram respectively. Total hospital stay was 5 and 4 days. Total duration of indwelling Foley's catheter (postoperative) was 5 days and 2 days. Patient satisfaction in term of urine flow, urinary control, improvement in frequency and nocturia were comparable in both groups. UTI and re-admission was more in hemi resection group. At the end of 2 years follow-up, there is no statistical difference between the safety and efficacy

  7. 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.

  8. 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...

  9. 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.

  10. Analysis of the Huge Immigration of Sogatella furcifera (Hemiptera: Delphacidae) to Southern China in the Spring of 2012.

    Science.gov (United States)

    Sun, Si-Si; Bao, Yun-Xuan; Wu, Yan; Lu, Min-Hong; Tuan, Hoang-Anh

    2018-02-08

    Sogatella furcifera (Horváth) is a migratory rice pest that periodically erupts across Asia, and early immigration is an important cause of its outbreak. The early immigration of S. furcifera into southern China shows evident annual fluctuations. In the spring of 2012, the huge size of the immigrant population and the large number of immigration peaks were at levels rarely seen prior to that year. However, little research has been done on the entire process of round-trip migration to clarify the development of the population, the long-distance migration and the final eruption. In this study, the light-trap data for S. furcifera in southern China and Vietnam in 2011-2016 were collected, and the trajectory modeling showed that the early immigrants to southern China came from the northern and central Vietnam, Laos, and northeastern Thailand. Analysis of the development of the population, the migration process and meteorological factors revealed the reasons for the huge size of the early immigration: 1) the expansion of the source area could be seen as a precondition; 2) the large size of the returned population in the last autumn and the warm temperature of southern Vietnam and Laos in the last winter increased the initial populations; 3) the sustained strong southwest winds were conducive to the northward migration of the population during the major immigration period in early May. Therefore, the large-scale immigration of S. furcifera to southern China in the spring of 2012 resulted from the combined effects of several factors involved in the process of round-trip migration. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

    Science.gov (United States)

    Kravatsky, Yuri V; Chechetkin, Vladimir R; Tchurikov, Nikolai A; Kravatskaya, Galina I

    2015-02-01

    The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  12. Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV).

    Science.gov (United States)

    Hick, Paul M; Subramaniam, Kuttichantran; Thompson, Patrick M; Waltzek, Thomas B; Becker, Joy A; Whittington, Richard J

    2017-11-01

    Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10 -4 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Epidemiology applied to health physics

    International Nuclear Information System (INIS)

    1983-01-01

    The technical program of the mid-year meeting of the Health Physics Society, entitled Epidemiology Applied to Health physics, was developed to meet three objectives: (1) give health physicists a deeper understanding of the basics of epidemiological methods and their use in developing standards, regulations, and criteria and in risk assessment; (2) present current reports on recently completed or on-going epidemiology studies; and (3) encourage greater interaction between the health physics and epidemiology disciplines. Included are studies relating methods in epidemiology to radiation protection standards, risk assessment from exposure to bone-seekers, from occupational exposures in mines, mills and nuclear facilities, and from radioactivity in building materials

  14. Epidemiology of Gout

    Science.gov (United States)

    Choi, Hyon

    2014-01-01

    Synopsis Gout is the most prevalent inflammatory arthritis in men. The findings of several epidemiological studies from a diverse range of countries suggest that the prevalence of gout has risen over the last few decades. Whilst incidence data are scarce, data from the US suggests that the incidence of gout is also rising. Evidence from prospective epidemiological studies has confirmed dietary factors (animal purines, alcohol and fructose), obesity, the metabolic syndrome, hypertension, diuretic use, and chronic kidney disease as clinically relevant risk factors for hyperuricemia and gout. Low-fat dairy products, coffee, and vitamin C appear to have a protective effect. Further prospective studies are required to examine other proposed risk factors for hyperuricaemia and gout such as the use of β-blockers and angiotension-II receptor antagonists (other than losartan), obstructive sleep apnoea, and osteoarthritis, and putative protective factors such as calcium-channel blockers and losartan. PMID:24703341

  15. 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...

  16. The leukemias: Epidemiologic aspects

    International Nuclear Information System (INIS)

    Linet, M.S.

    1984-01-01

    Particularly geared to physicians and cancer researchers, this study of the epidemiology and etiology of leukemia analyzes the four major leukemia subtypes in terms of genetic and familial determinant factors and examines the incidence, distribution and frequency of reported leukemia clusters. Linet discusses the connection between other types of malignancies, their treatments, and the subsequent development of leukemia and evaluates the impact on leukemia onset of such environmental factors as radiation therapy, drugs, and occupational hazards

  17. Worldwide Report, Epidemiology

    Science.gov (United States)

    1985-11-22

    caused by ingesting eggs of the pork tapeworm, Taenia solium . It has been described as the most com- mon parasitic disease of the central nervous...rather difficult to detect in stool specimens and at this stage it is impossible to distinguish between T. solium and T. saginata eggs either by...Knowledge and Perspectives, pp. 25-38. Academic Press, New York. 12. Pawlowskz S. (1982). Epidemiology and prevention of Taenia saginata infec- tion. In

  18. Epidemiology and moral philosophy.

    OpenAIRE

    Westrin, C G; Nilstun, T; Smedby, B; Haglund, B

    1992-01-01

    To an increasing extent ethical controversies affect and sometimes obstruct public health work and epidemiological research. In order to improve communication between the concerned parties a model for identification and analysis of ethical conflicts in individual-based research has been worked out in co-operation between epidemiologists and moral philosophers. The model has two dimensions. One dimension specifies relevant ethical principles (as beneficence, non-maleficence, autonomy and justi...

  19. Molecular epidemiology of Plum pox virus in Japan.

    Science.gov (United States)

    Maejima, Kensaku; Himeno, Misako; Komatsu, Ken; Takinami, Yusuke; Hashimoto, Masayoshi; Takahashi, Shuichiro; Yamaji, Yasuyuki; Oshima, Kenro; Namba, Shigetou

    2011-05-01

    For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.

  20. The emergence of translational epidemiology: from scientific discovery to population health impact.

    Science.gov (United States)

    Khoury, Muin J; Gwinn, Marta; Ioannidis, John P A

    2010-09-01

    Recent emphasis on translational research (TR) is highlighting the role of epidemiology in translating scientific discoveries into population health impact. The authors present applications of epidemiology in TR through 4 phases designated T1-T4, illustrated by examples from human genomics. In T1, epidemiology explores the role of a basic scientific discovery (e.g., a disease risk factor or biomarker) in developing a "candidate application" for use in practice (e.g., a test used to guide interventions). In T2, epidemiology can help to evaluate the efficacy of a candidate application by using observational studies and randomized controlled trials. In T3, epidemiology can help to assess facilitators and barriers for uptake and implementation of candidate applications in practice. In T4, epidemiology can help to assess the impact of using candidate applications on population health outcomes. Epidemiology also has a leading role in knowledge synthesis, especially using quantitative methods (e.g., meta-analysis). To explore the emergence of TR in epidemiology, the authors compared articles published in selected issues of the Journal in 1999 and 2009. The proportion of articles identified as translational doubled from 16% (11/69) in 1999 to 33% (22/66) in 2009 (P = 0.02). Epidemiology is increasingly recognized as an important component of TR. By quantifying and integrating knowledge across disciplines, epidemiology provides crucial methods and tools for TR.

  1. 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.

  2. 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.

  3. 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...

  4. 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. Copyright © 2012 Wiley Periodicals, Inc.

  5. Epidemiology of brain tumors in childhood--a review

    International Nuclear Information System (INIS)

    Baldwin, Rachel Tobias; Preston-Martin, Susan

    2004-01-01

    Malignant brain tumors are the leading cause of cancer death among children and the second most common type of pediatric cancer. Despite several decades of epidemiologic investigation, the etiology of childhood brain tumors (CBT) is still largely unknown. A few genetic syndromes and ionizing radiation are established risk factors. Many environmental exposures and infectious agents have been suspected of playing a role in the development of CBT. This review, based on a search of the medical literature through August 2003, summarizes the epidemiologic evidence to date. The types of exposures discussed include ionizing radiation, N-nitroso compounds (NOC), pesticides, tobacco smoke, electromagnetic frequencies (EMF), infectious agents, medications, and parental occupational exposures. We have chosen to focus on perinatal exposures and review some of the recent evidence indicating that such exposures may play a significant role in the causation of CBT. The scientific community is rapidly learning more about the molecular mechanisms by which carcinogenesis occurs and how the brain develops. We believe that advances in genetic and molecular biologic technology, including improved histologic subtyping of tumors, will be of huge importance in the future of epidemiologic research and will lead to a more comprehensive understanding of CBT etiology. We discuss some of the early findings using these technologies

  6. 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...

  7. National human genome projects: an update and an agenda.

    Science.gov (United States)

    An, Joon Yong

    2017-01-01

    Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions in defined population. This perspective summarizes national genome projects conducted in the past 10 years and introduces case studies to utilize genomic data in genetic research.

  8. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea

    DEFF Research Database (Denmark)

    Treusch, Alexander H; Kletzin, Arnulf; Raddatz, Guenter

    2004-01-01

    Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large-insert fosmid libraries in total...... (approximately 1% each) have been captured in our libraries. The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured...

  9. Hypercalcemia and huge splenomegaly presenting in an elderly patient with B-cell non-Hodgkin's lymphoma: a case report

    Directory of Open Access Journals (Sweden)

    Tirgari Farrokh

    2010-10-01

    Full Text Available Abstract Introduction Hypercalcemia is the major electrolyte abnormality in patients with malignant tumors. It can be due to localized osteolytic hypercalcemia or elaboration of humoral substances such as parathyroid hormone-related protein from tumoral cells. In hematological malignancies, a third mechanism of uncontrolled synthesis and secretion of 1-25(OH2D3 from tumoral cells or neighboring macrophages may contribute to the problem. However, hypercalcemia is quite unusual in patients with B-cell non-Hodgkin's lymphoma. Case presentation An 85-year-old Caucasian woman presented with low grade fever, anorexia, abdominal discomfort and fullness in her left abdomen for the last six months. She was mildly anemic and complained of fatigability. She had huge splenomegaly and was hypercalcemic. After correction of her hypercalcemia, she had a splenectomy. Microscopic evaluation revealed a malignant lymphoma. Her immunohistochemistry was positive for leukocyte common antigen, CD20 and parathyroid hormone-related peptide. Conclusion Immunopositivity for parathyroid hormone-related peptide clearly demonstrates that hypersecretion of a parathyroid hormone-like substance from the tumor had led to hypercalcemia in this case. High serum calcium is seen in only seven to eight percent of patients with B-cell non-Hodgkin's lymphoma, apparently due to different mechanisms. Evaluation of serum parathyroid hormone-related protein and 1-25(OH2D3 can be helpful in diagnosis and management. It should be noted that presentation with hypercalcemia has a serious impact on prognosis and survival.

  10. A huge ovarian mucinous cystadenoma associated with contralateral teratoma and polycystic ovary syndrome in an obese adolescent girl.

    Science.gov (United States)

    Thaweekul, Patcharapa; Thaweekul, Yuthadej; Mairiang, Karicha

    2016-12-01

    A 13-year-old, obese girl presented with acute abdominal pain with abdominal distension for a year. The physical examination revealed marked abdominal distension with a large well-circumscribed mass sized 13×20 cm. Her body mass index (BMI) was 37.8 kg/m2. An abdominal CT scan revealed a huge multiloculated cystic mass and a left adnexal mass. She had an abnormal fasting plasma glucose and low HDL-C. Laparotomy, right salpingooophorectomy, left cystectomy, lymph node biopsies and partial omentectomy were performed. The left ovary demonstrated multiple cystic follicles over the cortex. The histologic diagnosis was a mucinous cystadenoma of the right ovary and a matured cystic teratoma of the left ovary. Both obesity and polycystic ovary syndrome (PCOS) are associated with a greater risk of ovarian tumours, where PCOS could be either the cause or as a consequence of an ovarian tumour. We report an obese, perimenarchal girl with bilateral ovarian tumours coexistent with a polycystic ovary and the metabolic syndrome.

  11. Huge Inverse Magnetization Generated by Faraday Induction in Nano-Sized Au@Ni Core@Shell Nanoparticles.

    Science.gov (United States)

    Kuo, Chen-Chen; Li, Chi-Yen; Lee, Chi-Hung; Li, Hsiao-Chi; Li, Wen-Hsien

    2015-08-25

    We report on the design and observation of huge inverse magnetizations pointing in the direction opposite to the applied magnetic field, induced in nano-sized amorphous Ni shells deposited on crystalline Au nanoparticles by turning the applied magnetic field off. The magnitude of the induced inverse magnetization is very sensitive to the field reduction rate as well as to the thermal and field processes before turning the magnetic field off, and can be as high as 54% of the magnetization prior to cutting off the applied magnetic field. Memory effect of the induced inverse magnetization is clearly revealed in the relaxation measurements. The relaxation of the inverse magnetization can be described by an exponential decay profile, with a critical exponent that can be effectively tuned by the wait time right after reaching the designated temperature and before the applied magnetic field is turned off. The key to these effects is to have the induced eddy current running beneath the amorphous Ni shells through Faraday induction.

  12. Huge Inverse Magnetization Generated by Faraday Induction in Nano-Sized Au@Ni Core@Shell Nanoparticles

    Directory of Open Access Journals (Sweden)

    Chen-Chen Kuo

    2015-08-01

    Full Text Available We report on the design and observation of huge inverse magnetizations pointing in the direction opposite to the applied magnetic field, induced in nano-sized amorphous Ni shells deposited on crystalline Au nanoparticles by turning the applied magnetic field off. The magnitude of the induced inverse magnetization is very sensitive to the field reduction rate as well as to the thermal and field processes before turning the magnetic field off, and can be as high as 54% of the magnetization prior to cutting off the applied magnetic field. Memory effect of the induced inverse magnetization is clearly revealed in the relaxation measurements. The relaxation of the inverse magnetization can be described by an exponential decay profile, with a critical exponent that can be effectively tuned by the wait time right after reaching the designated temperature and before the applied magnetic field is turned off. The key to these effects is to have the induced eddy current running beneath the amorphous Ni shells through Faraday induction.

  13. Huge Inverse Magnetization Generated by Faraday Induction in Nano-Sized Au@Ni Core@Shell Nanoparticles

    Science.gov (United States)

    Kuo, Chen-Chen; Li, Chi-Yen; Lee, Chi-Hung; Li, Hsiao-Chi; Li, Wen-Hsien

    2015-01-01

    We report on the design and observation of huge inverse magnetizations pointing in the direction opposite to the applied magnetic field, induced in nano-sized amorphous Ni shells deposited on crystalline Au nanoparticles by turning the applied magnetic field off. The magnitude of the induced inverse magnetization is very sensitive to the field reduction rate as well as to the thermal and field processes before turning the magnetic field off, and can be as high as 54% of the magnetization prior to cutting off the applied magnetic field. Memory effect of the induced inverse magnetization is clearly revealed in the relaxation measurements. The relaxation of the inverse magnetization can be described by an exponential decay profile, with a critical exponent that can be effectively tuned by the wait time right after reaching the designated temperature and before the applied magnetic field is turned off. The key to these effects is to have the induced eddy current running beneath the amorphous Ni shells through Faraday induction. PMID:26307983

  14. 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.

  15. Epidemiology of Posttraumatic Osteoarthritis.

    Science.gov (United States)

    Thomas, Abbey C; Hubbard-Turner, Tricia; Wikstrom, Erik A; Palmieri-Smith, Riann M

    2017-06-02

    Osteoarthritis is a leading cause of disability whose prevalence and incidence continue to increase. History of joint injury represents an important risk factor for posttraumatic osteoarthritis and is a significant contributor to the rapidly growing percentage of the population with osteoarthritis. This review will present the epidemiology associated with posttraumatic osteoarthritis, with particular emphasis on the knee and ankle joints. It is important to understand the effect of posttraumatic osteoarthritis on the population so that sufficient resources can be devoted to countering the disease and promoting optimal long-term health for patients after joint injury.

  16. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  17. Worldwide Report, Epidemiology, No. 327

    National Research Council Canada - National Science Library

    1983-01-01

    Partial Contents: Epidemiology, Human Diseases, Health, Malaria, AIDS, Homosexual Male, Medical Administration, Rabies, Tuberculosis, Encephalitis Statistics, Gastroenteritie, Mystery Diseases, Children, Epidemics...

  18. Epidemiology in Latin America and the Caribbean: current situation and challenges.

    Science.gov (United States)

    Barreto, Sandhi M; Miranda, Jaime J; Figueroa, J Peter; Schmidt, Maria Inês; Munoz, Sergio; Kuri-Morales, P Pablo; Silva, Jarbas B

    2012-04-01

    This article analyses the epidemiological research developments in Latin America and the Caribbean (LAC). It integrates the series commissioned by the International Epidemiological Association to all WHO Regions to identify global opportunities to promote the development of epidemiology. Health situations of the regions were analysed based on published data on selected mortality, morbidity and risk factors. Epidemiological publication output by country was estimated by Medline bibliometrics. Internet and literature searches and data provided by key informants were used to describe perspectives on epidemiological training, research and funding. Despite important advances in recent decades, LAC remains the world's most unequal region. In 2010, 10% of the LAC's people still lived in conditions of multidimensional poverty, with huge variation among countries. The region has experienced fast and complex epidemiological changes in past decades, combining increasing rates of non-communicable diseases and injuries, and keeping uncontrolled many existing endemic and emerging diseases. Overall, epidemiological publications per year increased from 160 articles between 1961 and 1970 to 2492 between 2001 and 2010. The increase in papers per million inhabitants in the past three decades varied from 57% in Panama to 1339% in Paraguay. Universities are the main epidemiological training providers. There are at least 34 universities and other institutions in the region that offer postgraduate programmes at the master's and doctoral levels in epidemiology or public health. Most LAC countries rely largely on external funding and donors to initiate and sustain long-term research efforts. Despite the limited resources, the critical mass of LAC researchers has produced significant scientific contributions. FUTURE NEEDS: The health research panorama of the region shows enormous regional discrepancies, but great prospects. Improving research and human resources capacity in the region will

  19. Landscape Epidemiology of Tularemia Outbreaks in Sweden

    Science.gov (United States)

    Svensson, Kerstin; Bäck, Erik; Eliasson, Henrik; Berglund, Lennart; Granberg, Malin; Karlsson, Linda; Larsson, Pär; Forsman, Mats

    2009-01-01

    Summer outbreaks of tularemia that occurred from 1995 through 2005 in 2 locations in Sweden affected 441 persons. We performed an epidemiologic investigation of these outbreaks using a novel strategy, involving high-resolution genotyping of Francisella tularensis isolates obtained from 136 patients (using 18 genetic markers developed from 6 F. tularensis genome sequences) and interviews with the patients. Strong spatial associations were found between F. tularensis subpopulations and the places of disease transmission; infection by some subpopulations occurred within areas as small as 2 km2, indicating unidentified environmental point sources of tularemia. In both locations, disease clusters were associated with recreational areas beside water, and genetic subpopulations were present throughout the tularemia season and persisted over years. High-resolution genotyping in combination with patients’ statements about geographic places of disease transmission provided valuable indications of likely sources of infection and the causal genotypes during these tularemia outbreaks. PMID:19961673

  20. Epidemiology, hunger and development

    Directory of Open Access Journals (Sweden)

    Paulo H. Battaglin Machado

    2008-06-01

    Full Text Available Understanding the relationship between epidemiology and food security implies in disclosing famine causes, the way it is distributed in the society and to which extent it affects the populations. Building up from that perspective, this paper attempts to understand the famine logic throughout the various transitions accomplished in the past decades: epidemiologic, demographic, risk, nutritional and development. The reflexes of the demographic transition that took place in Brazil in the XXth century are related to the population nutritional status standard changes, that is, they shifted from malnutrition high prevalence to a significant increase in obesity. However, the paradox of this situation is due to the fact that most risk factors that bring about diseases of the modern world come from the “excess”, while millions die around the globe because of “deprivation”. The food production alone does not ensure its equitable distribution among the various groups of the society. The access alone does not lead to quality. The choices are made individually, but life style options imply in a set of correlations that go from economy to culture. It means that this field has a collective basis and encompasses environment and development.

  1. 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. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Sequencing and annotation of mitochondrial genomes from individual parasitic helminths.

    Science.gov (United States)

    Jex, Aaron R; Littlewood, D Timothy; Gasser, Robin B

    2015-01-01

    Mitochondrial (mt) genomics has significant implications in a range of fundamental areas of parasitology, including evolution, systematics, and population genetics as well as explorations of mt biochemistry, physiology, and function. Mt genomes also provide a rich source of markers to aid molecular epidemiological and ecological studies of key parasites. However, there is still a paucity of information on mt genomes for many metazoan organisms, particularly parasitic helminths, which has often related to challenges linked to sequencing from tiny amounts of material. The advent of next-generation sequencing (NGS) technologies has paved the way for low cost, high-throughput mt genomic research, but there have been obstacles, particularly in relation to post-sequencing assembly and analyses of large datasets. In this chapter, we describe protocols for the efficient amplification and sequencing of mt genomes from small portions of individual helminths, and highlight the utility of NGS platforms to expedite mt genomics. In addition, we recommend approaches for manual or semi-automated bioinformatic annotation and analyses to overcome the bioinformatic "bottleneck" to research in this area. Taken together, these approaches have demonstrated applicability to a range of parasites and provide prospects for using complete mt genomic sequence datasets for large-scale molecular systematic and epidemiological studies. In addition, these methods have broader utility and might be readily adapted to a range of other medium-sized molecular regions (i.e., 10-100 kb), including large genomic operons, and other organellar (e.g., plastid) and viral genomes.

  3. GDC 2: Compression of large collections of genomes.

    Science.gov (United States)

    Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

    2015-06-25

    The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.

  4. Cryptogenic transient ischemic attack after nose blowing: association of huge atrial septal aneurysm with patent foramen ovale as potential cause

    Directory of Open Access Journals (Sweden)

    Lotze U

    2013-07-01

    Full Text Available Ulrich Lotze,1 Uwe Kirsch,1 Marc-Alexander Ohlow,2 Thorsten Scholle,3 Jochen Leonhardi,3 Bernward Lauer,2 Gerhard Oltmanns,4 Hendrik Schmidt5,6 1Department of Internal Medicine, DRK Krankenhaus Sondershausen, Sondershausen, Germany; 2Department of Cardiology, Zentralklinik Bad Berka, Bad Berka, Germany; 3Institute of Diagnostic and Interventional Radiology, Zentralklinik Bad Berka, Germany; 4Department of Internal Medicine, DRK Krankenhaus Sömmerda; Sömmerda, Germany; 5Department of Cardiology and Diabetology, Klinikum Magdeburg, Magdeburg, Germany; 6Department of Internal Medicine III, Martin-Luther-Univeristy Halle-Wittenberg, Halle, Germany Abstract: Association of atrial septal aneurysm (ASA with patent foramen ovale (PFO is considered an important risk factor for cardioembolism frequently forwarding paradoxical embolism in patients with cryptogenic or unexplained cerebral ischemic events. We herein describe the case of a 69-year-old male patient reporting uncontrolled movements of the right arm due to a muscle weakness, slurred speech, and paresthesia in the oral region some seconds after he had blown his nose. These neurological symptoms had improved dramatically within a few minutes and were completely regressive at admission to our hospital about two hours later. On transesophageal echocardiography (TEE a huge ASA associated with PFO was detected. Diagnosis of the large-sized ASA was also confirmed by cardiac magnetic resonance imaging. Due to the early complete recovery from his neurological symptoms, the patient was diagnosed with a transient ischemic attack (TIA. After nine days he was discharged in a good clinical condition under the treatment with oral anticoagulation. It is concluded that in cryptogenic or unexplained stroke or TIA TEE should always be performed to rule out ASA and PFO as potential sources for paradoxical embolism in those inconclusive clinical situations. Keywords: congenital cardiac abnormality, atrial septal

  5. 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

  6. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  7. 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.

  8. Epidemiology of fibromyalgia.

    Science.gov (United States)

    Neumann, Lily; Buskila, Dan

    2003-10-01

    Chronic widespread pain, the cardinal symptom of fibromyalgia (FM), is common in the general population, with comparable prevalence rates of 7.3% to 12.9% across different countries. The prevalence of FM in the general population was reported to range from 0.5% to 5% and up to 15.7% in the clinic. The common association of FM with other rheumatic disorders, chronic viral infections, and systemic illnesses has been well documented in several studies. Up to 65% of patients with systemic lupus erythematosus meet the criteria for FM. FM is considered a member of the family of functional somatic syndromes. These syndromes are very common and share a similar phenomenology, epidemiologic characteristics, high rates of occurrence, a common pathogenesis, and similar management strategies. A high prevalence of FM was demonstrated among relatives of patients with FM and it may be attributed to genetic and environmental factors.

  9. [Epidemiology of osteoporosis].

    Science.gov (United States)

    Grazio, Simeon

    2006-01-01

    Osteoporosis represents a major and increasing public health problem with the aging of population. Major clinical consequences and economic burden of the disease are fractures. Many risk factors are associated with the fractures including low bone mass, hormonal disorders, personal and family history of fractures, low body weight, use of certain drugs (e.g. glucocorticoids), cigarette smoking, elevated intake of alchohol, low physical activity, insufficient level of vitamin D and low intake of calcium. This epidemiological review describes frequency, importance of risk factors and impact of osteoporosis and osteoporotic fractures. Objective measures of bone mineral density along with clinical assessment of risk factors can help identify patients who will benefit from prevention and intervention efforts and eventually reduce the morbidity and mortality associated with osteoporosis-related fractures.

  10. Temporal network epidemiology

    CERN Document Server

    Holme, Petter

    2017-01-01

    This book covers recent developments in epidemic process models and related data on temporally varying networks. It is widely recognized that contact networks are indispensable for describing, understanding, and intervening to stop the spread of infectious diseases in human and animal populations; “network epidemiology” is an umbrella term to describe this research field. More recently, contact networks have been recognized as being highly dynamic. This observation, also supported by an increasing amount of new data, has led to research on temporal networks, a rapidly growing area. Changes in network structure are often informed by epidemic (or other) dynamics, in which case they are referred to as adaptive networks. This volume gathers contributions by prominent authors working in temporal and adaptive network epidemiology, a field essential to understanding infectious diseases in real society.

  11. [Ethics and epidemiology].

    Science.gov (United States)

    Barata, Rita Barradas

    2005-01-01

    Human actions take place at the confluence of circumstances that require us to discern the proper way to act. Ethics falls within the terrain of practical knowledge, of knowledge about what is contingent. It belongs to the domain of moral judgments or value judgments. The counterpart of disenchantment with our contemporary world lies in an effort to re-establish an interest in ethics. There are basically three orders of relations between public health and human rights: the quest for balance between the collective good and individual rights; methods and techniques for identifying human rights violations and assessing their negative impact; and the tie between protecting individual rights and promoting health. The relationship between ethics and epidemiology goes beyond the ethical aspects involving research on human beings to encompass political commitments, practices within health services, and the production of knowledge.

  12. 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

  13. 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.

  14. 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

  15. National human genome projects: an update and an agenda

    OpenAIRE

    An, Joon Yong

    2017-01-01

    Population genetic and human genetic studies are being accelerated with genome technology and data sharing. Accordingly, in the past 10 years, several countries have initiated genetic research using genome technology and identified the genetic architecture of the ethnic groups living in the corresponding country or suggested the genetic foundation of a social phenomenon. Genetic research has been conducted from epidemiological studies that previously described the health or disease conditions...

  16. The Osceola Mudflow from Mount Rainier: Sedimentology and hazard implications of a huge clay-rich debris flow

    Science.gov (United States)

    Vallance, J.W.; Scott, K.M.

    1997-01-01

    altered rock in the preavalanche mass determines whether a debris avalanche will transform into a cohesive debris flow or remain a largely unsaturated debris avalanche. The distinction among cohesive lahar, noncohesive lahar, and debris avalanche is important in hazard assessment because cohesive lahars spread much more widely than noncohesive lahars that travel similar distances, and travel farther and spread more widely than debris avalanches of similar volume. The Osceola Mudflow is documented here as an example of a cohesive debris flow of huge size that can be used as a model for hazard analysis of similar flows.

  17. Participatory epidemiology: the contribution of participatory research to epidemiology

    Directory of Open Access Journals (Sweden)

    Mario Bach

    2017-02-01

    Full Text Available Abstract Background Epidemiology has contributed in many ways to identifying various risk factors for disease and to promoting population health. However, there is a continuing debate about the ability of epidemiology not only to describe, but also to provide results which can be better translated into public health practice. It has been proposed that participatory research approaches be applied to epidemiology as a way to bridge this gap between description and action. A systematic account of what constitutes participatory epidemiology practice has, however, been lacking. Methods A scoping review was carried out focused on the question of what constitutes participatory approaches to epidemiology for the purpose of demonstrating their potential for advancing epidemiologic research. Relevant databases were searched, including both the published and non-published (grey literature. The 102 identified sources were analyzed in terms of comparing common epidemiologic approaches to participatory counterparts regarding central aspects of the research process. Exemplary studies applying participatory approaches were examined more closely. Results A highly diverse, interdisciplinary body of literature was synthesized, resulting in a framework comprised of seven aspects of the research process: research goal, research question, population, context, data synthesis, research management, and dissemination of findings. The framework specifies how participatory approaches not only differ from, but also how they can enhance common approaches in epidemiology. Finally, recommendations for the further development of participatory approaches are given. These include: enhancing data collection, data analysis, and data validation; advancing capacity building for research at the local level; and developing data synthesis. Conclusion The proposed framework provides a basis for systematically developing the emergent science of participatory epidemiology.

  18. The epidemiology of endometriosis.

    Science.gov (United States)

    Cramer, Daniel W; Missmer, Stacey A

    2002-03-01

    Advances in understanding the epidemiology of endometriosis have lagged behind other diseases because of methodologic problems related to disease definition and control selection. Nevertheless, a better picture of the epidemiology of endometriosis has emerged over the past few decades. Prevalence estimates of the disease in clinic populations vary from about a 4% occurrence of largely asymptomatic endometriosis found in women undergoing tubal ligation to 50% of teenagers with intractable dysmenorrhea. General population incidence during the 1970s in this country has been suggested to be 1.6 per 1000 white females aged 15-49, while a more current study based upon hospital discharges finds endometriosis as a first listed diagnosis in 1.3 per 1000 discharges in women aged 15-44. There is a clinical impression that blacks have lower rates of endometriosis and Orientals have higher rates than whites. A variety of personal risk factors for endometriosis have also been described. Women with endometriosis may be taller and thinner. Menstrual factors reported to increase risk include dysmenorrhea, early menarche, and shorter cycle lengths. There is support for the idea that lifestyle exposures that might raise or lower estrogen levels could affect risk, including a decreased risk associated with smoking and exercise and an increased risk associated with caffeine or alcohol use. These risk factors appear to be compatible with the central importance of retrograde menstruation influenced by outflow obstruction that might affect its amount, immune factors that might affect its ability to be cleared, or hormonal stimuli that might affect its growth. In this model, dysmenorrhea could be either a disease symptom or a manifestation of outflow obstruction. Nulliparity could be either a consequence of disease or a cause since nulliparous women would not have the benefit of cervical dilation associated with labor and delivery. Since there is evidence that family history is a risk

  19. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    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...

  20. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; 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...

  1. 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

  2. Epidemiology of prostatitis

    Science.gov (United States)

    Krieger, John N.; Lee, Shaun Wen Huey; Jeon, Jeonseong; Cheah, Phaik Yeong; Liong, Men Long; Riley, Donald E.

    2008-01-01

    Background Prostatitis describes a combination of infectious diseases (acute and chronic bacterial prostatitis), chronic pelvic pain syndrome, and asymptomatic inflammation. Materials and methods We employed evidence-based methods to review the epidemiology of prostatitis syndromes. Results The prevalence of prostatitis symptoms could be compared in five studies surveying 10 617 men. Overall, 873 participants met various criteria for prostatitis, representing an overall rate of 8.2%, with prevalence ranging from 2.2 to 9.7%. A history of sexually transmitted diseases was associated with an increased risk for prostatitis symptoms. Men reporting a history of prostatitis symptoms had a substantially increased rate of benign prostatic hyperplasia, lower urinary tract symptoms and prostate cancer. In one study, the incidence of physician-diagnosed prostatitis was 4.9 cases per 1000 person-years. Two studies suggest that about one-third of men reporting prostatitis symptoms had resolution after 1 year. Patients with previous episodes and more severe symptoms are at higher risk for chronic pelvic pain. Discussion The prevalence of prostatitis symptoms is high, comparable to rates of ischamic heart disease and diabetes. Clinical evaluation appears necessary to verify that prostatitis is responsible for patients’ symptoms. Prostatitis symptoms may increase a man’s risk for benign prostate hypertrophy, lower urinary tract symptoms and prostate cancer. We need to define natural history and consequences of prostatitis, develop better algorithms for diagnosis and treatment, and develop strategies for prevention. PMID:18164907

  3. Epidemiology of Lung Cancer

    Science.gov (United States)

    Brock, Malcolm V.; Ford, Jean G.; Samet, Jonathan M.; Spivack, Simon D.

    2013-01-01

    Background: Ever since a lung cancer epidemic emerged in the mid-1900s, the epidemiology of lung cancer has been intensively investigated to characterize its causes and patterns of occurrence. This report summarizes the key findings of this research. Methods: A detailed literature search provided the basis for a narrative review, identifying and summarizing key reports on population patterns and factors that affect lung cancer risk. Results: Established environmental risk factors for lung cancer include smoking cigarettes and other tobacco products and exposure to secondhand tobacco smoke, occupational lung carcinogens, radiation, and indoor and outdoor air pollution. Cigarette smoking is the predominant cause of lung cancer and the leading worldwide cause of cancer death. Smoking prevalence in developing nations has increased, starting new lung cancer epidemics in these nations. A positive family history and acquired lung disease are examples of host factors that are clinically useful risk indicators. Risk prediction models based on lung cancer risk factors have been developed, but further refinement is needed to provide clinically useful risk stratification. Promising biomarkers of lung cancer risk and early detection have been identified, but none are ready for broad clinical application. Conclusions: Almost all lung cancer deaths are caused by cigarette smoking, underscoring the need for ongoing efforts at tobacco control throughout the world. Further research is needed into the reasons underlying lung cancer disparities, the causes of lung cancer in never smokers, the potential role of HIV in lung carcinogenesis, and the development of biomarkers. PMID:23649439

  4. 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.

  5. 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. Copyright © 2014 Elsevier España, S.L.U. y SEMICYUC. All rights reserved.

  6. Radiobiology and Epidemiology

    International Nuclear Information System (INIS)

    Desaintes, C; Holmstock, L.

    2001-01-01

    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

  7. 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.

  8. Indoor radon epidemiological study

    Energy Technology Data Exchange (ETDEWEB)

    Kunz, E; Tomasek, L; Mueller, T [National Radiation Protection Institute, Prague (Czech Republic); Placek, V [Inst. for Expertises and Emergencies, Pribram-Kamenna (Czech Republic); Matzner, J; Heribanova, A [State Office for Nuclear Safety, Prague (Czech Republic)

    1996-12-31

    The study is a long-term prospective cohort study of lung cancer and possibility other causes of death. The study population includes inhabitants of the area, who had resided there for at three years and at least one of these between 1.1.1960 and 21.12.1989. A total of 11865 inhabitants satisfied these criteria. The cumulative exposure of each respondent is being assessed on the basis of measurements in dwellings, time spent there and estimation of previous exposure levels by a model accounting for constructional changes in buildings. One year lasting measurements of radon daughter products by integral dosimeters (Kodak film LR 115) were performed in practically all dwellings of the specified area. Radon measurements in houses in term of equilibrium concentration are compared with the results of a pilot study in Petrovice in 1990-91 which gave the stimulus for the epidemiological study. The distribution of death causes and ratio of observed (O) to expected (E) cases among collected death cases in the cohort, generally, somewhat lower ratios than one reflect the non-industrial character of the region, with the exception of lung cancer in man. The differences in the O/E ratios for lung cancer among the separate communities indicate that even in the situation of generally lower mortality, the dependence of lung cancer mortality on radon.

  9. Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists

    Directory of Open Access Journals (Sweden)

    Matheus Sanitá Lima

    2017-11-01

    Full Text Available Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb, indicating that most of the organelle DNA—coding and noncoding—is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells.

  10. Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.

    Science.gov (United States)

    Sanitá Lima, Matheus; Smith, David Roy

    2017-11-06

    Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA-coding and noncoding-is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells. Copyright © 2017 Sanitá Lima and Smith.

  11. The mitochondrial genome of Toxocara canis.

    Science.gov (United States)

    Jex, Aaron R; Waeschenbach, Andrea; Littlewood, D Timothy J; Hu, Min; Gasser, Robin B

    2008-08-06

    Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.

  12. The mitochondrial genome of Toxocara canis.

    Directory of Open Access Journals (Sweden)

    Aaron R Jex

    2008-08-01

    Full Text Available Toxocara canis (Ascaridida: Nematoda, which parasitizes (at the adult stage the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secementean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida. The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts.

  13. The Mitochondrial Genome of Toxocara canis

    Science.gov (United States)

    Littlewood, D. Timothy J.; Hu, Min; Gasser, Robin B.

    2008-01-01

    Toxocara canis (Ascaridida: Nematoda), which parasitizes (at the adult stage) the small intestine of canids, can be transmitted to a range of other mammals, including humans, and can cause the disease toxocariasis. Despite its significance as a pathogen, the genetics, epidemiology and biology of this parasite remain poorly understood. In addition, the zoonotic potential of related species of Toxocara, such as T. cati and T. malaysiensis, is not well known. Mitochondrial DNA is known to provide genetic markers for investigations in these areas, but complete mitochondrial genomic data have been lacking for T. canis and its congeners. In the present study, the mitochondrial genome of T. canis was amplified by long-range polymerase chain reaction (long PCR) and sequenced using a primer-walking strategy. This circular mitochondrial genome was 14162 bp and contained 12 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes consistent for secernentean nematodes, including Ascaris suum and Anisakis simplex (Ascaridida). The mitochondrial genome of T. canis provides genetic markers for studies into the systematics, population genetics and epidemiology of this zoonotic parasite and its congeners. Such markers can now be used in prospecting for cryptic species and for exploring host specificity and zoonotic potential, thus underpinning the prevention and control of toxocariasis in humans and other hosts. PMID:18682828

  14. 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.

  15. Complete genome sequences of six measles virus strains

    NARCIS (Netherlands)

    Phan, M.V.T. (My V.T.); C.M.E. Schapendonk (Claudia); B.B. Oude Munnink (Bas B.); M.P.G. Koopmans D.V.M. (Marion); R.L. de Swart (Rik); Cotten, M. (Matthew)

    2018-01-01

    textabstractGenetic characterization of wild-type measles virus (MV) strains is a critical component of measles surveillance and molecular epidemiology. We have obtained complete genome sequences of six MV strains belonging to different genotypes, using random-primed next generation sequencing.

  16. Occupational reproductive epidemiology: Pt. 1

    International Nuclear Information System (INIS)

    Roman, Eve; Doyle, Pat

    1993-01-01

    The authors review the current state of knowledge about possible adverse effects of hazardous paternal workplace exposures on human reproduction is scant. The methodology for studying possible association between occupational exposures and adverse reproductive events is not well developed. More detailed laboratory and epidemiological research is clearly required, and better collaboration between these two disciplines is needed. Associations suggested in the course of epidemiological research need to be tested in the laboratory, and vice versa. (author)

  17. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  19. Multiple huge epiphrenic esophageal diverticula with motility disease treated with video-assisted thoracoscopic and hand-assisted laparoscopic esophagectomy: a case report

    OpenAIRE

    Taniguchi, Yoshiki; Takahashi, Tsuyoshi; Nakajima, Kiyokazu; Higashi, Shigeyoshi; Tanaka, Koji; Miyazaki, Yasuhiro; Makino, Tomoki; Kurokawa, Yukinori; Yamasaki, Makoto; Takiguchi, Shuji; Mori, Masaki; Doki, Yuichiro

    2017-01-01

    Background Epiphrenic esophageal diverticulum is a rare condition that is often associated with a concomitant esophageal motor disorder. Some patients have the chief complaints of swallowing difficulty and gastroesophageal reflux; traditionally, such diverticula have been resected via right thoracotomy. Here, we describe a case with huge multiple epiphrenic diverticula with motility disorder, which were successfully resected using a video-assisted thoracic and laparoscopic procedure. Case pre...

  20. On the prediction of hydroelastic behaviors of a huge floating structure in waves. 2nd Report; Choogata futai no harochu dansei kyodo no suiteiho ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Murai, M.; Kagemoto, H.; Fujino, M. [The University of Tokyo, Tokyo (Japan)

    1997-08-01

    On the hydroelastic behaviors of a huge floating structure, a mutual interaction theory based on the area division method is used for the analysis of a fluid problem and a mode analysis method is used for the analysis of deformation. On the continuous deformation of a floating structure, the structure is considered as a set of partial structures obtained when the plane shape was divided into squares and discretely handled as a series of rigid motions in the small partial structures obtained by dividing the partial structures more finely. The experimental result in a water tank and the distribution method at a singular point were compared on the deformation of the elastic floating structure estimated by calculation based on this formulation. The result showed that the estimation method on the hydroelastic problem proposed in this paper is valid. On the prediction of hydroelastic behaviors of a huge floating structure, various calculation examples indicate that the hydroelastic behavior is not only the relation between the structure length and wavelength, but also that the bending rigidity of a structure is a very important factor. For a huge floating structure in the 5,000 m class, up to shorter wavelength of about {lambda}/L = 1/100 must be investigated. 6 refs., 14 figs., 5 tabs.

  1. Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum.

    Science.gov (United States)

    Rao, Soumya; Nandineni, Madhusudan R

    2017-01-01

    Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.

  2. What can we learn about lyssavirus genomes using 454 sequencing?

    Science.gov (United States)

    Höper, Dirk; Finke, Stefan; Freuling, Conrad M; Hoffmann, Bernd; Beer, Martin

    2012-01-01

    The main task of the individual project number four"Whole genome sequencing, virus-host adaptation, and molecular epidemiological analyses of lyssaviruses "within the network" Lyssaviruses--a potential re-emerging public health threat" is to provide high quality complete genome sequences from lyssaviruses. These sequences are analysed in-depth with regard to the diversity of the viral populations as to both quasi-species and so-called defective interfering RNAs. Moreover, the sequence data will facilitate further epidemiological analyses, will provide insight into the evolution of lyssaviruses and will be the basis for the design of novel nucleic acid based diagnostics. The first results presented here indicate that not only high quality full-length lyssavirus genome sequences can be generated, but indeed efficient analysis of the viral population gets feasible.

  3. Origin and evolution of SINEs in eukaryotic genomes.

    Science.gov (United States)

    Kramerov, D A; Vassetzky, N S

    2011-12-01

    Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

  4. Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria.

    Science.gov (United States)

    Dittmann, Elke; Gugger, Muriel; Sivonen, Kaarina; Fewer, David P

    2015-10-01

    Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms. Copyright © 2015. Published by Elsevier Ltd.

  5. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  6. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

    Science.gov (United States)

    Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

    2017-04-01

    Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends.

    Directory of Open Access Journals (Sweden)

    José Ramos-Castañeda

    2017-01-01

    Full Text Available 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.

  8. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  9. 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

  10. 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

  11. Salmonella Typhi genomics: envisaging the future of typhoid eradication.

    Science.gov (United States)

    Yap, Kien-Pong; Thong, Kwai Lin

    2017-08-01

    Next-generation whole-genome sequencing has revolutionised the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of Salmonella Typhi genomes, which remarkably shape the genomic research of S. Typhi and other pathogens. Important new insights acquired from the genome sequencing of S. Typhi, pertaining to genomic variations, evolution, population structure, antibiotic resistance, virulence, pathogenesis, disease surveillance/investigation and disease control are discussed. As the numbers of sequenced genomes are increasing at an unprecedented rate, fine variations in the gene pool of S. Typhi are captured in high resolution, allowing deeper understanding of the pathogen's evolutionary trends and its pathogenesis, paving the way to bringing us closer to eradication of typhoid through effective vaccine/treatment development. © 2017 John Wiley & Sons Ltd.

  12. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  13. Molecular epidemiology and evolution of fish Novirhabdoviruses

    Science.gov (United States)

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  14. Genomic island excisions in Bordetella petrii

    Directory of Open Access Journals (Sweden)

    Levillain Erwan

    2009-07-01

    Full Text Available Abstract Background Among the members of the genus Bordetella B. petrii is unique, since it is the only species isolated from the environment, while the pathogenic Bordetellae are obligately associated with host organisms. Another feature distinguishing B. petrii from the other sequenced Bordetellae is the presence of a large number of mobile genetic elements including several large genomic regions with typical characteristics of genomic islands collectively known as integrative and conjugative elements (ICEs. These elements mainly encode accessory metabolic factors enabling this bacterium to grow on a large repertoire of aromatic compounds. Results During in vitro culture of Bordetella petrii colony variants appear frequently. We show that this variability can be attributed to the presence of a large number of metastable mobile genetic elements on its chromosome. In fact, the genome sequence of B. petrii revealed the presence of at least seven large genomic islands mostly encoding accessory metabolic functions involved in the degradation of aromatic compounds and detoxification of heavy metals. Four of these islands (termed GI1 to GI3 and GI6 are highly related to ICEclc of Pseudomonas knackmussii sp. strain B13. Here we present first data about the molecular characterization of these islands. We defined the exact borders of each island and we show that during standard culture of the bacteria these islands get excised from the chromosome. For all but one of these islands (GI5 we could detect circular intermediates. For the clc-like elements GI1 to GI3 of B. petrii we provide evidence that tandem insertion of these islands which all encode highly related integrases and attachment sites may also lead to incorporation of genomic DNA which originally was not part of the island and to the formation of huge composite islands. By integration of a tetracycline resistance cassette into GI3 we found this island to be rather unstable and to be lost from

  15. Epidemiological methods: a brief review

    International Nuclear Information System (INIS)

    Winkelstein, W. Jr.

    1983-01-01

    Epidemiology, the study of disease distributions in populations and the factors which influence these distributions, is an observational science, i.e., its data base consists of measurements made on free living individuals characterized by presence or absence of disease states and putative risk factors. Epidemiological studies are usually classified as descriptive or analytical. Descriptive studies are primarily used for planning and evaluating health programs or to generate etiological hypotheses. Analytical studies are primarily used for testing etiological hypotheses. Analytical studies are designed either as cohort investigations in which populations with and without a putative risk factor are followed through time to ascertain their differential incidence of disease, or case-control investigations in which the history of exposure to a putative risk factor is compared among persons with a disease and appropriate controls free of disease. Both descriptive and analytical epidemiological studies have been applied to health physics problems. Examples of such problems and the epidemiological methods used to explore them will be presented

  16. 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.

  17. Killing fields; The epidemiological evidence

    Energy Technology Data Exchange (ETDEWEB)

    Best, Simon

    1990-02-01

    The threat posed by low frequency fields emerged initially because a researcher, looking for environmental factors in childhood leukaemia, observed a link between low voltage, high current power lines and disease occurrence. Cellular evidence now supports the findings but epidemiology still leads the argument. (43 references). (author).

  18. 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.

  19. 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

  20. Panel 1 : Epidemiology and Diagnosis

    NARCIS (Netherlands)

    Homøe, Preben; Kværner, Kari; Casey, Janet R; Damoiseaux, Roger A M J; van Dongen, Thijs M A; Gunasekera, Hasantha; Jensen, Ramon G; Kvestad, Ellen; Morris, Peter S; Weinreich, Heather M

    Objective To create a literature review between 2011 and June 1, 2015, on advances in otitis media (OM) epidemiology and diagnosis (including relevant audiology studies). Data Sources Electronic search engines (PubMed, EMBASE, and Cochrane Library) with a predefined search strategy. Review Methods

  1. [Epidemiology of rabies in Algeria].

    Science.gov (United States)

    Benelmouffok, A; Belkaid, M; Benhassine, M

    An epidemiological study on rabies in Algeria has been carried out on data provided by the "Institut national de Santé publique" and the "Institut Pasteur d'Algérie". It showed that no region is unhurt. The animal reservoir is of the domestic type, essentially the dog. In 40% of cases, bites are due to stray dogs.

  2. TFOS DEWS II Epidemiology Report

    NARCIS (Netherlands)

    Stapleton, Fiona; Alves, Monica; Bunya, Vatinee Y.; Jalbert, Isabelle; Lekhanont, Kaevalin; Malet, Florence; Na, Kyung-Sun; Schaumberg, Debra; Uchino, Miki; Vehof, Jelle; Viso, Eloy; Vitale, Susan; Jones, Lyndon

    The subcommittee reviewed the prevalence, incidence, risk factors, natural history, morbidity and questionnaires reported in epidemiological studies of dry eye disease (DED). A meta-analysis of published prevalence data estimated the impact of age and sex. Global mapping of prevalence was

  3. Radiation epidemiology: Past and present

    International Nuclear Information System (INIS)

    Boice, J.D. Jr.

    1997-01-01

    Major advancements in radiation epidemiology have occurred during the last several years in studies of atomic bomb survivors, patients given medical radiation, and radiation workers, including underground miners. Risks associated with the Chernobyl accident, indoor radon and childhood exposure to I-131 have yet to be elucidated. Situations in the former Soviet Union around Chelyabinsk, a nuclear installation in the southern Urals, and in the Altai, which received radioactive fallout from weapons testing at Semipalatinsk, Kazakhstan, have the potential to provide information on the effects of chronic radiation exposure. Since Roentgen's discovery of x-rays just 100 years ago, a tremendous amount of knowledge has been accumulated about human health effects following irradiation. The 1994 UNSCEAR report contains the latest compilation and synthesis of radiation epidemiology. This overview will cover epidemiology from a radiation perspective. The different types of study methodologies will be described, followed by a kaleidoscope coverage of past and present studies; ending with some remaining questions in radiation epidemiology. This should set the stage for future chapters, and stimulate thinking about implications of the new data on radiation cancer risks

  4. [Occupational epidemiology: some methodological considerations].

    Science.gov (United States)

    Alvear-Galindo, María Guadalupe; del Pilar Paz-Román, María

    2006-01-01

    During the last decade, occupational epidemiology has gained a great importance, not only because of the increase of pollutants and their noxiousness, but also because it has gone from the descriptive to the analytic level. The purpose of this work is to present what has been reported on epidemiological studies, different ways of characterizing and measuring occupational exposure, by emphasizing slants of exposure and selection measurement. In the reviewed studies, an interest in improving the exposure evaluation has been shown. The mainly reported measurement slants are the ways of measuring and classifying the exposure. The main designs were transversal with the use of matrixes to improve the evaluation of exposure. Conditions of hygiene and security were considered in order to control the quality of the information. This information was analyzed with different criteria. Some of the elements that hinder the research on occupational epidemiology are a mixed exposure, small populations, lack of exposure data, low levels of exposure and long periods of illness latency. Some breakthroughs in the strategies of epidemiological analysis and some other areas of knowledge have made possible a better understanding of work and health conditions of workers.

  5. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  6. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  7. Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus.

    Science.gov (United States)

    Travassos da Rosa, Jorge Fernando; de Souza, William Marciel; Pinheiro, Francisco de Paula; Figueiredo, Mário Luiz; Cardoso, Jedson Ferreira; Acrani, Gustavo Olszanski; Nunes, Márcio Roberto Teixeira

    2017-05-01

    AbstractOropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal.

  8. A Huge Morel-Lavallée Lesion Treated Using a Quilting Suture Method: A Case Report and Review of the Literature.

    Science.gov (United States)

    Seo, Bommie F; Kang, In Sook; Jeong, Yeon Jin; Moon, Suk Ho

    2014-06-01

    The Morel-Lavallée lesion is a collection of serous fluid that develops after closed degloving injuries and after surgical procedures particularly in the pelvis and abdomen. It is a persistent seroma and is usually resistant to conservative methods of treatment such as percutaneous drainage and compression. Various methods of curative treatment have been reported in the literature, such as application of fibrin sealant, doxycycline, or alcohol sclerodhesis. We present a case of a huge recurrent Morel-Lavallée lesion in the lower back and buttock region that was treated with quilting sutures, fibrin sealant, and compression, with a review of the literature. © The Author(s) 2014.

  9. MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

    Science.gov (United States)

    Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

    2013-01-01

    The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

  10. Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

    Science.gov (United States)

    Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

    2015-04-01

    Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

  11. 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.

  12. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  13. The evolving epidemiology of inflammatory bowel disease.

    LENUS (Irish Health Repository)

    Shanahan, Fergus

    2009-07-01

    Epidemiologic studies in inflammatory bowel disease (IBD) include assessments of disease burden and evolving patterns of disease presentation. Although it is hoped that sound epidemiologic studies provide aetiological clues, traditional risk factor-based epidemiology has provided limited insights into either Crohn\\'s disease or ulcerative colitis etiopathogenesis. In this update, we will summarize how the changing epidemiology of IBD associated with modernization can be reconciled with current concepts of disease mechanisms and will discuss studies of clinically significant comorbidity in IBD.

  14. History and philosophy of modern epidemiology

    DEFF Research Database (Denmark)

    Andersen, Hanne

    2012-01-01

    Epidemiological studies of chronic diseases began around the mid-20th century. Contrary to the infectious disease epidemiology which had prevailed at the beginning of the 20th century and which had focused on single agents causing individual diseases, the chronic disease epidemiology which emerge...

  15. Multiple huge epiphrenic esophageal diverticula with motility disease treated with video-assisted thoracoscopic and hand-assisted laparoscopic esophagectomy: a case report.

    Science.gov (United States)

    Taniguchi, Yoshiki; Takahashi, Tsuyoshi; Nakajima, Kiyokazu; Higashi, Shigeyoshi; Tanaka, Koji; Miyazaki, Yasuhiro; Makino, Tomoki; Kurokawa, Yukinori; Yamasaki, Makoto; Takiguchi, Shuji; Mori, Masaki; Doki, Yuichiro

    2017-12-01

    Epiphrenic esophageal diverticulum is a rare condition that is often associated with a concomitant esophageal motor disorder. Some patients have the chief complaints of swallowing difficulty and gastroesophageal reflux; traditionally, such diverticula have been resected via right thoracotomy. Here, we describe a case with huge multiple epiphrenic diverticula with motility disorder, which were successfully resected using a video-assisted thoracic and laparoscopic procedure. A 63-year-old man was admitted due to dysphagia, heartburn, and vomiting. An esophagogram demonstrated an S-shaped lower esophagus with multiple epiphrenic diverticula (75 × 55 mm and 30 × 30 mm) and obstruction by the lower esophageal sphincter (LES). Esophageal manometry showed normal peristaltic contractions in the esophageal body, whereas the LES pressure was high (98.6 mmHg). The pressure vector volume of LES was 23,972 mmHg 2  cm. Based on these findings, we diagnosed huge multiple epiphrenic diverticula with a hypertensive lower esophageal sphincter and judged that resection might be required. We performed lower esophagectomy with gastric conduit reconstruction using a video-assisted thoracic and hand-assisted laparoscopic procedure. The postoperative course was uneventful, and the esophagogram demonstrated good passage, with no leakage, stenosis, or diverticula. The most common causes of mid-esophageal and epiphrenic diverticula are motility disorders of the esophageal body; appropriate treatment should be considered based on the morphological and motility findings.

  16. A case of huge colon carcinoma and right renal angiomyolipoma accompanied by proximal deep venous thrombosis, pulmonary embolism and tumor thrombus in the renal vein.

    Science.gov (United States)

    Ban, Daisuke; Yamamoto, Seiichiro; Kuno, Hirofumi; Fujimoto, Hiroyuki; Fujita, Shin; Akasu, Takayuki; Moriya, Yoshihiro

    2008-10-01

    A preoperative inferior vena cava (IVC) filter is reported to be effective in surgical cases with proximal deep venous thrombosis (DVT) or in which pulmonary embolism (PE) has already developed, and considered to be at high risk of developing secondary fatal PE during or after surgery. However, guidelines for using an IVC filter have yet to be established. The patient in the present report had two huge tumors, ascending colon cancer and renal angiomyolipoma, which occupied the entire right half of the abdomen, coexisting PE, DVT and tumor thrombus in the right renal vein. Secondary PE is fatal in the perioperative period, therefore, the vena cava filters were preoperatively inserted into the supra- and the infrarenal IVC. We successfully removed the tumors without complications. The patient is alive without tumor recurrence and PE or recurrent DVT 1 year and 6 months after surgery. The coexistence of two huge abdominal tumors as potential causes of PE and DVT is extremely rare, and we could have safely undergone the operation, using two vena cava filters in the supra- and infrarenal IVC.

  17. [Transcatheter embolization for huge pulmonary arteriovenous fistula using metallic "spider" and spring embolus--application of hand-made metallic "spider" using partial monorail technique].

    Science.gov (United States)

    Hirota, S; Sako, M; Fujita, Y; Hasegawa, Y; Sugimoto, K; Suzuki, Y; Kono, M

    1992-07-25

    We performed transcatheter embolization in two cases with huge pulmonary arteriovenous fistula (AVF) using a metallic "spider" and spring embolus. Conventional spring embolus or detachable balloon could not be used in these cases. Metallic spider was indicated for pulmonary AVF with a feeding artery diameter of more than 16 mm to prevent embolus passing through the AVF. In the first case, we used large handmade metallic spiders of 25 mm in diameter followed by embolization by numerous spring coils. At that time, a partial monorail technique was newly devised to carry the large metallic spider into the feeding artery, otherwise the spider could not pass into a 9F catheter. After embolization, symptoms and PaO2 in arterial blood improved remarkably in both cases. In the second case, a spring coil migrated into the normal pulmonary artery, but no infarction resulted. In conclusion, the metallic spider was very useful for embolization of hugee pulmonary AVF to avoid the embolus passing through and to tangle spring coils together with it. If commercially available "spiders" are too small, ones can be made easily.

  18. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  19. HCV and HCC molecular epidemiology

    Directory of Open Access Journals (Sweden)

    Flor H. Pujol

    2007-02-01

    Full Text Available

    iHepatitis C virus (HCV is a member of the family Flaviviridae, responsible for the majority of the non-A non-B post-transfusion hepatitis before 1990. Around 170 millions persons in the world are thought to be infected with this virus. A high number of HCV-infected people develop cirrhosis and from these, a significant proportion progresses to hepatocellular carcinoma (HCC. Six HCV genotypes and a large number of subtypes in each genotype have been described. Infections with HCV genotype 1 are associated with the lowest therapeutic success. HCV genotypes 1, 2, and 3 have a worldwide distribution. HCV subtypes 1a and 1b are the most common genotypes in the United States and are also are predominant in Europe, while in Japan, subtype 1b is predominant. Although HCV subtypes 2a and 2b are relatively common in America, Europe, and Japan, subtype 2c is found commonly in northern Italy. HCV genotype 3a is frequent in intravenous drug abusers in Europe and the United States. HCV genotype 4 appears to be prevalent in Africa and the Middle East, and genotypes 5 and 6 seem to be confined to South Africa and Asia, respectively. HCC accounts for approximately 6% of all human cancers. Around 500,000 to 1 million cases occur annually worldwide, with HCC being the fifth common malignancy in men and the ninth in women. HCC is frequently a consequence of infection by HBV and HCV. The first line of evidences comes from epidemiologic studies. While HBV is the most frequent cause of HCC in many countries of Asia and South America, both HBV and HCV are found at similar frequencies, and eventually HCV at a higher frequency than HBV, among HCC patients in Europe, North America, and Japan. The cumulative appearance rate of HCC might be higher for HCV

  20. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  1. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  2. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

    Science.gov (United States)

    Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.

    2014-01-01

    Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens. PMID:24574290

  3. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

    Science.gov (United States)

    Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S; Nielsen, Eva M; Aarestrup, Frank M

    2014-05-01

    Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all incoming isolates were concurrently subjected to WGS using IonTorrent PGM. Real-time bioinformatics analysis was performed using web-tools (www.genomicepidemiology.org) for species determination, multilocus sequence type (MLST) typing, and determination of phylogenetic relationship, and a specific VirulenceFinder for detection of E. coli virulence genes was developed as part of this study. In total, 46 suspected VTEC isolates were characterized in parallel during the study. VirulenceFinder proved successful in detecting virulence genes included in routine typing, explicitly verocytotoxin 1 (vtx1), verocytotoxin 2 (vtx2), and intimin (eae), and also detected additional virulence genes. VirulenceFinder is also a robust method for assigning verocytotoxin (vtx) subtypes. A real-time clustering of isolates in agreement with the epidemiology was established from WGS, enabling discrimination between sporadic and outbreak isolates. Overall, WGS typing produced results faster and at a lower cost than the current routine. Therefore, WGS typing is a superior alternative to conventional typing strategies. This approach may also be applied to typing and surveillance of other pathogens.

  4. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    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 MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  5. Microbial comparative pan-genomics using binomial mixture models

    DEFF Research Database (Denmark)

    Ussery, David; Snipen, L; Almøy, T

    2009-01-01

    The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter...... approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. RESULTS: We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection...... probabilities. Estimated pan-genome sizes range from small (around 2600 gene families) in Buchnera aphidicola to large (around 43000 gene families) in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely...

  6. Whole genome sequencing in clinical and public health microbiology.

    Science.gov (United States)

    Kwong, J C; McCallum, N; Sintchenko, V; Howden, B P

    2015-04-01

    Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

  7. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  8. Epidemiology of subtypes of depression

    DEFF Research Database (Denmark)

    Kessing, L V

    2007-01-01

    depression, dysthymia, and subsyndromal states; the association between stressful life events and depression appears to diminish with the number of depressive episodes. Finally, recent genetic findings are congruent with a model indicating that the majority of depressions develop in the interplay between...... genes and stressful experiences, whereas 'reactive' depressions and 'endogenous' depressions apparently exist at a lower prevalence. CONCLUSION: Further longitudinal, analytical, and genetic epidemiologic studies are needed to reveal which conditions are mild and transient, and which may be precursors......OBJECTIVE: There is a general clinical impression that depression differs qualitatively from non-depressive conditions, and that it can be identified as a categorical entity. In contrast, epidemiological studies support the view that depression is dynamic in nature and develops on a continuous...

  9. "Epidemiological criminology": coming full circle.

    Science.gov (United States)

    Akers, Timothy A; Lanier, Mark M

    2009-03-01

    Members of the public health and criminal justice disciplines often work with marginalized populations: people at high risk of drug use, health problems, incarceration, and other difficulties. As these fields increasingly overlap, distinctions between them are blurred, as numerous research reports and funding trends document. However, explicit theoretical and methodological linkages between the 2 disciplines remain rare. A new paradigm that links methods and statistical models of public health with those of their criminal justice counterparts is needed, as are increased linkages between epidemiological analogies, theories, and models and the corresponding tools of criminology. We outline disciplinary commonalities and distinctions, present policy examples that integrate similarities, and propose "epidemiological criminology" as a bridging framework.

  10. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  11. Viral marketing as epidemiological model

    OpenAIRE

    Rodrigues, Helena Sofia; Fonseca, Manuel

    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...

  12. Epidemiologic perspectives in radiation carcinogenesis

    International Nuclear Information System (INIS)

    Jablon, S.

    1984-01-01

    Epidemiological studies can tell much about carcinogenic effects at large doses, but not at small. To embark on large, long-term, expensive follow-up studies to learn something of scientific value about the effects of low doses-an average of three rads, say - is to waste time, effort, and money. It would be a fruitless effort even if the only problem to overcome was sampling variability - but it is not

  13. EPIDEMIOLOGICAL EVALUATION OF COLORECTAL CANCER

    OpenAIRE

    B. Shafayan M. Keyhani

    2003-01-01

    This study was carried out to analyze certain epidemiological variations in Iranian patients with colorectal cancer. (CRC): From March 1981 up to March 1993, 103 patients were analyzed retrospectively for age, gender, marital state, job, nutritional habits, presenting symptoms and histopathological features. Most of the patients with colorectal cancer were male, age range 20-75 (mean 56), 25.4 percent were long-term smokers and bleeding was the most common symptom. The rectum was the most com...

  14. Causal diagrams in systems epidemiology

    Directory of Open Access Journals (Sweden)

    Joffe Michael

    2012-03-01

    Full Text Available Abstract Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s. Transmitted causes ("causes of causes" tend not to be systematically analysed. The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties. The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets. Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback.

  15. Causal diagrams in systems epidemiology.

    Science.gov (United States)

    Joffe, Michael; Gambhir, Manoj; Chadeau-Hyam, Marc; Vineis, Paolo

    2012-03-19

    Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed.The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties.The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets.Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback.

  16. Biomarkers in Prostate Cancer Epidemiology

    Directory of Open Access Journals (Sweden)

    Mudit Verma

    2011-09-01

    Full Text Available Understanding the etiology of a disease such as prostate cancer may help in identifying populations at high risk, timely intervention of the disease, and proper treatment. Biomarkers, along with exposure history and clinical data, are useful tools to achieve these goals. Individual risk and population incidence of prostate cancer result from the intervention of genetic susceptibility and exposure. Biochemical, epigenetic, genetic, and imaging biomarkers are used to identify people at high risk for developing prostate cancer. In cancer epidemiology, epigenetic biomarkers offer advantages over other types of biomarkers because they are expressed against a person’s genetic background and environmental exposure, and because abnormal events occur early in cancer development, which includes several epigenetic alterations in cancer cells. This article describes different biomarkers that have potential use in studying the epidemiology of prostate cancer. We also discuss the characteristics of an ideal biomarker for prostate cancer, and technologies utilized for biomarker assays. Among epigenetic biomarkers, most reports indicate GSTP1 hypermethylation as the diagnostic marker for prostate cancer; however, NKX2-5, CLSTN1, SPOCK2, SLC16A12, DPYS, and NSE1 also have been reported to be regulated by methylation mechanisms in prostate cancer. Current challenges in utilization of biomarkers in prostate cancer diagnosis and epidemiologic studies and potential solutions also are discussed.

  17. Panel 1: Epidemiology and Diagnosis.

    Science.gov (United States)

    Homøe, Preben; Kværner, Kari; Casey, Janet R; Damoiseaux, Roger A M J; van Dongen, Thijs M A; Gunasekera, Hasantha; Jensen, Ramon G; Kvestad, Ellen; Morris, Peter S; Weinreich, Heather M

    2017-04-01

    Objective To create a literature review between 2011 and June 1, 2015, on advances in otitis media (OM) epidemiology and diagnosis (including relevant audiology studies). Data Sources Electronic search engines (PubMed, EMBASE, and Cochrane Library) with a predefined search strategy. Review Methods Articles with appropriate epidemiologic methodology for OM, including acute mastoiditis and eustachian tube dysfunction. Items included OM worldwide and in high-risk populations, OM-related hearing loss, news in OM diagnostics, prenatal risk factors and comorbidities, postnatal risk factors, genetics, microbiological epidemiology, guidelines, and quality of life. Conclusions Diagnostic evidence and genetic studies are increasing; guidelines are introduced worldwide; and there is evidence of benefit of pneumococcal conjugate vaccines. New risk factors and comordities are identified in the study period, and quality of life is affected in children and their families. Implications for Practice Chronic suppurative OM occurs worldwide and contributes to lifelong hearing loss. Uniform definitions are still lacking and should be provided. An association between HIV and chronic suppurative OM has been found. Tympanometry is recommended for diagnosis, with or without pneumatic otoscopy. Video otoscopy, algorithms, and validated questionnaires may assist clinicians. Childhood obesity is associated with OM. Heritability accounts for 20% to 50% of OM diagnoses. OM-prone children seem to produce weaker immunologic responses to pneumococcal conjugate vaccines. Clinicians tend to individualize treatment without adhering to guidelines.

  18. Parallel computing in genomic research: advances and applications

    Directory of Open Access Journals (Sweden)

    Ocaña K

    2015-11-01

    Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing

  19. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  20. The complete mitochondrial genome of rabbit pinworm Passalurus ambiguus: genome characterization and phylogenetic analysis.

    Science.gov (United States)

    Liu, Guo-Hua; Li, Sheng; Zou, Feng-Cai; Wang, Chun-Ren; Zhu, Xing-Quan

    2016-01-01

    Passalurus ambiguus (Nematda: Oxyuridae) is a common pinworm which parasitizes in the caecum and colon of rabbits. Despite its significance as a pathogen, the epidemiology, genetics, systematics, and biology of this pinworm remain poorly understood. In the present study, we sequenced the complete mitochondrial (mt) genome of P. ambiguus. The circular mt genome is 14,023 bp in size and encodes of 36 genes, including 12 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The mt gene order of P. ambiguus is the same as that of Wellcomia siamensis, but distinct from that of Enterobius vermicularis. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference (BI) showed that P. ambiguus was more closely related to W. siamensis than to E. vermicularis. This mt genome provides novel genetic markers for studying the molecular epidemiology, population genetics, systematics of pinworm of animals and humans, and should have implications for the diagnosis, prevention, and control of passaluriasis in rabbits and other animals.

  1. Huge opportunity for solar cooling

    International Nuclear Information System (INIS)

    Rowe, Daniel

    2014-01-01

    In Europe more than 400 solar cooling systems have been installed. By contrast, only a small number of solar cooling installations exist in Australia - primarily adsorption and absorption systems for commercial and hospitals - although these systems are growing. As with other renewable energy technologies, cost is a challenge. However solar cooling is currently competitive with other technologies, with some suggesting that system costs have been decreasing by about 20% per annum in recent times. Australia is also leading efforts in the development of residential solar desiccant technology, currently commercialising Australian-developed technology. Commercial and industrial enterprises are increasingly aware of the impact of demand charges, the potential to install technology as a hedge against future energy price rises and opportunities associated with increased on-site generation and reduced reliance on the grid, often necessitating on-site demand reduction and management. They are also driven by environmental and corporate social responsibility objectives as well as the opportunity for energy independence and uninterruptible operation. Interestingly, many of these interests are mirrdred at residential level, inspiring CSIRO's commercialisation of a domestic scale solar air conditioner with Australian manufacturer Brevis Climate Systems. Australia and other countries are increasingly aware of solar cooling as technology which can reduce or replace grid-powered cooling, particularly in applications where large building thermal energy requirements exist. In these applications, heating, cooling and hot water are generated and used in large amounts and the relative amounts of each can be varied dynamically, depending on building requirements. Recent demonstrations of solar cooling technology in Australia include Hunter TAFE's Solar Desiccant Cooling System - which provides heating, cooling and hot water to commercial training kitchens and classrooms - GPT's Charlestown Square Shopping Centre and Echuca Hospital. These systems join a number of others already in operation at the large commercial and industrial scale, as well as a smaller number of systems providing cooling to cafes and offices. The development in this area is being supported by CSIRO's Solar Cooling research team which provides development, modelling and design expertise across the spectrum of solar cooling variants, sizes and applications - from remote community food preservation in India, to large commercial and residential systems in Australia. The group also has industry test facilities to support the development and testing of solar air conditioning systems as well as conventional air conditioning technologies. The Australian Institute of Refrigeration Air Conditioning and Heating (AIRAH's) Solar Cooling Special Technical Group is also involved in developing the solar cooling industry in Australia with the aim of combating climate change by reducing greenhouse emissions from the residential and commercial building sectors. The group coordinates industry and research efforts and organises information exchange, educational and training events for interested technical and business representatives. Fact file- Solar cooling systems are essentially comprised of two parts - solar thermal collectors and a sorption chiller which convert the heat into useful cooling. Though a number of collector and chiller combinations exist, no one single approach has yet dominated. Corresponding with the type of chiller used, solar cooling systems are often grouped into three categories: absorption, adsorption and desiccant. During design, an appropriate collector technology will be chosen, typically either a parabolic, flat plate or evacuated tube collector. The optimal configuration is also determined in design, to align equipment characteristics with the conditions, environment and requirements presented by each application. Thus solar cooling has a number of variants which use different components or the same components in an alternate configuration. A number of variants are technically proven and available for commercial and industrial installations. Each variant uses standard 'off the shelf' FIVAC industry components which are available in both Australia and overseas. A typical solar cooling system is also able to supply broader energy needs of a building including space heating and hot water.

  2. Molecular epidemiology, and possible real-world applications in breast cancer.

    Science.gov (United States)

    Ito, Hidemi; Matsuo, Keitaro

    2016-01-01

    Gene-environment interaction, a key idea in molecular epidemiology, has enabled the development of personalized medicine. This concept includes personalized prevention. While genome-wide association studies have identified a number of genetic susceptibility loci in breast cancer risk, however, the application of this knowledge to practical prevention is still underway. Here, we briefly review the history of molecular epidemiology and its progress in breast cancer epidemiology. We then introduce our experience with the trial combination of GWAS-identified loci and well-established lifestyle and reproductive risk factors in the risk prediction of breast cancer. Finally, we report our exploration of the cumulative risk of breast cancer based on this risk prediction model as a potential tool for individual risk communication, including genetic risk factors and gene-environment interaction with obesity.

  3. Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

    Science.gov (United States)

    Abend, Michael; Port, Matthias

    2016-08-01

    The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers.

  4. DNA Sequence Patterns – A Successful Example of Grid Computing in Genome Research and Building Virtual Super-Computers for the Research Commons of e-Societies

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); A. Abuseiris (Anis); M. Lesnussa (Michael); F.N. Kepper (Nick); R.M. de Graaf (Rob); F.G. Grosveld (Frank)

    2011-01-01

    textabstractThe amount of information is growing exponentially with ever-new technologies emerging and is believed to be always at the limit. In contrast, huge resources are obviously available, which are underused in the IT sector, similar as e.g. in the renewable energy sector. Genome research is

  5. Development and simulation of the air-jack for emergency like a huge disaster; Kyujoyo eajakki no kaihatsu to sono simyureshon

    Energy Technology Data Exchange (ETDEWEB)

    Katsuyama, Kunihisa.; Ogata, Yuji.; Wada, Yuji. [National Institute for Resources and Environment, Tsukuba (Japan); Hashizume, Kiyoshi.; Nishida, Kenjiro. [Nippon Kayaku Corp., Tokyo (Japan)

    1999-02-28

    When a disaster is so huge like Kobe earthquake, every energy line is killed. Even if we want to help the sufferers, we have no energy to move machines to help them. As collapsed houses are very heavy, we need machines to remove collapsed stuff. Explosives include a lot of energy in themselves. So, an air-jack which has explosives inside was developed to remove collapsed stuff on suffered people. A simple air-jack was made and tested. One concrete block, 50cm x 50cm x 50cm, was lifted by the simple air-jack. A simulation of lifting the concrete block was carried out with a programme ANSYS on the super computer. (author)

  6. Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

    Science.gov (United States)

    Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

    2016-08-05

    The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Deep earth fluids and huge metallogenetic belt and fatal geological disaster: 60th anniversary of Professor Du Le-tian engaging in geology

    International Nuclear Information System (INIS)

    Ou Guangxi; Tao Shizhen; Liu Yinhe

    2012-01-01

    Professor Du Le-tian has been researching for a long time on scientific relationship between deep earth fluids and hydrocarbon accumulation and metallogenesis, as well as gestation and prediction of disasters. He has contributed greatly to the development of that scientific field. From 6 to 8, July, 2012, 'Workshop on Deep Earth Fluids and Huge Metallogenetic Belt, Fatal Geological Disaster, as well as 60 th Anniversary of Professor Du Le-tian Engaging in Geology' was successfully convened in Beijing, totally with 76 delegates present who were experts, scholars or students from USA, Hong Kong, or various institutes, colleges or universities of China. In the workshop, the scientific presentations discussed were counted up to 49, on aspects of geological processes of deep earth fluids, relationship between earth degassing and hydrocarbon accumulation or metallogenesis, gestating mechanism of volcanic eruptions and strong earthquakes as well as their relations with mine gas outburst, high-temperature and high-pressure experimental earth science, etc.. (authors)

  8. Epidemiology

    International Nuclear Information System (INIS)

    Hubert, D.

    2009-01-01

    Because of the concern of people, a study of mortality has previously been conducted in two Pennsylvania counties located near manufacturing and reprocessing plants of nuclear materials over the period 1950-1995. No excessive mortality has been identified in the population exposed counties in comparison to control counties. The current study is the continuation of the previous study of mortality over a period of eight additional years (up to 2004) and the addition of a study of cancer incidence over the period 1990-2004 and mortality for causes out of cancer from 1996 to 2004. Method: The population of each county of the study was compared to the population of three control counties selected according to socioeconomic and demographic characteristics, the same way as in the previous study. The demographic, mortality and incidence data for the different counties have been earned at the state of Pennsylvania. Results: over the period 1996-2004, mortality from cancer (10 457 deaths) in the two counties studied was comparable to that of six control counties (relative risk .97 [95% CI .94 -. 99]) and previous results. Similarly, the incidence of cancer was similar in the counties studied (39350 cases of cancer) and the control counties (relative risk .99 [95% CI .97-1.00]). The number of deaths unrelated to cancer was 36 565, very close to the expected number (relative risk .99 [95% CI 1.01-1.01]). Conclusion: Overall, no increase in cancer or non-cancer disease could be attributed to living in counties that had manufacturing and reprocessing plants of nuclear materials. (N.C.)

  9. The Future of Whole-Genome Sequencing for Public Health and the Clinic

    OpenAIRE

    Allard, Marc W.

    2016-01-01

    An American Society for Microbiology (ASM) conference titled the Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiological Investigation of Pathogens provided a venue for discussing how technologies surrounding whole-genome sequencing (WGS) are advancing microbiology. Several applications in microbial taxonomy, microbial forensics, and genomics for public health pathogen surveillance were presented at the meeting and are reviewed. All of...

  10. Epidemiology, molecular epidemiology, and risk factors for renal cell carcinoma

    Directory of Open Access Journals (Sweden)

    Chiara Paglino

    2011-12-01

    Full Text Available Despite only accounting for approximately 2% of all new primary cancer cases, renal cell carcinoma (RCC incidence has dramatically increased over time. Incidence rates vary greatly according to geographic areas, so that it is extremely likely that exogenous risk factors could play an important role in the development of this cancer. Several risk factors have been linked with RCC, including cigarette smoking, obesity, hypertension (and antihypertensive drugs, chronic kidney diseases (also dialysis and transplantation, as well as the use of certain analgesics. Furthermore, although RCC has not generally been considered an occupational cancer, several types of occupationally-derived exposures have been implicated in its pathogenesis. These include exposure to asbestos, chlorinated solvents, gasoline, diesel exhaust fumes, polycyclic aromatic hydrocarbons, printing inks and dyes, cadmium and lead. Finally, families with a predisposition to the development of renal neoplasms were identified and the genes involved discovered and characterized. Therefore, there are now four well-characterized, genetically determined syndromes associated with an increased incidence of kidney tumors, i.e., Von Hippel Lindau (VHL, Hereditary Papillary Renal Carcinoma (HPRC, Birt-Hogg-Dubé Syndrome (BHD, and Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC. This review will address present knowledge about the epidemiology, molecular epidemiology and risk factors of RCC.

  11. Statistical significance of epidemiological data. Seminar: Evaluation of epidemiological studies

    International Nuclear Information System (INIS)

    Weber, K.H.

    1993-01-01

    In stochastic damages, the numbers of events, e.g. the persons who are affected by or have died of cancer, and thus the relative frequencies (incidence or mortality) are binomially distributed random variables. Their statistical fluctuations can be characterized by confidence intervals. For epidemiologic questions, especially for the analysis of stochastic damages in the low dose range, the following issues are interesting: - Is a sample (a group of persons) with a definite observed damage frequency part of the whole population? - Is an observed frequency difference between two groups of persons random or statistically significant? - Is an observed increase or decrease of the frequencies with increasing dose random or statistically significant and how large is the regression coefficient (= risk coefficient) in this case? These problems can be solved by sttistical tests. So-called distribution-free tests and tests which are not bound to the supposition of normal distribution are of particular interest, such as: - χ 2 -independence test (test in contingency tables); - Fisher-Yates-test; - trend test according to Cochran; - rank correlation test given by Spearman. These tests are explained in terms of selected epidemiologic data, e.g. of leukaemia clusters, of the cancer mortality of the Japanese A-bomb survivors especially in the low dose range as well as on the sample of the cancer mortality in the high background area in Yangjiang (China). (orig.) [de

  12. Animal genomics and infectious disease resistance in poultry.

    Science.gov (United States)

    Smith, J; Gheyas, A; Burt, D W

    2016-04-01

    Avian pathogens are responsible for major costs to society, both in terms of huge economic losses to the poultry industry and their implications for human health. The health and welfare of millions of birds is under continued threat from many infectious diseases, some of which are increasing in virulence and thus becoming harder to control, such as Marek's disease virus and avian influenza viruses. The current era in animal genomics has seen huge developments in both technologies and resources, which means that researchers have never been in a better position to investigate the genetics of disease resistance and determine the underlying genes/mutations which make birds susceptible or resistant to infection. Avian genomics has reached a point where the biological mechanisms of infectious diseases can be investigated and understood in poultry and other avian species. Knowledge of genes conferring disease resistance can be used in selective breeding programmes or to develop vaccines which help to control the effects of these pathogens, which have such a major impact on birds and humans alike.

  13. Some aspects of cancer epidemiology

    International Nuclear Information System (INIS)

    Lilienfeld, A.M.

    1982-01-01

    Epidemiolgic studies have strongly suggested that a vast majority (80-90%) of cancers are caused by radiation, chemical and biologic agents; the remainder result from endogenous or genetic factors. Biologically, cancer is most probably the end result of a complex multistage process and therefore may be due to a sequence of exposures to different agents at each of these stages. This emphasizes the need to stress the study of interactions in epidemiologic studies to a greater extent than has been done thus far. Examples of the importance of interactions in several types of cancer are presented

  14. An introduction to mathematical epidemiology

    CERN Document Server

    Martcheva, Maia

    2015-01-01

    The book is a comprehensive, self-contained introduction to the mathematical modeling and analysis of infectious diseases. It includes model building, fitting to data, local and global analysis techniques. Various types of deterministic dynamical models are considered: ordinary differential equation models, delay-differential equation models, difference equation models, age-structured PDE models and diffusion models. It includes various techniques for the computation of the basic reproduction number as well as approaches to the epidemiological interpretation of the reproduction number. MATLAB code is included to facilitate the data fitting and the simulation with age-structured models.

  15. Intrathoracic neoplasia: Epidemiology and etiology

    Energy Technology Data Exchange (ETDEWEB)

    Weller, R.E.

    1992-05-01

    Neoplasms of the thorax encompass those derived from the thoracic wall, trachea, mediastinum, lungs and pleura. They represent a wide variety of lesions including benign and malignant tumors arising from many tissues. The large surface area, 60 to 90 m{sup 2} in man, represented by the respiratory epithelium and associated thoracic structures are ideal targets for carcinogens carried by inspired air. The topic of discussion in this report is the epidemiology, etiology, and mechanisms of spontaneous intrathoracic neoplasia in animals and man. Much of what we know or suspect about thoracic neoplasia in animals has been extrapolated from experimentally-induced neoplasms.

  16. A genomic overview of the population structure of Salmonella.

    Directory of Open Access Journals (Sweden)

    Nabil-Fareed Alikhan

    2018-04-01

    Full Text Available For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST] corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST, core genome MLST (cgMLST, and whole genome MLST (wgMLST and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs. eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

  17. A genomic overview of the population structure of Salmonella.

    Science.gov (United States)

    Alikhan, Nabil-Fareed; Zhou, Zhemin; Sergeant, Martin J; Achtman, Mark

    2018-04-01

    For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

  18. Air pollution and genomic instability: The role of particulate matter in lung carcinogenesis

    International Nuclear Information System (INIS)

    Santibáñez-Andrade, Miguel; Quezada-Maldonado, Ericka Marel; Osornio-Vargas, Álvaro; Sánchez-Pérez, Yesennia; García-Cuellar, Claudia M.

    2017-01-01

    In this review, we summarize and discuss the evidence regarding the interaction between air pollution, especially particulate matter (PM), and genomic instability. PM has been widely studied in the context of several diseases, and its role in lung carcinogenesis gained relevance due to an increase in cancer cases for which smoking does not seem to represent the main risk factor. According to epidemiological and toxicological evidence, PM acts as a carcinogenic factor in humans, inducing high rates of genomic alterations. Here, we discuss not only how PM is capable of inducing genomic instability during the carcinogenic process but also how our genetic background influences the response to the sources of damage. - Highlights: • Air pollution represents a worldwide problem with impact on human health. • Particulate matter (PM) has a recognized carcinogenic potential in humans. • Lung cancer susceptibility depends on gene-environment interactions. • Epidemiological and experimental evidence links PM exposure to genomic instability. • PM and genomic instability are co-dependent factors during cancer continuum. - We summarize the association between particulate matter (a component of air pollution) and genomic instability as well as discuss how new strategies to study the impact of air pollution on genomic instability and lung-cancer development could improve our understanding of the lung-cancer genome.

  19. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  20. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  1. Fertility and pregnancy: an epidemiologic perspective

    National Research Council Canada - National Science Library

    Wilcox, Allen J

    2010-01-01

    .... Weaving together history, biology, obstetrics, pediatrics, demography, infectious diseases, molecular genetics, and evolutionary biology, Allen Wilcox brings a fresh coherence to the epidemiologic...

  2. Clinical Epidemiology Unit - overview of research areas

    Science.gov (United States)

    Clinical Epidemiology Unit (CEU) conducts etiologic research with potential clinical and public health applications, and leads studies evaluating population-based early detection and cancer prevention strategies

  3. Shared genetics underlying epidemiological association between endometriosis and ovarian cancer

    DEFF Research Database (Denmark)

    Lu, Yi; Cuellar-Partida, Gabriel; Painter, Jodie N

    2015-01-01

    Epidemiological studies have demonstrated associations between endometriosis and certain histotypes of ovarian cancer, including clear cell, low-grade serous and endometrioid carcinomas. We aimed to determine whether the observed associations might be due to shared genetic aetiology. To address...... this, we used two endometriosis datasets genotyped on common arrays with full-genome coverage (3194 cases and 7060 controls) and a large ovarian cancer dataset genotyped on the customized Illumina Infinium iSelect (iCOGS) arrays (10 065 cases and 21 663 controls). Previous work has suggested...... that a large number of genetic variants contribute to endometriosis and ovarian cancer (all histotypes combined) susceptibility. Here, using the iCOGS data, we confirmed polygenic architecture for most histotypes of ovarian cancer. This led us to evaluate if the polygenic effects are shared across diseases. We...

  4. en epidemiología

    Directory of Open Access Journals (Sweden)

    Ana V. Diez Roux

    2008-01-01

    Full Text Available La epidemiología sociocultural se caracteriza por la integración de procesos sociales, culturales, económicos y políticos con procesos biológicos en el estudio de los determinantes de la salud. Por definición, esto implica la consideración de determinantes especificados a múltiples niveles, desde los genes hasta las características de la sociedad en su totalidad. En este artículo se analizan diversos problemas metodológicos que surgen en epidemiología (y en las ciencias sociales en general por la presencia de múltiples niveles de organización que pueden ser relevantes para entender las causas de la salud y la enfermedad. Se subraya la necesidad de investigar conjuntamente (o de integrar determinantes de la salud definidos a distintos niveles. El artículo concluye con un examen de las implicaciones de la presencia de múltiples niveles para el estudio de los determinantes sociales o culturales de la salud.

  5. Epidemiology: second-rate science?

    Science.gov (United States)

    Parascandola, M

    1998-01-01

    In recent years epidemiology has come under increasing criticism in regulatory and public arenas for being "unscientific." The tobacco industry has taken advantage of this, insisting for decades that evidence linking cigarettes and lung cancer falls short of proof. Moreover, many epidemiologists remain unduly skeptical and self-conscious about the status of their own causal claims. This situation persists in part because of a widespread belief that only the laboratory can provide evidence sufficient for scientific proof. Adherents of this view erroneously believe that there is no element of uncertainty or inductive inference in the "direct observation" of the laboratory researcher and that epidemiology provides mere "circumstantial" evidence. The historical roots of this attitude can be traced to philosopher John Stuart Mill and physiologist Claude Bernard and their influence on modern experimental thinking. The author uses the debate over cigarettes and lung cancer to examine ideas of proof in medical science and public health, concluding that inductive inference from a limited sample to a larger population is an element in all empirical science.

  6. Epidemiology of Clostridium difficile Infection

    Science.gov (United States)

    DePestel, Daryl D.; Aronoff, David M.

    2014-01-01

    There has been dramatic change in the epidemiology of Clostridium difficile infection (CDI) since the turn of the 21st Century noted by a marked increase in incidence and severity, occurring at a disproportionately higher frequency in older patients. Historically considered a nosocomial infection associated with antibiotic exposure, CDI has now also emerged in the community in populations previously considered low risk. Emerging risk factors and disease recurrence represent continued challenges in the management of CDI. The increased incidence and severity associated with CDI has coincided with the emergence and rapid spread of a previously rare strain, ribotype 027. Recent data from the U.S. and Europe suggest the incidence of CDI may have reached a crescendo in recent years and is perhaps beginning to plateau. The acute-care direct costs of CDI were estimated to be $4.8 billion in 2008. However, nearly all the published studies have focused on CDI diagnosed and treated in acute-care hospital setting and fail to measure the burden outside the hospital, including recently discharged patients, outpatients, and those in long-term care facilities. Enhanced surveillance methods are needed to monitor the incidence, identify populations at risk, and characterize the molecular epidemiology of strains causing CDI. PMID:24064435

  7. Childhood vitiligo: Clinical epidemiological profile

    Directory of Open Access Journals (Sweden)

    Asmae Lahlou

    2017-07-01

    Full Text Available Objective: To study the clinical and the epidemiologic profiles of childhood vitiligo. Patients and Methods: We prospectively analyzed the clinical data of children with vitiligo presented to the dermatology derpartement at University Hospital – Fès for 5 years from May 2011 to May 2016. This study included 31 patients. All patients were assessed for the natural history, clinical characteristics, family history, and associated abnormalities of vitiligo. Results: Of the 31 children with vitiligo 9 (29,03% were boys and 21 (67.74% were girls. The mean age of onset of the vitiligo was 10 years. The mean duration of the disease was 38,9 weeks. The most common type of vitiligo was vitiligo vulgaris (49.5% followed by focal vitiligo (39%, acrofacial vitiligo (32%, and segmental vitiligo (16% The most frequent site of onset was the extremities followed by the head and the neck, then the trunk and the genitalia. Of the 31 children with vitiligo, 39% had a family history and 4 % had an antecedent of autoimmune diesease like le diabète, une thyroïdite, l’anémie et le psoriasis, retrouvé. Conclusion: Our children have a strong family history of vitiligo and they are developing the disease at a slightly older age compared with those of other studies; however, other epidemiologic features appear to be similar to those reported in the previously published studies.

  8. Epidemiologic research program: Selected bibliography

    International Nuclear Information System (INIS)

    1993-05-01

    This bibliography is a current listing of scientific reports from epidemiologic and related activities sponsored by the Department of Energy. The Office of Epidemiology and Health Surveillance now is the departmental focal point for these activities and any others relating to the study of human health effects. The Office's mission is evolving to encompass the new role of the Department in environmental restoration, weapons dismantlement and nuclear material storage, and development of new energy technologies. Publications in these areas will be included in future editions of the bibliography. The present edition brings the listing up to date, and should facilitate access to specific reports. The program has been divided into several general areas of activity: the Radiation Effects Research Foundation, which supports studies of survivors of the atomic weapons in Hiroshima and Nagasaki; mortality and morbidity studies of DOE workers; studies on internally deposited alpha emitters; medical/histologic studies; studies on the genetic aspects of radiation damage; community health surveillance studies; and the development of computational techniques and of databases to make the results as widely useful as possible

  9. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  10. Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium?

    Science.gov (United States)

    Mohammed, Manal

    2017-11-07

    Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing. This study aimed to determine the efficacy of high-throughput CRISPR typing over conventional phage typing in epidemiological surveillance and outbreak investigation of S. Typhimurium. In silico analysis of whole genome sequences (WGS) of well-documented phage types of S. Typhimurium reveals the presence of different CRISPR type among strains belong to the same phage type. Furthermore, different phage types of S. Typhimurium share identical CRISPR type. Interestingly, identical spacers were detected among outbreak and non-outbreak associated DT8 strains of S. Typhimurium. Therefore, CRISPR typing is not useful for the epidemiological surveillance and outbreak investigation of S. Typhimurium and phage typing, until it is replaced by WGS, is still the gold standard method for epidemiological surveillance of S. Typhimurium.

  11. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  12. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  13. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  14. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  15. Recording Cultural Heritage Using Terrestrial Laserscanning - Dealing with the System, the Huge Datasets they Create and Ways to Extract the Necessary Deliverables you can Work with

    Science.gov (United States)

    Christofori, E.; Bierwagen, J.

    2013-07-01

    Recording Cultural Heritage objects using terrestrial laserscanning becomes more and more popular over the last years. Since terrestrial Laserscanning System (TLS) Manufacturers have strongly increased the amount and speed of data captured with a single scan at each system upgrade and cutting down system costs the use of TLS Systems for recording cultural heritage is an option for recording worth to think about beside traditional methods like Photogrammetric. TLS Systems can be a great tool for capturing complex cultural heritage object within a short amount of time beside the traditional methods but can be a nightmare to handle for further process if not used right while capturing. Furthermore TLS Systems still have to be recognized as survey equipment, even though some of the manufactures promote them as everyday tool. They have to be used in an intelligent way having in mind the clients and the individual cultural objects needs. Thus the efficient way to use TLS Systems for data recording becomes a relevant topic to deal with the huge Amount of data the Systems collect while recording. Already small projects can turn into huge Pointcloud Datasets that End user, like Architects or Archaeologist neither can't deal with as their technical equipment doesn't fit the requirements of the Dataset nor do they have the software tools to use the Data as the current software tools still are high prized. Even the necessary interpretation of the Dataset can be a tough task if the people who have to work on with the Pointcloud aren't educated right in order to understand TLS and the results it creates. The use of TLS Systems has to have in mind the project requirements of the individual Heritage Object, like the required accuracy, standards for Levels of Details (e.g. "Empfehlungen für die Baudokumentation, Günther Eckstein, Germany"), the required kind of Deliverables (Visualization, 2D Drawings, True Deformation Drawings, 3D Models, BIM or 4D - Animations) as well as the

  16. The Ovary of Tubifex tubifex (Clitellata, Naididae, Tubificinae Is Composed of One, Huge Germ-Line Cyst that Is Enriched with Cytoskeletal Components.

    Directory of Open Access Journals (Sweden)

    Anna Z Urbisz

    Full Text Available Recent studies on the ovary organization and oogenesis in Tubificinae have revealed that their ovaries are small polarized structures that are composed of germ cells in subsequent stages of oogenesis that are associated with somatic cells. In syncytial cysts, as a rule, each germ cell is connected to the central cytoplasmic mass, the cytophore, via only one stable intercellular bridge (ring canal. In this paper we present detailed data about the composition of germ-line cysts in Tubifex tubifex with special emphasis on the occurrence and distribution of the cytoskeletal elements. Using fixed material and live cell imaging techniques, we found that the entire ovary of T. tubifex is composed of only one, huge multicellular germ-line cyst, which may contain up to 2,600 cells. Its architecture is broadly similar to the cysts that are found in other clitellate annelids, i.e. a common, anuclear cytoplasmic mass in the center of the cyst and germ cells that are connected to it via intercellular bridges. The cytophore in the T. tubifex cyst extends along the long axis of the ovary in the form of elongated and branched cytoplasmic strands. Rhodamine-coupled phalloidin staining revealed that the prominent strands of actin filaments occur inside the cytophore. Similar to the cytophore, F-actin strands are branched and they are especially well developed in the middle and outermost parts of the ovary. Microfilaments are also present in the ring canals that connect the germ cells with the cytophore in the narrow end of the ovary. Using TubulinTracker, we found that the microtubules form a prominent network of loosely and evenly distributed tubules inside the cytophore as well as in every germ cell. The well-developed cytoskeletal elements in T. tubifex ovary seem to ensure the integrity of such a huge germ-line cyst of complex (germ cells-ring canals-cytophore organization. A comparison between the cysts that are described here and other well-known female

  17. RECORDING CULTURAL HERITAGE USING TERRESTRIAL LASERSCANNING – DEALING WITH THE SYSTEM, THE HUGE DATASETS THEY CREATE AND WAYS TO EXTRACT THE NECESSARY DELIVERABLES YOU CAN WORK WITH

    Directory of Open Access Journals (Sweden)

    E. Christofori

    2013-07-01

    Full Text Available Recording Cultural Heritage objects using terrestrial laserscanning becomes more and more popular over the last years. Since terrestrial Laserscanning System (TLS Manufacturers have strongly increased the amount and speed of data captured with a single scan at each system upgrade and cutting down system costs the use of TLS Systems for recording cultural heritage is an option for recording worth to think about beside traditional methods like Photogrammetric. TLS Systems can be a great tool for capturing complex cultural heritage object within a short amount of time beside the traditional methods but can be a nightmare to handle for further process if not used right while capturing. Furthermore TLS Systems still have to be recognized as survey equipment, even though some of the manufactures promote them as everyday tool. They have to be used in an intelligent way having in mind the clients and the individual cultural objects needs. Thus the efficient way to use TLS Systems for data recording becomes a relevant topic to deal with the huge Amount of data the Systems collect while recording. Already small projects can turn into huge Pointcloud Datasets that End user, like Architects or Archaeologist neither can't deal with as their technical equipment doesn't fit the requirements of the Dataset nor do they have the software tools to use the Data as the current software tools still are high prized. Even the necessary interpretation of the Dataset can be a tough task if the people who have to work on with the Pointcloud aren't educated right in order to understand TLS and the results it creates. The use of TLS Systems has to have in mind the project requirements of the individual Heritage Object, like the required accuracy, standards for Levels of Details (e.g. "Empfehlungen für die Baudokumentation, Günther Eckstein, Germany", the required kind of Deliverables (Visualization, 2D Drawings, True Deformation Drawings, 3D Models, BIM or 4D

  18. The New Epidemiology--A Challenge to Health Administration. Issues in Epidemiology for Administration.

    Science.gov (United States)

    Crichton, Anne, Ed.; Neuhauser, Duncan, Ed.

    The role of epidemiology in health administration is considered in 11 articles, and three course descriptions and a bibliography are provided. Titles and authors include the following: "The Need for Creative Managerial Epidemiology" (Gary L. Filerman); "The Growing Role of Epidemiology in Health Administration" (Maureen M.…

  19. Vitamin D and Colorectal Cancer: Molecular, Epidemiological, and Clinical Evidence

    Science.gov (United States)

    Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L.; Manson, JoAnn E.; Qian, Zhi Rong; Ogino, Shuji

    2016-01-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol, and binds to vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D metabolizing enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating effects of vitamin D. Preclinical and epidemiological studies provide evidence for anticancer effects of vitamin D (in particular, against colorectal cancer), though clinical trials have yet to prove its benefit. Additionally, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses, and clinical trials on vitamin D efficacy in colorectal cancer patients. Here we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies, and discuss the links and controversies within and between the two parts of evidence. PMID:27245104

  20. Vitamin D and colorectal cancer: molecular, epidemiological and clinical evidence.

    Science.gov (United States)

    Dou, Ruoxu; Ng, Kimmie; Giovannucci, Edward L; Manson, JoAnn E; Qian, Zhi Rong; Ogino, Shuji

    2016-05-01

    In many cells throughout the body, vitamin D is converted into its active form calcitriol and binds to the vitamin D receptor (VDR), which functions as a transcription factor to regulate various biological processes including cellular differentiation and immune response. Vitamin D-metabolising enzymes (including CYP24A1 and CYP27B1) and VDR play major roles in exerting and regulating the effects of vitamin D. Preclinical and epidemiological studies have provided evidence for anti-cancer effects of vitamin D (particularly against colorectal cancer), although clinical trials have yet to prove its benefit. In addition, molecular pathological epidemiology research can provide insights into the interaction of vitamin D with tumour molecular and immunity status. Other future research directions include genome-wide research on VDR transcriptional targets, gene-environment interaction analyses and clinical trials on vitamin D efficacy in colorectal cancer patients. In this study, we review the literature on vitamin D and colorectal cancer from both mechanistic and population studies and discuss the links and controversies within and between the two parts of evidence.

  1. Clostridium difficile infection: epidemiology, diagnosis and understanding transmission.

    Science.gov (United States)

    Martin, Jessica S H; Monaghan, Tanya M; Wilcox, Mark H

    2016-04-01

    Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potentially leading to 'silent' onward transmission. Modern technologies, such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis, are helping to track C. difficile transmission across health-care facilities, countries and continents, offering the potential to illuminate previously under-recognized sources of infection. These typing strategies have also demonstrated heterogeneity in terms of CDI incidence and strain types reflecting different stages of epidemic spread. However, comparison of CDI epidemiology, particularly between countries, is challenging due to wide-ranging approaches to sampling and testing. Diagnostic strategies for C. difficile are complicated both by the wide range of bacterial targets and tests available and the need to differentiate between toxin-producing and non-toxigenic strains. Multistep diagnostic algorithms have been recommended to improve sensitivity and specificity. In this Review, we describe the latest advances in the understanding of C. difficile epidemiology, transmission and diagnosis, and discuss the effect of these developments on the clinical management of CDI.

  2. Parallel computing in genomic research: advances and applications.

    Science.gov (United States)

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities.

  3. [Causal analysis approaches in epidemiology].

    Science.gov (United States)

    Dumas, O; Siroux, V; Le Moual, N; Varraso, R

    2014-02-01

    Epidemiological research is mostly based on observational studies. Whether such studies can provide evidence of causation remains discussed. Several causal analysis methods have been developed in epidemiology. This paper aims at presenting an overview of these methods: graphical models, path analysis and its extensions, and models based on the counterfactual approach, with a special emphasis on marginal structural models. Graphical approaches have been developed to allow synthetic representations of supposed causal relationships in a given problem. They serve as qualitative support in the study of causal relationships. The sufficient-component cause model has been developed to deal with the issue of multicausality raised by the emergence of chronic multifactorial diseases. Directed acyclic graphs are mostly used as a visual tool to identify possible confounding sources in a study. Structural equations models, the main extension of path analysis, combine a system of equations and a path diagram, representing a set of possible causal relationships. They allow quantifying direct and indirect effects in a general model in which several relationships can be tested simultaneously. Dynamic path analysis further takes into account the role of time. The counterfactual approach defines causality by comparing the observed event and the counterfactual event (the event that would have been observed if, contrary to the fact, the subject had received a different exposure than the one he actually received). This theoretical approach has shown limits of traditional methods to address some causality questions. In particular, in longitudinal studies, when there is time-varying confounding, classical methods (regressions) may be biased. Marginal structural models have been developed to address this issue. In conclusion, "causal models", though they were developed partly independently, are based on equivalent logical foundations. A crucial step in the application of these models is the

  4. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

    Science.gov (United States)

    Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

    2016-01-01

    Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and

  5. A unique case of a huge mixed squamous cell and glandular papilloma of non-endobronchial origin with a peripheral growth

    Directory of Open Access Journals (Sweden)

    Kei Yabuki

    Full Text Available We report a case of a huge solitary non-endobronchial pulmonary tumor in a 76-year-old male smoker. The tumor measured 11 × 10 × 8 cm. It was ill-defined, and it was located periphery of the right lower lobe with the subpleural cystic spaces. He underwent right lower lobectomy with mediastinal lymph node dissection and is free from tumor 30 months after surgery. Microscopically, it was composed of a proliferation of squamous and ciliated columnar epithelial cells with a few mucous cells. These cells were arranged in a papillary growth fashion extending along the fibrously thickened alveolar septa together with metaplastic bronchiolar and squamous epithelia displaying an usual interstitial pneumonia-pattern. Although the histologic features of the tumor were that of a mixed squamous cell and glandular papilloma (MSCGP, it was peripherally located and showed a lepidic growth, and it was much larger than previously reported MSCGPs. It is possible that the tumor developed in association with bronchial metaplasia in the periphery of the lung, and then extended along the surface of the reconstructed air spaces, which resulted in its unique histologic appearance. Further investigations of respiratory papilloma are needed to clarify the pathogenesis of these lesions. Keywords: Mixed squamous cell and glandular papilloma, Non-endobronchial, Cytology, Interstitial pneumonia, Pulmonary tumor

  6. Huge bilateral ovarian cysts in adulthood as the presenting feature of Van Wyk Grumbach syndrome due to chronic uncontrolled juvenile hypothyroidism

    Directory of Open Access Journals (Sweden)

    K S Shivaprasad

    2013-01-01

    Full Text Available Juvenile primary hypothyroidism causing cystic ovaries and pseudoprecocious puberty (Van-Wyk Grumbach syndrome (VWGS is well documented in literature. There are only a few reports of primary hypothyroidism presenting as ovarian cysts in adults. Here we present a case of huge bilateral ovarian cysts in adulthood as the presenting feature of VWGS due to chronic uncontrolled juvenile hypothyroidism. Large uniloculor right ovarian cyst (119 × 81 × 90 mm and a multicystic left ovary (55 × 45 × 49 mm were detected in a 24 year lady with secondary amenorrhea, galactorrhea, and palpable abdominal mass with history of neonatal jaundice, delayed milestones, short stature, and precocious menarche at age of 7.5 years age. She had elevated levels of cancer antigen (CA-125 which normalized post levothyroxine supplementation. Elevated CA-125 may lead to misdiagnosis of ovarian carcinoma and inadvertent treatment. Bilateral ovarian cysts in adults are a rare presentation of juvenile hypothyroidism. It is necessary to screen for primary hypothyroidism in patients presenting with bilateral ovarian cysts to prevent unnecessary evaluation and treatment.

  7. Topographical effects on wave exciting forces on huge floating structure. 2; Ogata futaishiki kaiyo kozobutsu ni sayosuru haryoku ni kansuru kenkyu. 2

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Y [Hiroshima University, Hiroshima (Japan); Okusu, M [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics

    1997-12-31

    A method to predict drift force acting on a floating structure has been developed for a marine structure consisting of a number of floating elements, positioned in a region having a slope at the sea bottom. When a huge marine structure, such as floating air port, is located in a coastal area, scale of the overall structure is very large, of the order of scale of water depth change. The new method assumes that a marine structure consisting of an infinite number of cylindrical floating elements is installed in parallel to the seashore, where symmetrical nature of the configuration allows to predict behavior of the whole system by analyzing one element. Integration of pressures acting on structure surfaces determines the horizontal component of the drift force acting on the structure. Being influenced by topography, drift force predicted peaks at a frequency different from that for the level predicted on the assumption of constant water depth. This indicates the necessity for consideration of seabottom slope and effects of broken waves at the seashore. 6 refs., 12 figs.

  8. On the sea-covering effect of a huge floating structure on the surrounding water; Choogata futai shuhen no kaisui ni taisuru kaimen shahei no eikyo ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, M; Kagemoto, H; Hamada, T [The University of Tokyo, Tokyo (Japan)

    1997-12-31

    The numerical analysis program based on the difference method for dynamics of sea water with sea-surface displacement, flow rate, salt content and temperature as the parameters is modified to more accurately assess the effects of a huge marine structure on surrounding environment by adding the effects of insolation and boundary conditions of the sea-covering effects of the floating structure. The numerical simulation was done for summer and winter seasons, not in a sea area but using a rectangular bay with the floating structure at the center. A new flow evolves around the floating structure, due to the sea-covering effect. The flow patterns in summer and winter are clearly different, due to difference in insolation. The predicted flow is also sensitive whether stratification is considered or not, by which is meant that it is important what stratification effect is taken into account. Daily insolation changes are accompanied by vertical distribution of water temperature and its temporal change. These effects are also observed under the floating structure which shields insolation. 10 refs., 17 figs., 4 tabs.

  9. Topographical effects on wave exciting forces on huge floating structure. 2; Ogata futaishiki kaiyo kozobutsu ni sayosuru haryoku ni kansuru kenkyu. 2

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Y. [Hiroshima University, Hiroshima (Japan); Okusu, M. [Kyushu Univ., Fukuoka (Japan). Research Inst. for Applied Mechanics

    1996-12-31

    A method to predict drift force acting on a floating structure has been developed for a marine structure consisting of a number of floating elements, positioned in a region having a slope at the sea bottom. When a huge marine structure, such as floating air port, is located in a coastal area, scale of the overall structure is very large, of the order of scale of water depth change. The new method assumes that a marine structure consisting of an infinite number of cylindrical floating elements is installed in parallel to the seashore, where symmetrical nature of the configuration allows to predict behavior of the whole system by analyzing one element. Integration of pressures acting on structure surfaces determines the horizontal component of the drift force acting on the structure. Being influenced by topography, drift force predicted peaks at a frequency different from that for the level predicted on the assumption of constant water depth. This indicates the necessity for consideration of seabottom slope and effects of broken waves at the seashore. 6 refs., 12 figs.

  10. On the sea-covering effect of a huge floating structure on the surrounding water; Choogata futai shuhen no kaisui ni taisuru kaimen shahei no eikyo ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Fujino, M.; Kagemoto, H.; Hamada, T. [The University of Tokyo, Tokyo (Japan)

    1996-12-31

    The numerical analysis program based on the difference method for dynamics of sea water with sea-surface displacement, flow rate, salt content and temperature as the parameters is modified to more accurately assess the effects of a huge marine structure on surrounding environment by adding the effects of insolation and boundary conditions of the sea-covering effects of the floating structure. The numerical simulation was done for summer and winter seasons, not in a sea area but using a rectangular bay with the floating structure at the center. A new flow evolves around the floating structure, due to the sea-covering effect. The flow patterns in summer and winter are clearly different, due to difference in insolation. The predicted flow is also sensitive whether stratification is considered or not, by which is meant that it is important what stratification effect is taken into account. Daily insolation changes are accompanied by vertical distribution of water temperature and its temporal change. These effects are also observed under the floating structure which shields insolation. 10 refs., 17 figs., 4 tabs.

  11. On the estimation method of hydrodynamic forces acting on a huge floating structure; Choogata futai ni hataraku haryoku ryutairyoku no suiteiho ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Kagemoto, H.; Fujino, M.; Zhu, T. [The University of Tokyo, Tokyo (Japan)

    1996-12-31

    A floating structure such as an international airport is anticipated to have a length of about 5,000 m and a width of about 1,000 m. A singular point method may be used as a method to estimate force that such a floating body is subjected to from waves. In order to derive a solution with practically sufficient accuracy, 1250 elements are required in the length direction and 250 elements in the width direction, or a total of 312,500 elements. Calculating this number of elements should use finally a linear equation system handling complex coefficients comprising 312,500 elements, which would require a huge amount of calculation time. This paper proposes a method to derive solution on wave forces acting on a super-large floating structure or fluid force coefficients such as added mass coefficients and decay coefficients at a practically workable calculation amount and still without degrading the accuracy. The structure was assumed to be a box-shaped structure. Strengths of the singular points to be distributed on each element were assumed to be almost constant except for edges in lateral, oblique and longitudinal waves. Under this assumption, the interior of the floating structure excepting its edges was represented by several large elements to have reduced the number of elements. A calculation method proposed based on this conception was verified of its effectiveness. 2 refs., 25 figs., 3 tabs.

  12. Epidemiology of extremity fractures in the Netherlands

    NARCIS (Netherlands)

    Beerekamp, M. S. H.; de Muinck Keizer, R. J. O.; Schep, N. W. L.; Ubbink, D. T.; Panneman, M. J. M.; Goslings, J. C.

    2017-01-01

    Insight in epidemiologic data of extremity fractures is relevant to identify people at risk. By analyzing age- and gender specific fracture incidence and treatment patterns we may adjust future policy, take preventive measures and optimize health care management. Current epidemiologic data on

  13. Complex epidemiological approach to human mutagenesis

    International Nuclear Information System (INIS)

    Czeizel, A.

    1980-01-01

    The main characteristics of the epidemiological approach are summarised and the criteria discussed for the adoption of this approach for the detection of human mutagenesis. Mutation monitoring systems are described and results of epidemiological studies of higher risk populations are presented. (C.F.)

  14. Maritim epidemiologi på Supercourse

    DEFF Research Database (Denmark)

    Jensen, Olaf

    2015-01-01

    Maritim epidemiologi er nu kommet med i samlingen af undervisningsmidler på ”Supercourse”. Der er oprettet en særlig mappe med Maritime Epidemiology og alle der har gode bidrag inden for området opfordres hermed til at publicere her. Supercourse er en samling af foredrag beregnet til at være en r...

  15. Retrospective study of epidemiological, clinicopathological and ...

    African Journals Online (AJOL)

    Retrospective study of epidemiological, clinicopathological and biological profils of 62 colorectal cancers cases in Jijel provence (Algeria) ... Our results were often compatible with the available literature and may provide reliable and relevant data on this disease. Key words: Colorectal cancer; Epidemiology; Therapy; ...

  16. Epidemiology, diagnosis and management of food allergy

    NARCIS (Netherlands)

    Le, T.T.M.

    2013-01-01

    This thesis describes the epidemiology, diagnosis and management of food allergy. Epidemiology This thesis shows that the prevalence of self-reported adverse food reactions in children and adults was high: 17-25% for all foods and 10-11% for 24 preselected, so-called priority foods. The prevalence

  17. 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....... Increasingly poor renal function, aberrations in calcium-phosphate metabolism and erythropoietin treatment seem to increase the risk of the disease and its severity. Up to 25-30% of patients with renal failure exposed to gadolinium-based contrast agents may develop nephrogenic systemic disease. The figure...... that gadolinium-containing contrast agents used for magnetic resonance imaging have an essential causative role in most, if not all, cases of nephrogenic systemic fibrosis. One particular agent, gadodiamide, caused the majority of cases, but gadopentetate dimeglumine has also been implicated in several cases...

  18. Epidemiological studies in mucus hypersecretion

    DEFF Research Database (Denmark)

    Vestbo, Jørgen

    2002-01-01

    Respiratory mucus in epidemiology has mainly been studied using standardized questionnaires including questions on cough and phlegm. In chronic obstructive pulmonary disease (COPD) much controversy exists regarding the importance of mucus hypersecretion. From being the key element in the 'British...... hypothesis' it was reduced to being an innocent disorder in the 1980s but is now again recognized as a potential risk factor for an accelerated loss of lung function. Whereas early studies in mainly occupational cohorts showed no effect of chronic mucus hypersecretion on decline in lung function......, such an effect has been shown in subsequent studies on general population samples. Chronic mucus hypersecretion also increases risk of hospital admission which may be due to an increased risk of lower respiratory tract infection. In severe COPD this may explain the increased mortality associated...

  19. [Scientific journalism and epidemiological risk].

    Science.gov (United States)

    Luiz, Olinda do Carmo

    2007-01-01

    The importance of the communications media in the construction of symbols has been widely acknowledged. Many of the articles on health published in the daily newspapers mention medical studies, sourced from scientific publications focusing on new risks. The disclosure of risk studies in the mass media is also a topic for editorials and articles in scientific journals, focusing the problem of distortions and the appearance of contradictory news items. The purpose of this paper is to explore the meaning and content of disclosing scientific risk studies in large-circulation daily newspapers, analyzing news items published in Brazil and the scientific publications used as their sources during 2000. The "risk" is presented in the scientific research projects as a "black box" in the meaning of Latour, with the news items downplaying scientific disputes and underscoring associations between behavioral habits and the occurrence of diseases, emphasizing individual aspects of the epidemiological approach, to the detriment of the group.

  20. Epidemiology of acute wrist trauma

    DEFF Research Database (Denmark)

    Larsen, C F; Lauritsen, Jens

    1993-01-01

    Epidemiological data on wrist injuries in a population can be used for planning by applying them to criteria for care and thus deriving estimates of provisions for care according to currently desirable standards. In a 1-year study all patients > or = 15 years with acute wrist trauma and treated...... in the emergency room were examined according to an algorithm until a diagnosis was established. The overall incidence of wrist trauma was 69 per 10,000 inhabitants per year. Incidence of wrist trauma requiring x-ray examination was 58 per 10,000 per year. The incidence of distal radius fractures was 27 per 10...... using data from a population-based study. A completeness rate of 0.56 (95% confidence interval: 0.31-0.78) was found. An x-ray had been taken for all patients reporting a fracture thus justifying the use of fractures as an incidence measure when comparing groups of patients with wrist trauma....

  1. Epidemiology of Haemophilus ducreyi Infections.

    Science.gov (United States)

    González-Beiras, Camila; Marks, Michael; Chen, Cheng Y; Roberts, Sally; Mitjà, Oriol

    2016-01-01

    The global epidemiology of Haemophilus ducreyi infections is poorly documented because of difficulties in confirming microbiological diagnoses. We evaluated published data on the proportion of genital and nongenital skin ulcers caused by H. ducreyi before and after introduction of syndromic management for genital ulcer disease (GUD). Before 2000, the proportion of GUD caused by H. ducreyi ranged from 0.0% to 69.0% (35 studies in 25 countries). After 2000, the proportion ranged from 0.0% to 15.0% (14 studies in 13 countries). In contrast, H. ducreyi has been recently identified as a causative agent of skin ulcers in children in the tropical regions; proportions ranged from 9.0% to 60.0% (6 studies in 4 countries). We conclude that, although there has been a sustained reduction in the proportion of GUD caused by H. ducreyi, this bacterium is increasingly recognized as a major cause of nongenital cutaneous ulcers.

  2. EPIDEMIOLOGICAL EVALUATION OF COLORECTAL CANCER

    Directory of Open Access Journals (Sweden)

    B. Shafayan M. Keyhani

    2003-07-01

    Full Text Available This study was carried out to analyze certain epidemiological variations in Iranian patients with colorectal cancer. (CRC: From March 1981 up to March 1993, 103 patients were analyzed retrospectively for age, gender, marital state, job, nutritional habits, presenting symptoms and histopathological features. Most of the patients with colorectal cancer were male, age range 20-75 (mean 56, 25.4 percent were long-term smokers and bleeding was the most common symptom. The rectum was the most common site and moderately differentiated carcinoma was considered as the main common histopathological variety. In conclusion, increasing incidence of colorectal cancer in younger Iranian population, below 30 and late admission and diagnosis were the main findings in the present study necessitating screening programs with annual fecal occult blood tests in high risk families.

  3. Genome-wide meta-analyses identify multiple loci associated with smoking behavior

    NARCIS (Netherlands)

    H. Furberg (Helena); Y. Kim (Yunjung); J. Dackor (Jennifer); E.A. Boerwinkle (Eric); N. Franceschini (Nora); D. Ardissino (Diego); L. Bernardinelli (Luisa); P.M. Mannucci (Pier); F. Mauri (Francesco); P.A. Merlini (Piera); D. Absher (Devin); T.L. Assimes (Themistocles); S.P. Fortmann (Stephen); C. Iribarren (Carlos); J.W. Knowles (Joshua); T. Quertermous (Thomas); L. Ferrucci (Luigi); T. Tanaka (Toshiko); J.C. Bis (Joshua); T. Haritunians (Talin); B. McKnight (Barbara); B.M. Psaty (Bruce); K.D. Taylor (Kent); E.L. Thacker (Evan); P. Almgren (Peter); L. Groop (Leif); C. Ladenvall (Claes); M. Boehnke (Michael); A.U. Jackson (Anne); K.L. Mohlke (Karen); H.M. Stringham (Heather); J. Tuomilehto (Jaakko); E.J. Benjamin (Emelia); S.J. Hwang; D. Levy (Daniel); S.R. Preis; R.S. Vasan (Ramachandran Srini); J. Duan (Jubao); P.V. Gejman (Pablo); D.F. Levinson (Douglas); A.R. Sanders (Alan); J. Shi (Jianxin); E.H. Lips (Esther); J.D. McKay (James); A. Agudo (Antonio); L. Barzan (Luigi); V. Bencko (Vladimir); S. Benhamou (Simone); X. Castellsagué (Xavier); C. Canova (Cristina); D.I. Conway (David); E. Fabianova (Eleonora); L. Foretova (Lenka); V. Janout (Vladimir); C.M. Healy (Claire); I. Holcátová (Ivana); K. Kjaerheim (Kristina); P. Lagiou; J. Lissowska (Jolanta); R. Lowry (Ray); T.V. MacFarlane (Tatiana); D. Mates (Dana); L. Richiardi (Lorenzo); P. Rudnai (Peter); N. Szeszenia-Dabrowska (Neonilia); D. Zaridze; A. Znaor (Ariana); M. Lathrop (Mark); P. Brennan (Paul); S. Bandinelli (Stefania); T.M. Frayling (Timothy); J.M. Guralnik (Jack); Y. Milaneschi (Yuri); J.R.B. Perry (John); D. Altshuler (David); R. Elosua (Roberto); S. Kathiresan (Sekar); G. Lucas (Gavin); O. Melander (Olle); V. Salomaa (Veikko); S.M. Schwartz (Stephen); B.F. Voight (Benjamin); B.W.J.H. Penninx (Brenda); J.H. Smit (Johannes); N. Vogelzangs (Nicole); D.I. Boomsma (Dorret); E.J.C. de Geus (Eco); J.M. Vink (Jacqueline); G.A.H.M. Willemsen (Gonneke); S.J. Chanock (Stephen); F. Gu (Fangyi); S.E. Hankinson (Susan); D. Hunter (David); A. Hofman (Albert); H.W. Tiemeier (Henning); A.G. Uitterlinden (André); P. Tikka-Kleemola (Päivi); S. Walter (Stefan); D.I. Chasman (Daniel); B.M. Everett (Brendan); G. Pare (Guillaume); P.M. Ridker (Paul); M.D. Li (Ming); H.H. Maes (Hermine); J. Audrain-Mcgovern (Janet); D. Posthuma (Danielle); L.M. Thornton (Laura); C. Lerman (Caryn); J. Kaprio (Jaakko); J.E. Rose (Jed); J.P.A. Ioannidis (John); P. Kraft (Peter); D.Y. Lin (Dan); P.F. Sullivan (Patrick); C.J. O'Donnell (Christopher)

    2010-01-01

    textabstractConsistent but indirect evidence has implicated genetic factors in smoking behavior. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology

  4. Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorum

    Science.gov (United States)

    Kelly Ivors; Matteo Garbelotto; Ineke De Vries; Peter Bonants

    2006-01-01

    Investigating the population genetics of Phytophthora ramorum, the causal agent of sudden oak death (SOD), is critical to understanding the biology and epidemiology of this important phytopathogen. Raw sequence data (445,000 reads) of P. ramorum was provided by the Joint Genome Institute. Our objective was to develop and utilize...

  5. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  6. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  7. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  8. On the epidemiology of influenza

    Directory of Open Access Journals (Sweden)

    Scragg Robert

    2008-02-01

    Full Text Available Abstract The epidemiology of influenza swarms with incongruities, incongruities exhaustively detailed by the late British epidemiologist, Edgar Hope-Simpson. He was the first to propose a parsimonious theory explaining why influenza is, as Gregg said, "seemingly unmindful of traditional infectious disease behavioral patterns." Recent discoveries indicate vitamin D upregulates the endogenous antibiotics of innate immunity and suggest that the incongruities explored by Hope-Simpson may be secondary to the epidemiology of vitamin D deficiency. We identify – and attempt to explain – nine influenza conundrums: (1 Why is influenza both seasonal and ubiquitous and where is the virus between epidemics? (2 Why are the epidemics so explosive? (3 Why do they end so abruptly? (4 What explains the frequent coincidental timing of epidemics in countries of similar latitude? (5 Why is the serial interval obscure? (6 Why is the secondary attack rate so low? (7 Why did epidemics in previous ages spread so rapidly, despite the lack of modern transport? (8 Why does experimental inoculation of seronegative humans fail to cause illness in all the volunteers? (9 Why has influenza mortality of the aged not declined as their vaccination rates increased? We review recent discoveries about vitamin D's effects on innate immunity, human studies attempting sick-to-well transmission, naturalistic reports of human transmission, studies of serial interval, secondary attack rates, and relevant animal studies. We hypothesize that two factors explain the nine conundrums: vitamin D's seasonal and population effects on innate immunity, and the presence of a subpopulation of "good infectors." If true, our revision of Edgar Hope-Simpson's theory has profound implications for the prevention of influenza.

  9. Global epidemiology of celiac disease

    Directory of Open Access Journals (Sweden)

    S. V. Bykova

    2018-01-01

    Full Text Available The review presents the data on the prevalence of celiac disease in various world regions. The numbers of patients with celiac disease continues to rise every year. According to some authors, this is to be related not only to improvement in diagnosis, but to other extrinsic factors, as well, that require additional studies. In the 1980s the prevalence of this disease was 1.05%, and by the beginning of 2000s, it amounted to 1.99%. In particular, from 1993 to 2002 in Britain its incidence increased from 6 to 13.3 per 100,000. Both raised awareness of doctors and conduction of epidemiological studies play a decisive role in the improvement of the diagnosis of celiac disease. The information cumulated up to now makes it possible to conclude that the highest diagnostic rates of celiac disease can be found in the risk groups. They include 1st and 2nd degree relatives of patients with celiac disease, patients with autoimmune disorders (type 1 diabetes mellitus, autoimmune thyroiditis; those with clinical signs of an intestinal disorder, such as chronic diarrhea, as well as patients with anemia, osteoporosis and high transaminase levels of unknown origin. According to the Finnish epidemiological study, the prevalence of celiac disease, depending on the risk group, may vary from 6.6 to 16.3%. The guidelines by the American College of Gastroenterology, British Society of Gastroenterology, North-American Society of Pediatric Gastroenterology, and the Russian Consensus on Diagnosis and Treatment of Celiac Disease in Adults and Children all recommend thorough examination of patients from the risk groups. Active diagnosis of celiac disease (screening has been recognized as one of the approaches to primary prevention to autoimmune disorders and cancer.

  10. Microbial comparative pan-genomics using binomial mixture models

    Directory of Open Access Journals (Sweden)

    Ussery David W

    2009-08-01

    Full Text Available Abstract Background The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. Results We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection probabilities. Estimated pan-genome sizes range from small (around 2600 gene families in Buchnera aphidicola to large (around 43000 gene families in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely occurring genes in the population. Conclusion Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes.

  11. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  12. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  13. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  14. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  15. First insights in the variability of Borrelia recurrentis genomes.

    Directory of Open Access Journals (Sweden)

    Durdica Marosevic

    2017-09-01

    Full Text Available Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45 reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in different years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen.Two historical isolates from Ethiopia and four isolates from migrants from Somalia (n = 3 and Ethiopia (n = 1 obtained in 2015 were cultured in MPK-medium supplemented with 50% foetal calf serum. Whole DNA was sequenced using Illumina MiSeq technology and analysed using the CLC Genomics Workbench and SPAdes de novo assembler. Compared to the reference B. recurrentis A1 29-38 SNPs were identified in the genome distributed on the chromosome and plasmids. In addition to that, plasmids of differing length, compared to the available reference genome were identified.The observed low genetic variability of B. recurrentis isolates is possibly due to the adaptation to a very conserved vector-host (louse-human cycle, or influenced by the fastidious nature of the pathogen and their resistance to in vitro growth. Nevertheless, isolates obtained in 2015 were bearing the same chromosomal SNPs and could be distinguished from the historical isolates by means of whole genome sequencing, but not hitherto used typing methods. This is the first study examining the molecular epidemiology of B. recurrentis and provides the necessary background for the development of better diagnostic tools.

  16. Epidemiology of acute lymphoblastic leukemia

    International Nuclear Information System (INIS)

    Pendergrass, T.W.

    1985-01-01

    Although the etiology of acute leukemia is largely unknown, some facets of the puzzle are becoming clarified. Recognition of important patterns in age-specific mortality rates has suggested that events early in life, perhaps even prenatally, may have an influence on developing leukemia in childhood. The racial differences evident in mortality, incidence, and immunologic subtype of ALL suggest either differences in exposures to certain factors or differences in responses to those factors by white children. Hereditary factors appear to play a role. Familial and hereditary conditions exist that have high incidences of acute leukemia. Chromosomal anomalies are common in these conditions. Viral infections may play a role by contributing to alteration in genetic material through incorporation of the viral genome. How that virus is dealt with after primary infection seems important. The presence of immunodeficiency may allow wider dissemination or enhanced replication of such viruses, thereby increasing the likelihood of cellular transformation to an abnormal cell. Proliferation of that malignant cell to a clone may depend on other cofactors. Perhaps prolonged exposure to substances like benzene or alkylating agents may enhance these interactions between virus and genetic material. Does this change DNA repair mechanisms. Are viral infections handled differently. Is viral genomic information more easily integrated into host cells. Ionizing radiation has multiple effects. Alteration in genetic material occurs both at the molecular and chromosomal levels. DNA may be altered, lost, or added in the cell's attempt to recover from the injury

  17. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  18. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.

    OpenAIRE

    Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf Sommer; Nielsen, Eva M.; Aarestrup, Frank Møller

    2014-01-01

    Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-prod...

  19. Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

    OpenAIRE

    Joensen, Katrine Grimstrup; Scheutz, Flemming; Lund, Ole; Hasman, Henrik; Kaas, Rolf S.; Nielsen, Eva M.; Aarestrup, Frank M.

    2014-01-01

    Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-prod...

  20. Epidemiology and genetics of intracranial aneurysms

    Energy Technology Data Exchange (ETDEWEB)

    Caranci, F., E-mail: ferdinandocaranci@libero.it [Unit of Neuroradiology, Department of Diagnostic Radiology and Radiotherapy, Federico II University, Naples (Italy); Briganti, F., E-mail: frabriga@unina.it [Unit of Neuroradiology, Department of Diagnostic Radiology and Radiotherapy, Federico II University, Naples (Italy); Cirillo, L.; Leonardi, M. [Neuroradiology service, Bellaria Hospital, Bologna (Italy); Muto, M., E-mail: mutomar@tiscali.it [Neuroradiology Service Cardarelli Hospital Naples (Italy)

    2013-10-01

    Intracranial aneurysms are acquired lesions (5–10% of the population), a fraction of which rupture leading to subarachnoid hemorrhage with devastating consequences. Until now, the exact etiology of intracranial aneurysms formation remains unclear. The low incidence of subarachnoid hemorrhage in comparison with the prevalence of unruptured IAs suggests that the vast majority of intracranial aneurysms do not rupture and that identifying those at highest risk is important in defining the optimal management. The most important factors predicting rupture are aneurysm size and site. In addition to ambiental factors (smoking, excessive alcohol consumption and hypertension), epidemiological studies have demonstrated a familiar influence contributing to the pathogenesis of intracranial aneurysms, with increased frequency in first- and second-degree relatives of people with subarachnoid hemorrhage. In comparison to sporadic aneurysms, familial aneurysms tend to be larger, more often located at the middle cerebral artery, and more likely to be multiple. Other than familiar occurrence, there are several heritable conditions associated with intracranial aneurysm formation, including autosomal dominant polycystic kidney disease, neurofibromatosis type I, Marfan syndrome, multiple endocrine neoplasia type I, pseudoxanthoma elasticum, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II and IV. The familial occurrence and the association with heritable conditions indicate that genetic factors may play a role in the development of intracranial aneurysms. Genome-wide linkage studies in families and sib pairs with intracranial aneurysms have identified several loci on chromosomes showing suggestive evidence of linkage, particularly on chromosomes 1p34.3–p36.13, 7q11, 19q13.3, and Xp22. For the loci on 1p34.3–p36.13 and 7q11, a moderate positive association with positional candidate genes has been demonstrated (perlecan gene, elastin gene, collagen type 1 A2

  1. Epidemiology and genetics of intracranial aneurysms

    International Nuclear Information System (INIS)

    Caranci, F.; Briganti, F.; Cirillo, L.; Leonardi, M.; Muto, M.

    2013-01-01

    Intracranial aneurysms are acquired lesions (5–10% of the population), a fraction of which rupture leading to subarachnoid hemorrhage with devastating consequences. Until now, the exact etiology of intracranial aneurysms formation remains unclear. The low incidence of subarachnoid hemorrhage in comparison with the prevalence of unruptured IAs suggests that the vast majority of intracranial aneurysms do not rupture and that identifying those at highest risk is important in defining the optimal management. The most important factors predicting rupture are aneurysm size and site. In addition to ambiental factors (smoking, excessive alcohol consumption and hypertension), epidemiological studies have demonstrated a familiar influence contributing to the pathogenesis of intracranial aneurysms, with increased frequency in first- and second-degree relatives of people with subarachnoid hemorrhage. In comparison to sporadic aneurysms, familial aneurysms tend to be larger, more often located at the middle cerebral artery, and more likely to be multiple. Other than familiar occurrence, there are several heritable conditions associated with intracranial aneurysm formation, including autosomal dominant polycystic kidney disease, neurofibromatosis type I, Marfan syndrome, multiple endocrine neoplasia type I, pseudoxanthoma elasticum, hereditary hemorrhagic telangiectasia, and Ehlers-Danlos syndrome type II and IV. The familial occurrence and the association with heritable conditions indicate that genetic factors may play a role in the development of intracranial aneurysms. Genome-wide linkage studies in families and sib pairs with intracranial aneurysms have identified several loci on chromosomes showing suggestive evidence of linkage, particularly on chromosomes 1p34.3–p36.13, 7q11, 19q13.3, and Xp22. For the loci on 1p34.3–p36.13 and 7q11, a moderate positive association with positional candidate genes has been demonstrated (perlecan gene, elastin gene, collagen type 1 A2

  2. Epidemiological study around La Hague

    International Nuclear Information System (INIS)

    1999-01-01

    The North Cotentin is in France, the area where have been led until now, the biggest number of epidemiology studies on the effects of ionizing radiations on man, in order to assess the leukemia incidences and other cancer pathologies around nuclear facilities. The North Cotentin concentrates four nuclear installations.The objective of this file is to take stock of the situation in this field. In 1995 and 1998 have been published two sections of an epidemiology study about the incidence of leukemia in North Cotentin (J.F. Viel study for the period 1978-1992, Spira study for 1993-1997). The study of the Professor Spira does not bring to the fore a significant excess of leukemia for the period 1978-1997. The report of the professor Spira advocates several complementary epidemiology studies to precise or complete the data and lighten the causes of leukemia in North Cotentin. The studies of J.F.Viel shows that it does not exist a significant excess of cases in the studied area (25 cases for 22.8 expected cases, so a non significant difference) but notices an aggregate at the limit to be significant in the Beaumont-Hague canton (4 cases for 1.4 expected cases). J.F.Viel puts forward a relationship between the risk increase (of leukemia incidence) and some individual characteristics linked to the way of life of the studied persons: the North Cotentin beaches frequenting by the mothers or the children at least one time by month, the consumption of fish or shellfish having a local origin at least one time by week. This study suggests that it is the radioactivity, on the beaches on in fishes and shellfish that would be at the origin of the additional noticed leukemia. The authorities asked at the beginning of 1997, a scientific commission directed by the Professor Souleau to propose a new epidemiology study on the leukemia risk around La Hague. The report concludes that the leukemia incidence in the North Cotentin is in accordance with the expected incidence (25 observed

  3. Superposition model analysis of nickel(II) ions in trigonal bipyramidal complexes exhibiting huge zero field splitting (aka ‘giant magnetic anisotropy’)

    Energy Technology Data Exchange (ETDEWEB)

    Rudowicz, Czesław, E-mail: crudowicz@zut.edu.pl [Faculty of Chemistry, A. Mickiewicz University, 61-614 Poznań (Poland); Institute of Physics, West Pomeranian University of Technology, Szczecin (Poland); Açıkgöz, Muhammed [Department of Chemistry, Rutgers University, Newark, New Jersey 07102 (United States); Gnutek, Paweł [Institute of Physics, West Pomeranian University of Technology, Szczecin (Poland)

    2017-07-15

    Graphical abstract: Using crystal structure data for [Ni(Me{sub 6}tren)Cl](ClO{sub 4}) and [Ni(Me{sub 6}tren)Br](Br) as well as taking into account the Jahn-Teller distortions of five-fold coordinated Ni-complexes revealed by DFT geometry optimization, the ZFSPs are predicted for several structural models and wide ranges of model parameters. - Highlights: • Semiempirical study of potential SMM [Ni(Me{sub 6}tren)Cl](ClO{sub 4}) and [Ni(Me{sub 6}tren)Br](Br). • Superposition model analysis of zero field splitting (ZFS) parameters carried out. • Jahn-Teller distortions revealed by DFT geometry optimization considered. • SPM predicts D(ZFS) of observed magnitudes with positive or negative signs. • Results corroborate giant ZFS, which shall not be equated with magnetic anisotropy. - Abstract: Potential single-ion magnet Ni{sup 2+} systems: [Ni(Me{sub 6}tren)Cl](ClO{sub 4}) and [Ni(Me{sub 6}tren)Br](Br) reveal unusually high zero field splitting (ZFS). The ZFS parameter (ZFSP) D{sub expt} = −120 to −180 cm{sup −1} was determined indirectly by high-magnetic field, high-frequency electron magnetic resonance (HMF-EMR). Modeling ZFSPs using the density functional theory (DFT) codes predicts D values: −100 to −200 cm{sup −1}. Such ZFSP values may seem controversial in view of the D values usually not exceeding several tens of cm{sup −1} for Ni{sup 2+} ions. To corroborate or otherwise these results and elucidate the origin of the huge ZFS (named inappropriately as ‘giant uniaxial magnetic anisotropy’) and respective wavefunctions, we have undertaken semiempirical modeling based on the crystal field (CF) and spin Hamiltonians (SH) theory. In this paper, a feasibility study is carried out to ascertain if superposition model (SPM) calculations may yield such huge D values for these Ni{sup 2+} systems. Using crystal structure data for [Ni(Me{sub 6}tren)Cl](ClO{sub 4}) and [Ni(Me{sub 6}tren)Br](Br) as well as taking into account the Jahn

  4. Evidence and causality assessment in environmental epidemiology: methodological aspects

    International Nuclear Information System (INIS)

    Valleron, A.J.

    2000-01-01

    There are usually three major steps in the study of the possible impact of environmental factors on health: 1) to demonstrate that there is an association between exposure to the factor and the disease under study; 2) to demonstrate that this association is causal; 3) to evaluate the health benefit that could be obtained by removing the source of exposure. Statistical methods are commonly assumed to provide an objective way of achieving these three steps. This paper reviews some of the conditions that have to be met to allow proper interpretations and to avoid some of the controversies that are often found in health-environment studies. First, it should be remembered that the so-called P value which is used to qualify 'statistically significant' associations between risk factors and diseases does not give any indication of the probability that this association is actual, while far too often it is believed that it does. The probability that an association between an environmental factor and a disease is real could, however, be estimated by using Bayesian methods. These methods require that the a priori probabilities be stated, which is difficult to do in practice. Some directions to overcome this difficulty are presented. Second, the analysis of causality cannot be carried out on statistical grounds alone and the so-called 'causality criteria' are of limited practical interest. Definition of what is a cause, and upon which conditions a candidate factor of a disease can be considered as a cause, deserves much research effort, and careful consideration of the huge literature (mostly outside of the epidemiological field, for example in logic) which is devoted to this subject. Finally, the measurement of the role of a factor in a disease is very often assessed through the use of 'attributable fraction' or 'attributable mortality'. This should be done only when it is demonstrated that the considered factor is causal. Moreover, the interpretation of attributable fractions

  5. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  6. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  7. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  8. An animated depiction of major depression epidemiology

    Directory of Open Access Journals (Sweden)

    Patten Scott B

    2007-06-01

    Full Text Available Abstract Background Epidemiologic estimates are now available for a variety of parameters related to major depression epidemiology (incidence, prevalence, etc.. These estimates are potentially useful for policy and planning purposes, but it is first necessary that they be synthesized into a coherent picture of the epidemiology of the condition. Several attempts to do so have been made using mathematical modeling procedures. However, this information is not easy to communicate to users of epidemiological data (clinicians, administrators, policy makers. Methods In this study, up-to-date data on major depression epidemiology were integrated using a discrete event simulation model. The mathematical model was animated in Virtual Reality Modeling Language (VRML to create a visual, rather than mathematical, depiction of the epidemiology. Results Consistent with existing literature, the model highlights potential advantages of population health strategies that emphasize access to effective long-term treatment. The paper contains a web-link to the animation. Conclusion Visual animation of epidemiological results may be an effective knowledge translation tool. In clinical practice, such animations could potentially assist with patient education and enhanced long-term compliance.

  9. An animated depiction of major depression epidemiology.

    Science.gov (United States)

    Patten, Scott B

    2007-06-08

    Epidemiologic estimates are now available for a variety of parameters related to major depression epidemiology (incidence, prevalence, etc.). These estimates are potentially useful for policy and planning purposes, but it is first necessary that they be synthesized into a coherent picture of the epidemiology of the condition. Several attempts to do so have been made using mathematical modeling procedures. However, this information is not easy to communicate to users of epidemiological data (clinicians, administrators, policy makers). In this study, up-to-date data on major depression epidemiology were integrated using a discrete event simulation model. The mathematical model was animated in Virtual Reality Modeling Language (VRML) to create a visual, rather than mathematical, depiction of the epidemiology. Consistent with existing literature, the model highlights potential advantages of population health strategies that emphasize access to effective long-term treatment. The paper contains a web-link to the animation. Visual animation of epidemiological results may be an effective knowledge translation tool. In clinical practice, such animations could potentially assist with patient education and enhanced long-term compliance.

  10. [Kidney transplantation epidemiology in France].

    Science.gov (United States)

    Hiesse, Christian

    2013-11-01

    Kidney transplantation activity in France is among the most important worldwide: in 2011, 2976 transplants have been performed (47.5 per million population), and the number of patients living with a functional graft is estimated around 30,000, representing 44.7% of all patients (n = 67,270) treated for end-stage renal failure. However, the rate of preemptive kidney transplants remains very low, only 3.3% of incident patients starting renal replacement therapy. The analysis of demand showed a progressive increase in recent years, as demonstrated by the registration rate on the kidney transplantation waiting list, increasing by 5% yearly between 2006 and 2010, but with huge differences according to age categories and regional registration areas, reflecting discrepant appreciations in indications for kidney transplantation. The median waiting time between registration and transplantation increased progressively in recent years, reaching 22.3 months with considerable variations according to regional areas and transplantation teams. Kidney transplantation activity, while increasing continuously, is far to cover the rising demand, and inexorably patients accumulate on the waiting list (around 9000 patients were registered by January 2012). This situation is the consequence of insufficient organ procurement activity. The deceased organ procurement rate remained high: 1572 harvested donors in 2011 (24.1 per million population), but the proportion of older donors rose in recent years, to reach the rate of 26% of donors older than 65 years in 2011. The procurement activity of donors after cardiac arrest was reintroduced in 2006, but increased slowly: 65 transplants were performed in 2011 using kidney procured in non heart-beating donors. The living donor kidney transplantation activity has markedly increased recently: 302 living donor transplantations were performed in 2011, representing 10.1% of the kidney transplantations. Facing the predictable increase in the number of

  11. An estimation of the prevalence of genomic disorders using chromosomal microarray data.

    Science.gov (United States)

    Gillentine, Madelyn A; Lupo, Philip J; Stankiewicz, Pawel; Schaaf, Christian P

    2018-04-24

    Multiple genomic disorders result from recurrent deletions or duplications between low copy repeat (LCR) clusters, mediated by nonallelic homologous recombination. These copy number variants (CNVs) often exhibit variable expressivity and/or incomplete penetrance. However, the population prevalence of many genomic disorders has not been estimated accurately. A subset of genomic disorders similarly characterized by CNVs between LCRs have been studied epidemiologically, including Williams-Beuren syndrome (7q11.23), Smith-Magenis syndrome (17p11.2), velocardiofacial syndrome (22q11.21), Prader-Willi/Angelman syndromes (15q11.2q12), 17q12 deletion syndrome, and Charcot-Marie-Tooth neuropathy type 1/hereditary neuropathy with liability to pressure palsy (PMP22, 17q11.2). We have generated a method to estimate prevalence of highly penetrant genomic disorders by (1) leveraging epidemiological data for genomic disorders with previously reported prevalence estimates, (2) obtaining chromosomal microarray data on genomic disorders from a large medical genetics clinic; and (3) utilizing these in a linear regression model to determine the prevalence of this syndromic copy number change among the general population. Using our algorithm, the prevalence for five clinically relevant recurrent genomic disorders: 1q21.1 microdeletion (1/6882 live births) and microduplication syndromes (1/6309), 15q13.3 microdeletion syndrome (1/5525), and 16p11.2 microdeletion (1/3021) and microduplication syndromes (1/4216), were determined. These findings will inform epidemiological strategies for evaluating those conditions, and our method may be useful to evaluate the prevalence of other highly penetrant genomic disorders.

  12. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Nielsen, Eva M.; Kaas, Rolf Sommer

    2014-01-01

    Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly ‘real-time’ monitoring and identification of outbreaks, reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for using as a routine epidemiological typing....... Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatics approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the association...... of the isolates to specific outbreaks. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 88%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic...

  13. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  14. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  15. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  16. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  17. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  18. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  19. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  20. Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

    Science.gov (United States)

    Murray, Gemma G R; Soares, André E R; Novak, Ben J; Schaefer, Nathan K; Cahill, James A; Baker, Allan J; Demboski, John R; Doll, Andrew; Da Fonseca, Rute R; Fulton, Tara L; Gilbert, M Thomas P; Heintzman, Peter D; Letts, Brandon; McIntosh, George; O'Connell, Brendan L; Peck, Mark; Pipes, Marie-Lorraine; Rice, Edward S; Santos, Kathryn M; Sohrweide, A Gregory; Vohr, Samuel H; Corbett-Detig, Russell B; Green, Richard E; Shapiro, Beth

    2017-11-17

    The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction. Copyright © 2017, American Association for the Advancement of Science.

  1. Epidemiological issues related to dose reconstruction

    International Nuclear Information System (INIS)

    Shore, R.E.

    1996-01-01

    When a dose reconstruction is performed around some nuclear site, a decision has to be made as to whether an epidemiologic study should be performed there and, if so, what form the study should take. The goal of this paper is to provide an overview of epidemiologic and biostatistical issues that help determine whether an epidemiologic study around a nuclear facility is worthwhile doing from a scientific standpoint. We are all aware that public health and sociopolitical concerns often assume considerable importance in these decisions, but they will not be considered here. 27 refs., 2 tabs

  2. Radon epidemiology: A guide to the literature

    International Nuclear Information System (INIS)

    Marks, S.

    1988-12-01

    This document was written as a comprehensive overview of the voluminous literature on both uranium miner and residential radon epidemiology studies. This document provides the reader with a fairly complete list of radon epidemiology publications and key features of each, so that readers may further pursue only those publications of interest in the vast body of radon literature. A companion document, exploring all on-going residential radon epidemiology studies will be published by the Office of Health and Environmental Research (OHER), the Department of Energy (DOE) in the spring of 1989

  3. Internal dosimetry for epidemiologic studies

    International Nuclear Information System (INIS)

    Groer, P.G.

    1987-01-01

    In traditional epidemiologic analyses, a single valued summary index, the standardized mortality ratio (SMR), is quite popular. The SMR is simply the ratio of the number of deaths observed in the study population to the number of deaths expected if the study population were subject to the age-specific rates of a standard population. SMRs for all causes or specific causes can be calculated. For such a simple analysis an exposed cohort is often characterized by an average organ or whole body dose or dose interval, and the necessary dose estimation effort is relatively minor. Modern statistical methods focus on the estimation of the cause-specific mortality rate λ for study populations exposed to ionizing radiations or toxic chemicals. The dependence of λ on factors other than demographic characteristics, such as race and sex, is usually described through a parametric model. Such factors, often called covariates or covariables, are incorporated in the mathematical expression for the hazard rate. The external gamma dose or the internal lung dose from inhaled uranium are good examples for covariates. This type of analysis permits the use of individual doses and gives a detailed and quantitative description of the mortality rate as a function of the covariables, but at the cost of a major dosimetric effort. The generation of the necessary dose information and also the calculational efforts become especially taxing for time-dependent covariates such as an internal, cumulative organ dose. 4 refs

  4. The epidemiology of premature ejaculation.

    Science.gov (United States)

    Saitz, Theodore Robert; Serefoglu, Ege Can

    2016-08-01

    Vast advances have occurred over the past decade with regards to understanding the epidemiology, pathophysiology and management of premature ejaculation (PE); however, we still have much to learn about this common sexual problem. As a standardized evidence-based definition of PE has only recently been established, the reported prevalence rates of PE prior to this definition have been difficult to interpret. As a result, a large range of conflicting prevalence rates have been reported. In addition to the lack of a standardized definition and operational criteria, the method of recruitment for study participation and method of data collection have obviously contributed to the broad range of reported prevalence rates. The new criteria and classification of PE will allow for continued research into the diverse phenomenology, etiology and pathogenesis of the disease to be conducted. While the absolute pathophysiology and true prevalence of PE remains unclear, developing a better understanding of the true prevalence of the disease will allow for the completion of more accurate analysis and treatment of the disease.

  5. Epidemiology of Ciguatera in Florida.

    Science.gov (United States)

    Radke, Elizabeth G; Reich, Andrew; Morris, John Glenn

    2015-08-01

    Ciguatera is the most commonly reported marine food-borne illness worldwide. Because there is a biological plausibility that ciguatera may be impacted by long-term climate variability and Florida is on the northern border of the geographic distribution of ciguatera, it is important to update our understanding of its epidemiology in Florida. We performed an analysis of 291 reports in Florida from 2000 to 2011 and an e-mail survey of 5,352 recreational fishers to estimate incidence and underreporting and identify high risk demographic groups, fish types, and catch locations. Incidence was 5.6 per 100,000 adjusted for underreporting. Hispanics had the highest incidence rate (relative risk [RR] = 3.4) and were more likely to eat barracuda than non-Hispanics. The most common catch locations for ciguatera-causing fish were the Bahamas and Florida Keys. Cases caused by fish from northern Florida were infrequent. These results indicate that ciguatera incidence is higher than estimated from public health reports alone. There is little evidence that incidence or geographic range has increased because of increased seawater temperatures since earlier studies. © The American Society of Tropical Medicine and Hygiene.

  6. Foot burns: epidemiology and management.

    Science.gov (United States)

    Hemington-Gorse, S; Pellard, S; Wilson-Jones, N; Potokar, T

    2007-12-01

    This is a retrospective study of the epidemiology and management of isolated foot burns presenting to the Welsh Centre for Burns from January 1998 to December 2002. A total of 289 were treated of which 233 were included in this study. Approximately 40% were in the paediatric age group and the gender distribution varied dramatically for adults and children. In the adult group the male:female ratio was 3.5:1, however in the paediatric group the male:female ratio was more equal (1.6:1). Scald burns (65%) formed the largest group in children and scald (35%) and chemical burns (32%) in adults. Foot burns have a complication rate of 18% and prolonged hospital stay. Complications include hypertrophic scarring, graft loss/delayed healing and wound infection. Although isolated foot burns represent a small body surface area, over half require treatment as in patients to allow for initial aggressive conservative management of elevation and regular wound cleansing to avoid complications. This study suggests a protocol for the initial acute management of foot burns. This protocol states immediate referral of all foot burns to a burn centre, admission of these burns for 24-48 h for elevation, regular wound cleansing with change of dressings and prophylactic antibiotics.

  7. Epidemiology of sporotrichosis in Venezuela.

    Science.gov (United States)

    Mata-Essayag, Sofia; Delgado, Alejandro; Colella, Maria T; Landaeta-Nezer, Maria E; Rosello, Arantza; Perez de Salazar, Celina; Olaizola, Carolina; Hartung, Claudia; Magaldi, Sylvia; Velasquez, Etna

    2013-08-01

    Sporotrichosis is one of the most common subcutaneous mycoses in Venezuela. It is a granulomatous chronic infection with cutaneous or subcutaneous tissue lesions. Regional lymphatic involvement may be present; extracutaneous disease is rare. The causal fungus Sporothrix schenckii has been isolated from soil, vegetation, and animals on numerous occasions and in many localities throughout the world. The aim of this study is to describe clinical and epidemiological features of cases of sporotrichosis observed in Venezuela and review of the literature. We included the demographic data, clinical features, diagnostic methods, treatment, and follow-up of patients with sporotrichosis from 1963 to 2009, diagnosed at the Department of Medical Mycology. One-hundred and thirty-three sporotrichosis cases were diagnosed. Most patients were under the age of 30 years (66.15%). In 61.6% of them, the mode of transmission was not identified. The predominant clinical form in this population was lymphocutaneous (63.15%). Direct microscopic diagnosis was performed in 123 cases, and 57.9% yielded positive results for asteroid body. Sporotrichosis is an endemic subcutaneous mycosis in Venezuela. There are no reports to this date of disseminated forms of the disease, even amongst patients with acquired immunodeficiency syndrome. Direct microscopic examination of wet mount slides with saline solution or distilled water in the search for asteroid bodies is paramount. Saturated sodium and potassium iodine solutions continue to be extremely efficacious and affordable to most of our patients, therefore our treatment of choice. © 2013 The International Society of Dermatology.

  8. Epidemiology of cancer in children

    International Nuclear Information System (INIS)

    Greenberg, R.S.; Shuster, J.L. Jr.

    1985-01-01

    The epidemiologic features of cancers among children have stimulated abundant descriptive and analytic investigation. The descriptive work has demonstrated consistent differences in the incidence rates of these cancers by anatomic site, age, race, and gender. It is clear that the various forms of cancer during childhood have distinctive patterns of occurrence. To a large extent, the characteristic population distributions of these diseases may represent differences in the underlying etiologic processes. Analytic studies of cancer during childhood have addressed possible genetic and environmental risk factors for these diseases. The demonstration of cancers induced by transplacental exposure to diethylstilbestrol has confirmed the speculation that the prenatal environment may influence subsequent carcinogenesis. Although possible leukemogenic effects of intrauterine diagnostic irradiation remain controversial, the issue may become unimportant clinically as prenatal irradiation is replaced by other diagnostic modalities (194). To date, studies of prenatal ultrasound have provided no evidence of an overall excess of subsequent malignancies. Postnatal exposure to high doses of irradiation is known to produce considerable excesses of leukemias and other cancers. At present, there are insufficient data available to reach a firm conclusion on the possible carcinogenic effects of exposure during childhood to low doses of irradiation, fringe magnetic fields, or chemicals

  9. Epidemiology of radiogenic breast cancer

    International Nuclear Information System (INIS)

    Howe, G.R.

    1984-01-01

    The primary objective of epidemiologic studies of radiogenic breast cancer is to use empirical data from human populations exposed to radiation, in order to delineate increases in risk of breast cancer as a function of the radiation characteristics and the characteristics of the women exposed. In addition, such empirical data may be used to test hypotheses concerning the biological mechanism of radiation-induced breast cancer, and this mechanism in turn may serve as a useful model both for other radiogenic solid tumors, and for breast tumors induced by other carcinogens. Specifically, the objective may be formulated in terms of developing an appropriate relatively simple mathematical model, whose functional form may be tested and whose parameters may be estimated from the relevant human data. It is necessary to derive such a model, both because of the sampling instability of estimates based on small subgroups of populations and also because observations may not be available in populations with the characteristics of interest. These latter two restrictions are exemplified by the problem of estimating an increase in risk for individuals with relatively small exposures, and the problem of estimating lifetime risk

  10. TFOS DEWS II Epidemiology Report.

    Science.gov (United States)

    Stapleton, Fiona; Alves, Monica; Bunya, Vatinee Y; Jalbert, Isabelle; Lekhanont, Kaevalin; Malet, Florence; Na, Kyung-Sun; Schaumberg, Debra; Uchino, Miki; Vehof, Jelle; Viso, Eloy; Vitale, Susan; Jones, Lyndon

    2017-07-01

    The subcommittee reviewed the prevalence, incidence, risk factors, natural history, morbidity and questionnaires reported in epidemiological studies of dry eye disease (DED). A meta-analysis of published prevalence data estimated the impact of age and sex. Global mapping of prevalence was undertaken. The prevalence of DED ranged from 5 to 50%. The prevalence of signs was higher and more variable than symptoms. There were limited prevalence studies in youth and in populations south of the equator. The meta-analysis confirmed that prevalence increases with age, however signs showed a greater increase per decade than symptoms. Women have a higher prevalence of DED than men, although differences become significant only with age. Risk factors were categorized as modifiable/non-modifiable, and as consistent, probable or inconclusive. Asian ethnicity was a mostly consistent risk factor. The economic burden and impact of DED on vision, quality of life, work productivity, psychological and physical impact of pain, are considerable, particularly costs due to reduced work productivity. Questionnaires used to evaluate DED vary in their utility. Future research should establish the prevalence of disease of varying severity, the incidence in different populations and potential risk factors such as youth and digital device usage. Geospatial mapping might elucidate the impact of climate, environment and socioeconomic factors. Given the limited study of the natural history of treated and untreated DED, this remains an important area for future research. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Snowboard traumatology: an epidemiological study.

    Science.gov (United States)

    Pigozzi, F; Santori, N; Di Salvo, V; Parisi, A; Di-Luigi, L

    1997-06-01

    In the past 10 years, snowboarding has become a popular winter sport among young people, and the number of accidents has increased proportionately. The incidence of traumas from snowboarding is shown to be 4 to 6 for every 1000 medical examinations, which is similar to that of downhill skiing. However, other important statistical differences exist between the two sports. This study of 106 snowboarding-related injury cases analyzes the epidemiology of these injuries in Italy. Results found that 45.1% of injuries are located in the upper limbs and that significant advantages are obtained with the introduction of guards to protect the upper limbs during descent. Serious ligament injuries to the knee are more rare in snowboarding than in downhill skiing. In both sports, injuries are more common with rigid boots, which lead to a higher incidence of injury to the upper limbs. Finally, a high percentage of injury to beginners was found in this study. Training courses for those who are considering taking up the sport of snowboarding could significantly lower their risk of trauma.

  12. [Epidemiology of pain in Gabon].

    Science.gov (United States)

    Nzoghe Nguema, Pierre; Ngaka Nsafu, D

    2004-01-01

    The authors report on a prospective survey which took place from January 1999 to December 2000 - the epidemiology of pain in Gabon - to determine its distribution in the population. Ninety-eight women and eighty-four men aged 17 to 80 years old (mean age: 50) who consulted at the pain clinic were included in the study, a majority of the patients being aged between 21 and 60 years. Lower back pains and gonalgias secondary to osteo-arthritis or arthritis were more common in the North of the country, where the patients represented 57.7% of the sample, these two previous localisations along with cephalagias accounting for 52.7% of the motives for the visits. Thoracic and abdominal pains common in both men and women in the South were psychological. Patients working in the tertiary sector represented 45.3% of the patients, those of the secondary sector 24.4%, and those of the primary 20.3%. The non-steroidal anti-inflammatory analgesics (NSAI) associated with WHO grade 1 and 2 analgesics were effective in 50% of cases, some of whom also needed steroidal articular infiltration. Psychological pains were soothed by amitriptyline. A specific training of doctors and paramedics in pain treatment is necessary to improve care and assistance in this area. Copyright John Libbey Eurotext 2003.

  13. Epidemiological features of brain tumors

    Directory of Open Access Journals (Sweden)

    Živković Nenad

    2013-01-01

    Full Text Available Brain tumors account for 1.4% of all cancers and 2.4% of all cancer-related deaths. The incidence of brain tumors varies and it is higher in developed countries of Western Europe, North America, Australia and New Zealand. In Serbia, according to data from 2009, malignant brain tumors account for 2. 2 of all tumors, and from all cancer­related deaths, 3.2% is caused by malignant brain tumors. According to recent statistical reports, an overall incidence of brain tumors for benign and malignant tumors combined is 18.71 per 100,000 persons/year. The most common benign brain tumor in adults is meningioma, which is most present in women, and the most common malignant tumor is glioblastoma, which is most present in adult men. Due to high mortality, especially in patients diagnosed with glioblastoma and significant brain tumor morbidity, there is a constant interest in understanding its etiology in order to possibly prevent tumor occurrence in future and enable more efficient treatment strategies for this fatal brain disease. Despite the continuously growing number of epidemiological studies on possible factors of tumor incidence, the etiology remains unclear. The only established environmental risk factor of gliomas is ionizing radiation exposure. Exposure to radiofrequency electromagnetic fields via cell phone use has gained a lot of attention as a potential risk factor of brain tumor development. However, studies have been inconsistent and inconclusive, so more definite results are still expected.

  14. One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions.

    Science.gov (United States)

    Mueller, Linda; Bertelli, Claire; Pillonel, Trestan; Salamin, Nicolas; Greub, Gilbert

    2017-06-01

    Amoeba-resisting microorganisms raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion, and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year. Despite a low number of mutations, the virus showed a genome reduction of 3.7% after 12 months. Lausannevirus genome evolution in sympatric conditions was investigated by its co-culture with Estrella lausannensis, an obligate intracellular bacterium, in the amoeba A. castellanii during one year. Cultures were split every 3 months. Genome sequencing revealed that in these conditions both, Lausannevirus and E. lausannensis, show stable genome, presenting no major rearrangement. In fact, after one year they acquired from 2 to 7 and from 4 to 10 mutations per culture for Lausannevirus and E. lausannensis, respectively. Interestingly, different mutations in the endonuclease encoding genes of Lausannevirus were observed in different subcultures, highlighting the importance of this gene product in the replication of Lausannevirus. Conversely, mutations in E. lausannensis were mainly located in a gene encoding for a phosphoenolpyruvate-protein phosphotransferase (PtsI), implicated in sugar metabolism. Moreover, in our conditions and with our analyses we detected no horizontal gene transfer during one year of co-culture. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  16. Genomics and fish adaptation

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2015-12-01

    Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

  17. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  18. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  19. Genomic definition of species

    Energy Technology Data Exchange (ETDEWEB)

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  20. Structural genomics in endocrinology

    NARCIS (Netherlands)

    Smit, J. W.; Romijn, J. A.

    2001-01-01

    Traditionally, endocrine research evolved from the phenotypical characterisation of endocrine disorders to the identification of underlying molecular pathophysiology. This approach has been, and still is, extremely successful. The introduction of genomics and proteomics has resulted in a reversal of