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Sample records for survey ngs 1st

  1. NGS Survey Control Map

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

  2. AIDS. 1st annual George H. Gallup Memorial Survey.

    Science.gov (United States)

    1988-06-01

    Acquired immunodeficiency syndrome (AIDS) was selected as the subject for the 1st annual George H Gallup Memorial Survey. This survey, conducted in August 1987-April 1988 in 35 countries, measured the level of awareness of AIDS, the extent of concern about AIDS, knowledge, changes in behavior resulting form the AIDS epidemic, and attitudes toward people with AIDS. Overall, the poll's findings attest to the effectiveness of the health education efforts of governmental and nongovernmental organizations. Awareness that AIDS poses an urgent international health problem was almost universal in the 35 samples. In about half of these countries, AIDS was identified as the most important national health problem; in the remaining countries, AIDS was ranked 2nd to cancer. The proportion of respondents expressing a fear of personally contracting the AIDS virus ranged from lows of under 10% in most of Europe to a high of 45% among South African blacks. A majority of respondents in the US, Colombia, the Philippines, Brazil, Nigeria, Ecuador, El Salvador, and Chile believed that AIDS will soon spread beyond current risk groups to the general population. Despite widespread awareness of the grave threat posed by AIDS, insufficient numbers of respondents reported that they had made specific behavioral changes intended to protect themselves form HIV infection. Overall, about half of those interviewed indicated they are now more cautious in their choice of sexual partners; similarly, about half are using condoms more or for the 1st time.

  3. Stress and mental health problems in 1st year medical students: a survey of two medical colleges in Kanpur, India

    Directory of Open Access Journals (Sweden)

    Shivendra Jena

    2015-01-01

    Full Text Available Background: Incidence of stress among medical students has been reported to be between high and very high. Medical students in pre-clinical phase are more likely to develop psychological distress than medical students in clinical phase. It may affect academic performance and lead to anxiety, depression and substance abuse. Methods: First year students of one government medical college and one private medical college of Kanpur, Uttar Pradesh, India, were surveyed to find out stress and mental health problems shortly after their admission. Results: The two colleges showed difference in the frequencies of a number of factors- current stress, sleep problem, sad mood, both parents working, parents giving sufficient time, non-participation in extra-curricular activities, sharing problem with their families, having break-up in a romantic relationship and poor relationships with classmates and roommate. More students of the government medical college reported to have current stress compared to the students of the private medical college. While all students of the government medical who had stress since admission did not recover from it, 55.56% of students of the private medical college recovered from it at the time of our survey. Conclusion: a Psychiatry Department of every medical college should be involved in screening 1st year students having stress and mental health problems and managing them. b Medical education should be imparted in more relaxed and fun filled manner to help students cope with the long and difficult course. [Int J Res Med Sci 2015; 3(1.000: 130-134

  4. NOS/NGS activities to support development of radio interferometric surveying techniques

    Science.gov (United States)

    Carter, W. E.; Dracup, J. F.; Hothem, L. D.; Robertson, D. S.; Strange, W. E.

    1980-01-01

    National Geodetic Survey activities towards the development of operational geodetic survey systems based on radio interferometry are reviewed. Information about the field procedures, data reduction and analysis, and the results obtained to date is presented.

  5. National Geodetic Survey (NGS) Geodetic Control Stations, (Horizontal and/or Vertical Control), March 2009

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  6. NgsRelate

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    . Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.pop gen.dk/software. CONTACT: ida...

  7. NgsRelate

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    be called with high certainty. RESULTS: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account....... Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.pop gen.dk/software. CONTACT: ida...

  8. A Survey on Knowledge and Attitude of Rational Use of Antibiotics on Predesigned Proforma among Interns and 1st year Postgraduate Students’

    Directory of Open Access Journals (Sweden)

    Dr.Poonam Patel

    2016-08-01

    Full Text Available BACKGROUND-In the present era we are facing the major problem called antibiotics resistance. Appropriate knowledge of antibiotics of medical student can greatly help to combat this problem. Keeping these points in mind we have planned the study to assess the knowledge, attitude and practice of antibiotics prescribing among the medical student and sensitizing the student regarding antibiotics resistance. METHODOLOGY- In this study, 181students (interns and 1st year PG resident were included to participate in the questionnaire survey on students’ knowledge, attitude and practice toward antibiotic usage. The forms were collected immediately after completion. RESULT-total 181 students participated. Our study reveal that attitude, behaviour towards prescribing antibiotics and awareness of students for antibiotics resistance are adequate but they have less knowledge about clinical situation faced in wards and OPD. 98.34% student says yes to get more education about antibiotics. 94.47% student says yes for sensitization program to be scheduled every 3-5yrs for all the doctors regarding rational use of antibiotics CONCLUSION-This study shows that there is a need for interventions (like strict antibiotics policy, scheduled antibiotics sensitization programme, integrated teaching that support rational use of antibiotics.

  9. NGS Absolute Gravity Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Absolute Gravity data (78 stations) was received in July 1993. Principal gravity parameters include Gravity Value, Uncertainty, and Vertical Gradient. The...

  10. 2013 NOAA National Geodetic Survey (NGS) LIDAR of New Jersey: Barnegat Light Integrated Ocean and Coastal Mapping Product

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  11. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    Science.gov (United States)

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation.

  12. Airborne Gravity Data Enhances NGS Experimental Gravimetric Geoid in Alaska

    Science.gov (United States)

    Holmes, S. A.; Childers, V. A.; Li, X.; Roman, D. R.

    2014-12-01

    The U.S. National Geodetic Survey [NGS], through their Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, continues to update its gravimetry holdings by flying new airborne gravity surveys over a large fraction of the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field by using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Several airborne campaigns have already been flown over Alaska and its coastline. Some of this Alaskan coastal data have been incorporated into a new NGS experimental geoid model - xGEOID14. The xGEOID14 model is the first in a series of annual experimental geoid models that will incorporate NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques by which the airborne and land-survey data are filtered and cleaned, and then combined with satellite gravity models, elevation data (etc.) with the ultimate aim of computing a geoid model that can support a national physical height system by 2022. Here we will examine the NGS GRAV-D airborne data in Alaska, and assess its contribution to xGEOID14. Future prospects for xGEOID15 will also be considered.

  13. NGS-based deep bisulfite sequencing.

    Science.gov (United States)

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  14. Toward Better Oversight of NGS Tests.

    Science.gov (United States)

    2016-09-01

    The FDA has published two draft guidance documents aimed at streamlining its oversight of tests based on next-generation sequencing (NGS). One contains preliminary recommendations addressing the analytic validity of NGS-based tests for hereditary diseases; the other explains how test developers can obtain official recognition of their genetic variant databases, potentially speeding marketing clearance or approval.

  15. 76 FR 77208 - Affirmation of Vertical Datum for Surveying and Mapping Activities for the Islands of St. Croix...

    Science.gov (United States)

    2011-12-12

    ...: National Geodetic Survey (NGS), National Ocean Service (NOS), National Oceanic and Atmospheric... (NOS), National Geodetic Survey (NGS), has completed the definition and implementation of VIVD09... monuments is available in digital form, from the NGS Web site:...

  16. National Geodetic Survey's Airport Aerial Photography

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The National Geodetic Survey (NGS), formerly part of the U.S. Coast and Geodetic Survey, has been performing Aeronautical surveys since the 1920's. NGS, in...

  17. CDC WONDER: Population - Bridged-Race July 1st Estimates

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Population - Bridged-Race July 1st Estimates online databases report bridged-race population estimates of the July 1st resident population of the United States,...

  18. Estimating inbreeding coefficients from NGS data

    DEFF Research Database (Denmark)

    Vieira, Filipe Garrett; Fumagalli, Matteo; Albrechtsen, Anders;

    2013-01-01

    Most methods for Next-Generation Sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy-Weinberg Equilibrium (HWE) as a prior. However, many organisms including domesticated, partially selfing or with asexual life cycles show strong...... deviations from HWE. For such species, and specially for low coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual beforecalling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an Expectation...

  19. 1st Applied Electromagnetic International Conference

    CERN Document Server

    Othman, Mohd; Aziz, Mohamad; Malek, Mohd

    2015-01-01

    In this book, experts from academia and industry present the latest advances in scientific theory relating to applied electromagnetics and examine current and emerging applications particularly within the fields of electronics, communications, and computer technology. The book is based on presentations delivered at APPEIC 2014, the 1st Applied Electromagnetic International Conference, held in Bandung, Indonesia in December 2014. The conference provided an ideal platform for researchers and specialists to deliver both theoretically and practically oriented contributions on a wide range of topics relevant to the theme of nurturing applied electromagnetics for human technology. Many novel aspects were addressed, and the contributions selected for this book highlight the relevance of advances in applied electromagnetics to a variety of industrial engineering problems and identify exciting future directions for research.

  20. Statistical modelling of spatio-temporal dependencies in NGS data

    NARCIS (Netherlands)

    Ranciati, Saverio

    2016-01-01

    Next-generation sequencing (NGS) heeft zich snel gevestigd als de huidige standaard in de genetische analyse. Deze omschakeling van microarray naar NGS vereist nieuwe statistische strategieën om de onderzoeksvragen aan te pakken. Ten eerste, NGS data bestaat uit discrete waarnemingen, meestal gekenm

  1. The potential of whole genome NGS for infectious disease diagnosis.

    Science.gov (United States)

    Lecuit, Marc; Eloit, Marc

    2015-01-01

    Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.

  2. The CERN Neutrino beam to Gran Sasso (NGS)

    CERN Document Server

    Bailey, R; Ball, A E; Bonnal, P; Buhler-Broglin, Manfred; Détraz, C; Elsener, Konrad; Ereditato, A; Faugeras, Paul E; Ferrari, A; Fortuna, G; Grant, A L; Guglielmi, A M; Hilaire, A; Hübner, Kurt; Jonker, M; Kissler, Karl Heinz; López-Hernandez, L A; Maugain, J M; Migliozzi, P; Palladino, Vittorio; Pietropaolo, F; Revol, Jean Pierre Charles; Sala, P R; Sanelli, C; Stevenson, Graham Roger; Vassilopoulos, N; Vincke, H H; Weisse, E; Wilhemsson, M

    1999-01-01

    The conceptual technical design of the NGS (CERN neutrino beam to Gran Sasso) facility has been presented in the report CERN 98-02 / INFN-AE/98-05. Additional information, in particular an update on various neutrino beam options for the NGS facility, has been provided in a memorandum to the CERN-SPSC Committee (CERN-SPSC/98-35). In the present report, further improvements on the NGS design and performance, in particular new scenarios for SPS proton cycles for NGS operation and a new version of the NGS "high energy" neutrino beam for nt appearance experiments, are described. This new NGS reference beam is estimated to provide three times more nt events per year than the beam presented in the 1998 report. The radiological aspects of the NGS facility have been re-examined with the new beam design. An updated version of the construction schedule is also presented.

  3. An Assessment of Airborn Gravimetry Collected under the NGS GRAV-D Project

    Science.gov (United States)

    Holmes, S. A.

    2009-12-01

    In the United States, the National Geodetic Survey [NGS] holds the official charter to maintain the vertical datum for the USA and its territories. This includes the responsibility to maintain a current geoid model for transforming between orthometric (H) and geodetic (h) heights. The latest (2009) NGS geoid model incorporates the latest GRACE-based satellite-only geopotential solutions, very-high-resolution digital elevation models [DEMs] derived from the Shuttle Radar Topography Mission [SRTM], and other additional data and processing improvements. This recent geoid model also benefited greatly from the prior release of the National Geospatial-Intelligence Agency’s [NGA] Earth Gravitational Model 2008 [EGM2008], which served as a computational reference field for the new geoid, but was also particularly useful for identifying and removing corrupted data from the NGS gravimetry database. Looking forwards, NGS intends to increase its efforts to refine and improve its future national geoid models. To this end, their ambitious "Gravity for the Re-definition of the American Datum” [GRAV-D] project aims to update the NGS gravimetry holdings by flying new airborn gravity surveys over a large fraction of the USA and it territories. Concurrent efforts will focus on developing new processing techniques for optimally incorporating improved gravimetry into the final geoid solution. To this end, the GRAV-D team has already flown several surveys in the Gulf of Mexico, Puerto Rico, US Virgin Islands, and Alaska. Testing and analysis aimed at calibrating and validating the preliminary survey data is already underway. The latest assessment of these recent efforts, including the extent to which this new data can be expected to contribute to an improved gravimetric geoid model, is presented here.

  4. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis.

    Science.gov (United States)

    Ruark, Elise; Renwick, Anthony; Clarke, Matthew; Snape, Katie; Ramsay, Emma; Elliott, Anna; Hanks, Sandra; Strydom, Ann; Seal, Sheila; Rahman, Nazneen

    2016-01-01

    To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 730 sites; 409 sites with variants and 321 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 286 indel variants and 275 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.

  5. Identification and characterization of two novel cytosolic sulfotransferases, SULT1 ST7 and SULT1 ST8, from zebrafish

    Energy Technology Data Exchange (ETDEWEB)

    Liu, T.-A. [Department of Pharmacology, College of Pharmacy, University of Toledo, Toledo, OH 43606 (United States); Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan (China); Bhuiyan, Shakhawat [Division of Arts and Sciences, Jarvis Christian College, Hawkins, TX 75765 (United States); Snow, Rhodora [School of Mathematics and Science, J. Sargeant Reynolds Community College, Richmond, VA 23285 (United States); Yasuda, Shin; Yasuda, Tomoko [Department of Pharmacology, College of Pharmacy, University of Toledo, Toledo, OH 43606 (United States); Yang, Y.-S. [Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan (China); Williams, Frederick E.; Liu, M.-Y.; Suiko, Masahito [Department of Pharmacology, College of Pharmacy, University of Toledo, Toledo, OH 43606 (United States); Carter, Glendora [School of Mathematics and Science, J. Sargeant Reynolds Community College, Richmond, VA 23285 (United States); Liu, M.-C. [Department of Pharmacology, College of Pharmacy, University of Toledo, Toledo, OH 43606 (United States)], E-mail: ming.liu@utoledo.edu

    2008-08-29

    Cytosolic sulfotransferases (SULTs) constitute a family of Phase II detoxification enzymes that are involved in the protection against potentially harmful xenobiotics as well as the regulation and homeostasis of endogenous compounds. Compared with humans and rodents, the zebrafish serves as an excellent model for studying the role of SULTs in the detoxification of environmental pollutants including environmental estrogens. By searching the expressed sequence tag database, two zebrafish cDNAs encoding putative SULTs were identified. Sequence analysis indicated that these two putative zebrafish SULTs belong to the SULT1 gene family. The recombinant form of these two novel zebrafish SULTs, designated SULT1 ST7 and SULT1 ST8, were expressed using the pGEX-2TK glutathione S-transferase (GST) gene fusion system and purified from transformed BL21 (DE3) cells. Purified GST-fusion protein form of SULT1 ST7 and SULT1 ST8 exhibited strong sulfating activities toward environmental estrogens, particularly hydroxylated polychlorinated biphenyls (PCBs), among various endogenous and xenobiotic compounds tested as substrates. pH-dependence experiments showed that SULT1 ST7 and SULT1 ST8 displayed pH optima at 6.5 and 8.0, respectively. Kinetic parameters of the two enzymes in catalyzing the sulfation of catechin and chlorogenic acid as well as 3-chloro-4-biphenylol were determined. Developmental expression experiments revealed distinct patterns of expression of SULT1 ST7 and SULT1 ST8 during embryonic development and throughout the larval stage onto maturity.

  6. EMSL Quarterly Highlights Report: 1st Quarter, Fiscal Year 2009

    Energy Technology Data Exchange (ETDEWEB)

    Showalter, Mary Ann; Kathmann, Loel E.; Manke, Kristin L.

    2009-02-02

    The EMSL Quarterly Highlights Report covers the science, staff and user recognition, and publication activities that occurred during the 1st quarter (October 2008 - December 2008) of Fiscal Year 2009.

  7. Electronic Health Records Place 1st at Indy 500

    Science.gov (United States)

    ... Navigation Bar Home Current Issue Past Issues EHR Electronic Health Records Place 1st at Indy 500 Past ... last May's Indy 500 had thousands of personal Electronic Health Records on hand for those attending—and ...

  8. EMSL Quarterly Highlights Report: 1st Quarter, FY08

    Energy Technology Data Exchange (ETDEWEB)

    Showalter, Mary Ann

    2008-01-28

    The EMSL Quarterly Highlights Report covers the science, staff and user recognition, and publication activities that occurred during the 1st quarter (October 2007 - December 2007) of Fiscal Year 2008.

  9. Texas Reports 1st Likely Case of Local Zika Infection

    Science.gov (United States)

    ... html Texas Reports 1st Likely Case of Local Zika Infection Woman had no travel-related risk factors, ... reported its first possible case of locally transmitted Zika infection on Monday. If confirmed, Texas would join ...

  10. FDA OKs 1st Drug to Treat Duchenne Muscular Dystrophy

    Science.gov (United States)

    ... html FDA OKs 1st Drug to Treat Duchenne Muscular Dystrophy Exondys 51 seems to fill unmet need ... the first drug for a rare form of muscular dystrophy. Exondys 51 (eteplirsen) was granted accelerated approval ...

  11. Geodetic Control Points, Approx 3 mile survey grade GPS grid incorporating NGS and Davenport & Bettendorf existing control (re-occupied), Published in 2005, 1:600 (1in=50ft) scale, Scott County.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Geodetic Control Points dataset, published at 1:600 (1in=50ft) scale, was produced all or in part from Field Survey/GPS information as of 2005. It is described...

  12. NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

    Science.gov (United States)

    May, Ali; Abeln, Sanne; Buijs, Mark J; Heringa, Jaap; Crielaard, Wim; Brandt, Bernd W

    2015-07-01

    Massively parallel sequencing of microbial genetic markers (MGMs) is used to uncover the species composition in a multitude of ecological niches. These sequencing runs often contain a sample with known composition that can be used to evaluate the sequencing quality or to detect novel sequence variants. With NGS-eval, the reads from such (mock) samples can be used to (i) explore the differences between the reads and their references and to (ii) estimate the sequencing error rate. This tool maps these reads to references and calculates as well as visualizes the different types of sequencing errors. Clearly, sequencing errors can only be accurately calculated if the reference sequences are correct. However, even with known strains, it is not straightforward to select the correct references from databases. We previously analysed a pyrosequencing dataset from a mock sample to estimate sequencing error rates and detected sequence variants in our mock community, allowing us to obtain an accurate error estimation. Here, we demonstrate the variant detection and error analysis capability of NGS-eval with Illumina MiSeq reads from the same mock community. While tailored towards the field of metagenomics, this server can be used for any type of MGM-based reads. NGS-eval is available at http://www.ibi.vu.nl/programs/ngsevalwww/.

  13. Orthogonal NGS for High Throughput Clinical Diagnostics.

    Science.gov (United States)

    Chennagiri, Niru; White, Eric J; Frieden, Alexander; Lopez, Edgardo; Lieber, Daniel S; Nikiforov, Anastasia; Ross, Tristen; Batorsky, Rebecca; Hansen, Sherry; Lip, Va; Luquette, Lovelace J; Mauceli, Evan; Margulies, David; Milos, Patrice M; Napolitano, Nichole; Nizzari, Marcia M; Yu, Timothy; Thompson, John F

    2016-04-19

    Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.

  14. CRCDA--Comprehensive resources for cancer NGS data analysis.

    Science.gov (United States)

    Thangam, Manonanthini; Gopal, Ramesh Kumar

    2015-01-01

    Next generation sequencing (NGS) innovations put a compelling landmark in life science and changed the direction of research in clinical oncology with its productivity to diagnose and treat cancer. The aim of our portal comprehensive resources for cancer NGS data analysis (CRCDA) is to provide a collection of different NGS tools and pipelines under diverse classes with cancer pathways and databases and furthermore, literature information from PubMed. The literature data was constrained to 18 most common cancer types such as breast cancer, colon cancer and other cancers that exhibit in worldwide population. NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization. Pipelines for variant detection, quality control and data analysis were listed to provide out-of-the box solution for NGS data analysis, which may help researchers to overcome challenges in selecting and configuring individual tools for analysing exome, whole genome and transcriptome data. An extensive search page was developed that can be queried by using (i) type of data [literature, gene data and sequence read archive (SRA) data] and (ii) type of cancer (selected based on global incidence and accessibility of data). For each category of analysis, variety of tools are available and the biggest challenge is in searching and using the right tool for the right application. The objective of the work is collecting tools in each category available at various places and arranging the tools and other data in a simple and user-friendly manner for biologists and oncologists to find information easier. To the best of our knowledge, we have collected and presented a comprehensive package of most of the resources available in cancer for NGS data analysis. Given these factors, we believe that this website will be an useful resource to the NGS research community working on cancer. Database URL: http://bioinfo.au-kbc.org.in/ngs/ngshome.html.

  15. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  16. Analysis of stresses on the 1st phase support of the monitoring drifts of the radioactive waste repository

    Directory of Open Access Journals (Sweden)

    Hatala Jozef

    1999-09-01

    Full Text Available In the paper, the stability analysis of the radioactive waste repository monitoring drifts’ support by means of the numerical modelling - finite element method is described. The aim of this analysis was to judge to what extent the designed 1st phase support’s parameters correspond with the geomechanical conditions determined by the engineering-geological survey.

  17. Proceedings of the 1st LAK Data Challenge

    NARCIS (Netherlands)

    d'Aquin, Mathieu; Dietze, Stefan; Drachsler, Hendrik; Herder, Eelco; Taibi, Davide

    2013-01-01

    d'Aquin, M., Dietze, S., Drachsler, H., Herder, E., & Taibi, D. (Eds.) (2013, April). Proceedings of the 1st LAK Data Challenge, held at LAK 2013, the Third Conference on Learning Analytics and Knowledge. Published by CEUR Workshop Proceedings, 2013, Vol. 974.

  18. MULTIPLE OSSIFIED COSTAL CARTILAGES FOR 1ST RIB

    Directory of Open Access Journals (Sweden)

    Raghavendra D.R.

    2014-12-01

    Full Text Available Costal cartilages are flattened bars of hyaline cartilages. All ribs except the last two, join with the sternum through their respective costal cartilages directly or indirectly. During dissection for 1st MBBS students in the Department of Anatomy, JJMMC, Davangere, variation was found in a male cadaver aged 45 –50 years. Multiple ossified costal cartilages for 1st rib were present on left side. There were 3 costal cartilages connecting 1st rib to manubrium. There were two small intercostal spaces between them. The lower two small costal cartilages fused together to form a common segment which in turn fused with large upper costal cartilage. The large upper costal cartilage forms costochondral joint with 1st rib. All costal cartilages showed features of calcification. The present variation of multiple ossified costal cartilages are due to bifurcation of costal cartilage. It may cause musculoskeletal pain, intercostal nerve entrapment or vascular compression. Awareness of these anomalies are important for radiologists for diagnostic purpose and for surgeons for performing various clinical and surgical procedures.

  19. RESTAURANT AND CAFETERIA SERVICES ARRANGEMENTS FOR MAY 1ST, 2001

    CERN Multimedia

    Restaurant Supervisory Committee

    2001-01-01

    1. Restaurants As Tuesday, May 1st, is an official CERN holiday, restaurants no 2 (DSR : Bldg. 504 - Meyrin) and no 3 (Avenance : Bldg. 866 - Prévessin) will be closed as from Monday, April 30 at 18h00. They will reopen on Wednesday, May 2nd at 6h30 (rest. no 2) and at 7h00 (rest. no 3). On May 1st, a limited service will be provided by restaurant no. 1 (COOP : Bldg. 501 - Meyrin) from 8h00 to 21h00 with hot meals served from 11h30 to 14h00 and from 18h00 to 19h30. 2. Satellite cafétérias All satellite cafétérias will be closed on May 1st. They will all operate normally on Monday, April 30, except for buildings 17 (Meyrin), 865 and 892 (Prévessin) which will be closed. 3. Newspaper stand The newspaper kiosque in building 501 will be closed on May 1st.

  20. Evaluation of the 1st DIGIT field trial

    OpenAIRE

    Lund, Mass Soldal; Bogya, Emese Lujza

    2008-01-01

    This report evaluates the 1st DIGIT field trial, a security risk analysis conducted for Santander in the autumn of 2007. The evaluation includes lessons learned from the analysis and an empirical investigation into the use of the CORAS language in the analysis.

  1. 1st International Workshop on Learning Analytics and Linked Data

    NARCIS (Netherlands)

    Drachsler, Hendrik; Dietze, Stefan; Greller, Wolfgang; D'Aquin, Mathieu; Jovanovich, Jelena; Pardo, Abelardo; Reinhardt, Wolfgang; Verbert, Katrien

    2012-01-01

    Drachsler, H., Dietze, S., Greller, W., D'Aquin, M., Jovanovic, J., Pardo, A., Reinhardt, W., & Verbert, K. (2012). 1st International Workshop on Learning Analytics and Linked Data. In S. Dawson, C. Haythornthwaite, S. Buckingham Shum, D. Gasevic, & R. Fergusson (Eds.), LAK '12 Proceedings of the

  2. The Use of GOCE/GRACE Information in the Latest NGS xGeoid15 Model for the USA

    Science.gov (United States)

    Holmes, S. A.; Li, X.; Youngman, M.

    2015-12-01

    The U.S. National Geodetic Survey [NGS], through its Gravity for the Redefinition of the American Vertical Datum [GRAV-D] program, is flying airborne gravity surveys over the USA and its territories. By 2022, NGS intends that all orthometric heights in the USA will be determined in the field using a reliable national gravimetric geoid model to transform from geodetic heights obtained from GPS. Towards this end, all available airborne data has been incorporated into a new NGS experimental geoid model - xGEOID15. The xGEOID15 model is the second in a series of annual experimental geoid models that incorporates NGS GRAV-D airborne data. This series provides a useful benchmark for assessing and improving current techniques, to ultimately compute a geoid model that can support a national physical height system by 2022. Here, we focus on the combination of the latest GOCE/GRACE models with the terrestrial gravimetry (land/airborne) that was applied for xGeoid15. Comparisons against existing combination gravitational solutions, such as EGM2008 and EIGEN6C4, as well as recent geoid models, such as xGeoid14 and CGG2013, are interesting for what they reveal about the respective use of the GOCE/GRACE satgrav information.

  3. 75 FR 57263 - New Policy Announcing That Traditional Horizontal Survey Projects Performed With Terrestrial...

    Science.gov (United States)

    2010-09-20

    ... Into NGS Databases AGENCY: National Geodetic Survey (NGS), National Ocean Service (NOS), National..., 2011 the National Geodetic Survey (NGS) will cease accepting data, all orders and classes, from... September 1984 ``Standards and Specifications for Geodetic Control Networks'' for inclusion into the...

  4. RESTAURANT and CAFETERIA SERVICES: ARRANGEMENTS for MAY 1st, 2003

    CERN Multimedia

    2003-01-01

    1. Restaurants As Thursday, May 1st, is an official CERN holiday, restaurants no. 2 (DSR : Bldg. 504 - Meyrin) and no. 3 (Avenance : Bldg. 866 - Prévessin) will be closed as from Wednesday, April 30 at 18h00. They will reopen on Friday, May 2nd at 6h30 (rest. no. 2) and at 7h00 (rest. no. 3). On May 1st, a limited service will be provided by restaurant no. 1 (COOP : Bldg. 501 - Meyrin) from 8h00 to 21h00 with hot meals served from 11h30 to 14h00 and from 18h00 to 19h30. 2. Newspaper stand The newspaper kiosque run by restaurant no. 1 in building 501 will be closed. 3. Decentralised services No decentralised services (satellite cafétérias etc.) will operate on May 1st, but will resume their normal activites on Friday, May 2nd, except for those dependent on restaurant no. 3 (Prévessin site) which will not reopen until Monday, May 5, 2003.

  5. [Granuloma Gravidarum in a 37-year-old 1st Gravida, 1st Para--A Case Report].

    Science.gov (United States)

    Findeklee, S

    2015-10-01

    The granuloma gravidarum is a rare benign tumour with gingival origin. It occurs in circa 0.2% of pregnancies. Mostly we see an asymptomatic course of disease terminated by hormonal changes after delivery. If the granuloma is associated with complaints of the pregnant woman, for example masticational pain or recurrent bleedings, therapeutic options are conservative therapy, surgery or delivery. We report the case of a 37-year-old 1st gravida, 1st para who had an induced delivery in the 39+2 gestational week because of a symptomatic granuloma gravidarum. We saw a spontaneous remission of the granuloma within 3 months post partum. The case report underlines the importance of suitable information for pregnant women about oral hygiene and the necessity of regular dental controls during pregnancy for prophylaxis of granuloma gravidarum.

  6. Precise GPS ephemerides from DMA and NGS tested by time transfer

    Science.gov (United States)

    Lewandowski, Wlodzimierz W.; Petit, Gerard; Thomas, Claudine

    1992-01-01

    It was shown that the use of the Defense Mapping Agency's (DMA) precise ephemerides brings a significant improvement to the accuracy of GPS time transfer. At present a new set of precise ephemerides produced by the National Geodetic Survey (NGS) has been made available to the timing community. This study demonstrates that both types of precise ephemerides improve long-distance GPS time transfer and remove the effects of Selective Availability (SA) degradation of broadcast ephemerides. The issue of overcoming SA is also discussed in terms of the routine availability of precise ephemerides.

  7. 2014 NOAA NGS Topobathy Lidar: Connecticut

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  8. NGS catalog: A database of next generation sequencing studies in humans.

    Science.gov (United States)

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2012-06-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits.

  9. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. II - Surface photometry

    Science.gov (United States)

    Cutri, Roc M.; Low, Frank J.; Guhathakurta, Puragra

    1993-01-01

    In this paper we present a method to calibrate surface photometry of faint sources measured from direct photographic plates, such as those of the NGS/POSS and ESO/SRC Sky Survey. This calibration procedure does not require scanning sensitometer spots on the plates, but instead uses measurements of the brightness profiles of many faint stars of known brightness to fit a linearized approximation to the characteristic curve. The approximation is valid for only low- to medium-density emulsions, so this technique is appropriate only for relatively faint emission. Comparison between measurements of representative extended sources on the NGS/POSS and CCD images indicates that surface photometry can be obtained from the Sky Survey plates accurate to 0.1-0.3 mag in the range mu(B) between 23 and 27 and mu(R) between 22 and 26 mag/sq arcsec.

  10. Stress study in 1st year medical students

    OpenAIRE

    Ranade, Amita; Kulkarni, Ganesh; Dhanumali, Sameer

    2015-01-01

    As stress is a very common feature in medical students, we performed a cross-sectional study in 1st year medical students to know the prevalence of stress in students, severity of stress & to find the symptoms associated with stress. A pre-designed & pre-tested questionnaire was distributed to 60 students (31 girls & 29 boys) randomly selected. After analyzing the data in the questionnaires, we found that major cases of stress were stress of school performance, stress of school/le...

  11. The 1st All-Russian Workshop on Archaeoastronomy

    Science.gov (United States)

    Bochkarev, Nikolai G.

    2007-08-01

    The 1st All-Russia Workshop on Archaeoastronomy “Astronomical and World-Outlook Meaning of the Archaeological Monuments of South Ural” was held on June 19-25, 2006, at the ground of the archaeological center “Arkaim” (Chelyabinsk Region). Besides about 30 talks, astronomical measurements were performed at two archaeological objects under intensive study: Arkaim Site (Bronze Epoch, XVIII-XVI c. B.C.) and tumuli “with whiskers” complex Kondurovsky (V-VIII c. A.D.). The promising character of the megalithic complex on the Vera Island (Lake Turgoyak) was stated.

  12. Proceedings of the 1st symposium on advanced science research

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-09-01

    The 1st symposium on advanced science research was held in Tokai-mura, Ibaraki-ken, on 23-24 March, 1995, under the auspices of JAERI. Two hundred and sixty scientists attended the symposium; over 40% of the attendants were from universities and laboratories outside JAERI. This proceedings consists of 6 oral presentations of the research activities in the Advanced Science Research Center, 70 poster presentations on the field of basic science from both the inside and outside of JAERI and 2 panel discussions on the actinide physics and biocrystallography. (author).

  13. 2003 - 2004 ACADEMIC TRAINING PROGRAMME 1st TERM

    CERN Multimedia

    Françoise Benz

    2003-01-01

    1st TERM 29 September to 19 December 2003 REGULAR LECTURE PROGRAMME (Renewable) Energy Policy in the EU Members States and the Accession States By D. Reiche, Free University of Berlin, D 13, 14, 15, 16, 17 October LECTURES SERIES FOR POSTGRADUATE STUDENTS Introduction to QCD By B. Webber, CERN-TH 20, 21, 22, 23, 24 October The lectures are open to all those interested, without application. The abstract of the lectures, as well as any change to the above information (title, dates, time, place etc) will be published in the CERN Bulletin, the WWW, and by notices before each term and for each series of lectures.

  14. Structural thermal model tests on exposed facility of Japanese experiment module for international space station `Alpha`. 1st Report. Static load/fluid loop performance test and modal survey; Kokusai uchu station `Alpha` JEM bakurobu no netsukozo model shiken. 1. Seikaju shiken, ryudo tokusei shiken oyoboi modal survey

    Energy Technology Data Exchange (ETDEWEB)

    Mizuno, M.; Nakao, K.; Ikami, T.; Arafune, K.; Nakahara, S. [Ishikawajima-Harima Heavy Industries Co. Ltd., Tokyo (Japan)

    1995-03-01

    Static load/fluid loop performance test and modal survey results among structural thermal model (STM) tests of an exposed facility are reported for the Japanese Experiment Module (JEM) mounted on the international space station `Alpha`. In the static load test, the strength and rigidity of STM were ascertained to be reasonable against the loads applied to the facility at launch and reentry, and the structural mathematical model was also reasonable based on the comparison between test and analytical results. In the fluid performance test to verify the fundamental fluid loop performance of the thermal control system for the exposed facility, the test results on pressure losses of STM which has a strong effect on the accuracy of coolant fluid distribution at each branch point, well agreed with analytical ones. In the modal survey to verify dynamic characteristics of the structural mathematical model, some appropriate modal parameters were obtained by modal analysis of test data, and the survey results also well agreed with analytical ones on the structural mathematical model. 1 ref., 10 figs., 2 tabs.

  15. Estimating IBD tracts from low coverage NGS data

    DEFF Research Database (Denmark)

    Garrett Vieira, Filipe Jorge; Albrechtsen, Anders; Nielsen, Rasmus

    2016-01-01

    that the new method provides a marked increase in accuracy even at low coverage. AVAILABILITY AND IMPLEMENTATION: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM CONTACT: fgvieira@snm.ku.dk SUPPLEMENTARY...

  16. Geodetic Survey Water Level Observations

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Over one million images of National Coast & Geodetic Survey (now NOAA's National Geodetic Survey/NGS) forms captured from microfiche. Tabular forms and charts...

  17. NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

    OpenAIRE

    Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

    2012-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages a...

  18. 1st International Conference on Advancements of Medical Electronics

    CERN Document Server

    Bag, Sandip; Ganguly, Karabi; Sarkar, Indranath; Biswas, Papun

    2015-01-01

    The book is a collection of peer-reviewed scientific papers submitted by active researchers in the 1st International Conference on Advancements of Medical Electronics (ICAME2015). The conference is organized jointly by the Department of Biomedical Engineering and Electronics and Communication Engineering, JIS College of Engineering, West Bengal, India. The primary objective of the conference is to strengthen interdisciplinary research and its applications for the welfare of humanity. A galaxy of academicians, professionals, scientists, statesman and researchers from different parts of the country and abroad got together and shared their knowledge. The book presents research articles of medical image processing & analysis, biomedical instrumentation & measurements, DSP & clinical applications, embedded systems & its applications in healthcare. The book can be referred as a tool for further research.

  19. 1st Workshop of the Canadian Society for Virology

    Science.gov (United States)

    McCormick, Craig; Grandvaux, Nathalie

    2017-01-01

    The 1st Workshop of the Canadian Society for Virology (CSV2016) was a Special Workshop of the 35th Annual Meeting for the American Society for Virology, held on 18 June 2016 on the beautiful Virginia Tech campus in Blacksburg, Virginia. The workshop provided a forum for discussion of recent advances in the field, in an informal setting conducive to interaction with colleagues. CSV2016 featured two internationally-renowned Canadian keynote speakers who discussed translational virology research; American Society for Virology President Grant McFadden (then from University of Florida, now relocated to Arizona State University) who presented his studies of oncolytic poxviruses, while Matthew Miller (McMaster University) reviewed the prospects for a universal influenza vaccine. The workshop also featured a variety of trainee oral and poster presentations, and a panel discussion on the topic of the future of the CSV and virus research in Canada. PMID:28335511

  20. 1st International Conference on Communication and Computer Engineering

    CERN Document Server

    Othman, Mohd; Othman, Mohd; Rahim, Yahaya; Pee, Naim

    2015-01-01

    This book covers diverse aspects of advanced computer and communication engineering, focusing specifically on industrial and manufacturing theory and applications of electronics, communications, computing, and information technology. Experts in research, industry, and academia present the latest developments in technology, describe applications involving cutting-edge communication and computer systems, and explore likely future directions. In addition, access is offered to numerous new algorithms that assist in solving computer and communication engineering problems. The book is based on presentations delivered at ICOCOE 2014, the 1st International Conference on Communication and Computer Engineering. It will appeal to a wide range of professionals in the field, including telecommunication engineers, computer engineers and scientists, researchers, academics, and students.

  1. 1st International Conference on Calcined Clays for Sustainable Concrete

    CERN Document Server

    Favier, Aurélie

    2015-01-01

    This volume focuses on research and practical issues linked to Calcined Clays for Sustainable Concrete. The main subjects are geology of clays, hydration and performance of blended systems with calcined clays, alkali activated binders, economic and environmental impacts of the use of calcined clays in cement based materials. Topics addressed in this book include the influence of processing on reactivity of calcined clays, influence of clay mineralogy on reactivity, geology of clay deposits, Portland-calcined clay systems, hydration, durability, performance, Portland-calcined clay-limestone systems, hydration, durability, performance, calcined clay-alkali systems, life cycle analysis, economics and environmental impact of use of calcined clays in cement and concrete, and field applications. This book compiles the different contributions of the 1st International Conference on Calcined Clays for Sustainable Concrete, which took place in Lausanne, Switzerland, June, 23-25, 2015.The papers present the latest  res...

  2. 1st International Conference on Computational and Experimental Biomedical Sciences

    CERN Document Server

    Jorge, RM

    2015-01-01

    This book contains the full papers presented at ICCEBS 2013 – the 1st International Conference on Computational and Experimental Biomedical Sciences, which was organized in Azores, in October 2013. The included papers present and discuss new trends in those fields, using several methods and techniques, including active shape models, constitutive models, isogeometric elements, genetic algorithms, level sets, material models, neural networks, optimization, and the finite element method, in order to address more efficiently different and timely applications involving biofluids, computer simulation, computational biomechanics, image based diagnosis, image processing and analysis, image segmentation, image registration, scaffolds, simulation, and surgical planning. The main audience for this book consists of researchers, Ph.D students, and graduate students with multidisciplinary interests related to the areas of artificial intelligence, bioengineering, biology, biomechanics, computational fluid dynamics, comput...

  3. 1st International Conference on Robot Intelligence Technology and Applications

    CERN Document Server

    Matson, Eric; Myung, Hyun; Xu, Peter

    2013-01-01

    In recent years, robots have been built based on cognitive architecture which has been developed to model human cognitive ability. The cognitive architecture can be a basis for intelligence technology to generate robot intelligence. In this edited book the robot intelligence is classified into six categories: cognitive intelligence, social intelligence, behavioral intelligence, ambient intelligence, collective intelligence and genetic intelligence. This classification categorizes the intelligence of robots based on the different aspects of awareness and the ability to act deliberately as a result of such awareness. This book aims at serving researchers and practitioners with a timely dissemination of the recent progress on robot intelligence technology and its applications, based on a collection of papers presented at the 1st International Conference on Robot Intelligence Technology and Applications (RiTA), held in Gwangju, Korea, December 16-18, 2012. For a better readability, this edition has the total 101 ...

  4. 1st Latin American Congress on Automation and Robotics

    CERN Document Server

    Baca, José; Moreno, Héctor; Carrera, Isela; Cardona, Manuel

    2017-01-01

    This book contains the proceedings of the 1st Latin American Congress on Automation and Robotics held at Panama City, Panama in February 2017. It gathers research work from researchers, scientists, and engineers from academia and private industry, and presents current and exciting research applications and future challenges in Latin American. The scope of this book covers a wide range of themes associated with advances in automation and robotics research encountered in engineering and scientific research and practice. These topics are related to control algorithms, systems automation, perception, mobile robotics, computer vision, educational robotics, robotics modeling and simulation, and robotics and mechanism design. LACAR 2017 has been sponsored by SENACYT (Secretaria Nacional de Ciencia, Tecnologia e Inovacion of Panama).

  5. Next generation sequencing (NGS): a golden tool in forensic toolkit.

    Science.gov (United States)

    Aly, S M; Sabri, D M

    2015-01-01

    The DNA analysis is a cornerstone in contemporary forensic sciences. DNA sequencing technologies are powerful tools that enrich molecular sciences in the past based on Sanger sequencing and continue to glowing these sciences based on Next generation sequencing (NGS). Next generation sequencing has excellent potential to flourish and increase the molecular applications in forensic sciences by jumping over the pitfalls of the conventional method of sequencing. The main advantages of NGS compared to conventional method that it utilizes simultaneously a large number of genetic markers with high-resolution of genetic data. These advantages will help in solving several challenges such as mixture analysis and dealing with minute degraded samples. Based on these new technologies, many markers could be examined to get important biological data such as age, geographical origins, tissue type determination, external visible traits and monozygotic twins identification. It also could get data related to microbes, insects, plants and soil which are of great medico-legal importance. Despite the dozens of forensic research involving NGS, there are requirements before using this technology routinely in forensic cases. Thus, there is a great need to more studies that address robustness of these techniques. Therefore, this work highlights the applications of forensic sciences in the era of massively parallel sequencing.

  6. T1/ST2 promotes T helper 2 cell activation and polyfunctionality in bronchopulmonary mycosis.

    Science.gov (United States)

    Piehler, D; Grahnert, A; Eschke, M; Richter, T; Köhler, G; Stenzel, W; Alber, G

    2013-03-01

    Interleukin (IL)-33 enhances T helper (Th)2 immunity via its receptor T1/ST2. Infection with the yeast-like pathogen Cryptococcus neoformans is usually controlled by a Th1-mediated immune response. The mechanisms responsible for nonprotective Th2 immunity leading to allergic inflammation in pulmonary cryptococcosis are still not fully understood. Using a murine pulmonary model of C. neoformans infection, we report that T1/ST2 expression correlates with the intensity of Th2 activation, as demonstrated by the expression of CD25 and CD44 and downregulation of CD62L. Antigen-specific T1/ST2(+) Th cells are the primary source of the Th2 cytokines IL-5 and IL-13 as compared with wild-type T1/ST2(-) Th cells or Th cells from T1/ST2(-/-) mice. In addition, T1/ST2(+) Th cells almost exclusively contain bi- and trifunctional Th2 cytokine-producing Th cells compared with T1/ST2(-) Th cells or Th cells from T1/ST2(-/-) mice. Finally, T1/ST2-driven Th2 development resulted in defective pulmonary fungal control. These data demonstrate that T1/ST2 directs Th2 cell activation and polyfunctionality in allergic bronchopulmonary mycosis.

  7. 1st Advanced Marine Renewable Energy Instrumentation Experts Workshop

    Energy Technology Data Exchange (ETDEWEB)

    none,

    2011-10-01

    The U.S. marine energy industry is actively pursuing development of offshore wind and marine hydrokinetic (MHK) energy systems. Experience in the wind energy sector demonstrates that new technology development requires thorough measurement and characterization of the environmental conditions prevalent at installation sites and of technology operating in the field. Presently, there are no turn-key instrumentation system solutions that meet the measurement needs of the marine energy industry. The 1st Advanced Marine Renewable Energy Instrumentation Experts Workshop brought together technical experts from government laboratories, academia, and industry representatives from marine energy, wind, offshore oil and gas, and instrumentation developers to present and discuss the instrumentation needs of the marine energy industry. The goals of the meeting were to: 1. Share the latest relevant knowledge among technical experts; 2. Review relevant state-of-the-art field measurement technologies and methods; 3. Review lessons learned from recent field deployments; 4. Identify synergies across different industries; 5. Identify gaps between existing and needed instrumentation capabilities; 6. Understand who are the leading experts; 7. Provide a forum where stakeholders from the marine energy industry could provide substantive input in the development of new marine energy field deployable instrumentation packages.

  8. National Geodetic Control Stations, Geographic NAD83, NGS (2004) [geodetic_ctrl_point_la_NGS_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  9. The National Geochemical Survey - database and documentation

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS, in collaboration with other federal and state government agencies, industry, and academia, is conducting the National Geochemical Survey (NGS) to produce...

  10. The National Geochemical Survey - database and documentation

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS, in collaboration with other federal and state government agencies, industry, and academia, is conducting the National Geochemical Survey (NGS) to produce a...

  11. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

    OpenAIRE

    Jian Li; Aarif Mohamed Nazeer Batcha; Björn Grüning; Mansmann, Ulrich R.

    2016-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic ...

  12. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.

    Science.gov (United States)

    Li, Jian; Batcha, Aarif Mohamed Nazeer; Grüning, Björn; Mansmann, Ulrich R

    2015-01-01

    Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.

  13. NGS WFSs module for MAORY at E-ELT

    Science.gov (United States)

    Esposito, S.; Agapito, G.; Antichi, J.; Bonanno, A.; Carbonaro, L.; Giordano, C.; Spanò, P.

    We report on the natural guide star (NGS) wavefront sensors (WFS) module for MAORY, the multi-cojugate adaptive optics (MCAO) system for the ESO E-ELT. Three low-order, near-infrared (H-band), Shack-Hartmann sensors provide fast acquisition of the first 5 modes (tip, tilt, focus, astigmatism) on 3 natural guide stars over a 160 arcsec field of view. Three moderate-order (20x20), visible (600-800 nm), pyramid WFSs provide the slow Truth sensing to correct LGS wavefront estimates of low-order modes. These sensors are mounted onto three R-theta stages to patrol the field of view. The module is also equipped with a retractable, on-axis, high-order (80x80), visible, pyramid WFS for the single-conjugate AO (SCAO) mode of MAORY and MICADO. The visible WFSs share the same 80x80 pyramid WFS design. This choice enables also a MCAO NGS capability. Simulations show that Strehl ratios (SR) over 40% are reached with MCAO and three, 2x2 sub-apertures, NIR low-order WFSs working with H-mag=20 reference stars. In SCAO mode, 90% SR for a 8mag stars with a contrast down to 10-5, and 45% SR for a 16mag star, are achieved.

  14. IPv6与下一代服务(NGS)

    Institute of Scientific and Technical Information of China (English)

    雷振洲

    2005-01-01

    大家知道现在我们都在走PSTN电信网络NGN,下一代Internet就是NGI,移动网要走向3G/B3G.那么他们为什么要走向NGS,实际上特别是上个世纪90年代的移动通信告诉我们现在的网络不能适应将来的要求,为什么?互联网的大发展说明人对信息的需求、对数据的需求、对未来更有价值的服务应用的需求越来越高.移动的大发展说明移动性对个性化对无所不在的需求是越来越强烈了.

  15. Clinical validation of NGS technology for HLA: An early adopter's perspective.

    Science.gov (United States)

    Weimer, Eric T

    2016-10-01

    Clinical validation of NGS for HLA typing has been a topic of interest with many laboratories investigating the merits. NGS has proven effective at reducing ambiguities and costs while providing more detailed information on HLA genes not previously sequenced. The ability of NGS to multiplex many patients within a single run presents unique challenges and sequencing new regions of HLA genes requires application of our knowledge of genetics to accurately determine HLA typing. This review represents my laboratory's experience in validation of NGS for HLA typing. It describes the obstacles faced with validation of NGS and is broken down into pre-analytic, analytic, and post-analytic challenges. Each section includes solutions to address them.

  16. Normal and compound poisson approximations for pattern occurrences in NGS reads.

    Science.gov (United States)

    Zhai, Zhiyuan; Reinert, Gesine; Song, Kai; Waterman, Michael S; Luan, Yihui; Sun, Fengzhu

    2012-06-01

    Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS

  17. The 1st Fermi Lat Supernova Remnant Catalog

    CERN Document Server

    Acero, Fabio; Ajello, Marco; Baldini, Luca; Ballet, Jean; Barbiellini, Guido; Bastieri, Denis; Bellazzini, Ronaldo; Bissaldi, E; Blandford, Roger; Bloom, E D; Bonino, Raffaella; Bottacini, Eugenio; Bregeon, J; Bruel, Philippe; Buehler, Rolf; Buson, S; Caliandro, G A; Cameron, Rob A; Caputo, R; Caragiulo, Micaela; Caraveo, Patrizia A; Casandjian, Jean Marc; Cavazzuti, Elisabetta; Cecchi, Claudia; Chekhtman, A; Chiang, J; Chiaro, G; Ciprini, Stefano; Claus, R; Cohen, J M; Cohen-Tanugi, Johann; Cominsky, L R; Condon, B; Conrad, Jan; Cutini, S; D'Ammando, F; Angelis, A; Palma, F; Desiante, Rachele; Digel, S W; Venere, L; Drell, Persis S; Drlica-Wagner, Alex; Favuzzi, C; Ferrara, E C; Franckowiak, Anna; Fukazawa, Prof Yasushi; Funk, Prof Stefan; Fusco, P; Gargano, Fabio; Gasparrini, Dario; Giglietto, Nicola; Giommi, Paolo; Giordano, Francesco; Giroletti, Marcello; Glanzman, Tom; Godfrey, Gary; Gomez-Vargas, G A; Grenier, I A; Grondin, M -H; Guillemot, L; Guiriec, Sylvain; Gustafsson, M; Hadasch, D; Harding, A K; Hayashida, M; Hays, Elizabeth; Hewitt, J W; Hill, A B; Horan, Deirdre; Hou, X; Iafrate, Giulia; Jogler, Tobias; J'ohannesson, G; Johnson, Anthony S; Kamae, T; Katagiri, Hideaki; Kataoka, Prof Jun; Katsuta, Junichiro; Kerr, Matthew; Knodlseder, J; Kocevski, Prof Dale; Kuss, M; Laffon, Helene; Lande, J; Larsson, S; Latronico, Luca; Lemoine-Goumard, Marianne; Li, J; Li, L; Longo, Francesco; Loparco, Francesco; Lovellette, Michael N; Lubrano, Pasquale; Magill, J; Maldera, S; Marelli, Martino; Mayer, Michael; Mazziotta, M N; Michelson, Peter F; Mitthumsiri, Warit; Mizuno, Tsunefumi; Moiseev, Alexander A; Monzani, Maria Elena; Moretti, E; Morselli, Aldo; Moskalenko, Igor V; Murgia, Prof Simona; Nemmen, Prof Rodrigo; Nuss, Eric; Ohsugi, Takashi; Omodei, Nicola; Orienti, Monica; Orlando, Elena; Ormes, Jonathan F; Paneque, David; Perkins, J S; Pesce-Rollins, Melissa; Petrosian, Prof Vahe'; Piron, Frederic; Pivato, Giovanna; Porter, Troy; Rain`o, S; Rando, Riccardo; Razzano, Massimiliano; Razzaque, Soebur; Reimer, Anita; Reimer, Prof Olaf; Renaud, Matthieu; Reposeur, Thierry; Rousseau, Mr Romain; Parkinson, P M; Schmid, J; Schulz, A; Sgr`o, C; Siskind, Eric J; Spada, Francesca; Spandre, Gloria; Spinelli, Paolo; Strong, Andrew W; Suson, Daniel; Tajima, Hiro; Takahashi, Hiromitsu; Tanaka, T; Thayer, Jana B; Thompson, D J; Tibaldo, L; Tibolla, Omar; Torres, Prof Diego F; Tosti, Gino; Troja, Eleonora; Uchiyama, Yasunobu; Vianello, G; Wells, B; Wood, Kent; Wood, M; Yassine, Manal; Zimmer, Stephan

    2015-01-01

    To uniformly determine the properties of supernova remnants (SNRs) at high energies, we have developed the first systematic survey at energies from 1 to 100 GeV using data from the Fermi Large Area Telescope. Based on the spatial overlap of sources detected at GeV energies with SNRs known from radio surveys, we classify 30 sources as likely GeV SNRs. We also report 14 marginal associations and 245 flux upper limits. A mock catalog in which the positions of known remnants are scrambled in Galactic longitude, allows us to determine an upper limit of 22% on the number of GeV candidates falsely identified as SNRs. We have also developed a method to estimate spectral and spatial systematic errors arising from the diffuse interstellar emission model, a key component of all Galactic Fermi LAT analyses. By studying remnants uniformly in aggregate, we measure the GeV properties common to these objects and provide a crucial context for the detailed modeling of individual SNRs. Combining our GeV results with multiwavele...

  18. Introduction to the 1st International Symposium on Phytochemicals in Medicine and Food (ISPMF 2015).

    Science.gov (United States)

    Zheng, Yafeng; Jassbi, Amir Reza; Xiao, Jianbo

    2016-03-30

    The 1st International Symposium on Phytochemicals in Medicine and Food (ISPMF 2015) was held in Shanghai, China, from June 26th to 29th, 2015. The 1st ISPMF was organized by the Phytochemical Society of Europe (PSE) and the Phytochemical Society of Asia (PSA). More than 270 scientists from 48 countries attended this meeting. The program of ISPMF 2015 consisted of 12 plenary lectures, 20 invited talks, and 55 short oral presentations in 16 sessions, including phytochemistry, phytomedicine, pharmacology, and application of phytochemicals in medicine and food. The 1st ISPMF has obtained support from Critical Reviews in Food Science and Nutrition, Food Chemistry, Phytochemistry Reviews, and Nutrients. As supported by Prof. Thomas F. Hofmann, a special issue on Journal of Agricultural and Food Chemistry (ACS) for the 1st ISPMF was initiated in January 2015.

  19. Feedback Equivalence of 1-dimensional Control Systems of the 1-st Order

    OpenAIRE

    2008-01-01

    The problem of local feedback equivalence for 1-dimensional control systems of the 1-st order is considered. The algebra of differential invariants and criteria for the feedback equivalence for regular control systems are found.

  20. A New Class of Group Field Theories for 1st Order Discrete Quantum Gravity

    OpenAIRE

    Oriti, D; Tlas, T.

    2007-01-01

    Group Field Theories, a generalization of matrix models for 2d gravity, represent a 2nd quantization of both loop quantum gravity and simplicial quantum gravity. In this paper, we construct a new class of Group Field Theory models, for any choice of spacetime dimension and signature, whose Feynman amplitudes are given by path integrals for clearly identified discrete gravity actions, in 1st order variables. In the 3-dimensional case, the corresponding discrete action is that of 1st order Regg...

  1. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  2. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Directory of Open Access Journals (Sweden)

    Ping Qiu

    Full Text Available Genotyping of hepatitis C virus (HCV plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  3. File list: His.Lar.20.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lar.20.AllAg.1st_instar dm3 Histone Larvae 1st instar SRX013009,SRX013088,SRX01...3044,SRX013064,SRX013097 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/His.Lar.20.AllAg.1st_instar.bed ...

  4. File list: His.Lar.50.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  5. File list: ALL.Lar.50.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Lar.50.AllAg.1st_instar dm3 All antigens Larvae 1st instar SRX013009,SRX013072,...SRX013088,SRX013044,SRX013064,SRX013097,SRX013056,SRX013055 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/ALL.Lar.50.AllAg.1st_instar.bed ...

  6. File list: His.Lar.10.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available His.Lar.10.AllAg.1st_instar dm3 Histone Larvae 1st instar SRX013088,SRX013064,SRX01...3044,SRX013009,SRX013097 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/His.Lar.10.AllAg.1st_instar.bed ...

  7. File list: ALL.Lar.10.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  8. File list: ALL.Lar.20.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Lar.20.AllAg.1st_instar dm3 All antigens Larvae 1st instar SRX013009,SRX013072,...SRX013088,SRX013044,SRX013064,SRX013097,SRX013055,SRX013056 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/ALL.Lar.20.AllAg.1st_instar.bed ...

  9. File list: His.Lar.05.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

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  10. File list: ALL.Lar.05.AllAg.1st_instar [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available ALL.Lar.05.AllAg.1st_instar dm3 All antigens Larvae 1st instar SRX013088,SRX013009,...SRX013064,SRX013044,SRX013072,SRX013055,SRX013097,SRX013056 http://dbarchive.biosciencedbc.jp/kyushu-u/dm3/assembled/ALL.Lar.05.AllAg.1st_instar.bed ...

  11. Cas-analyzer: an online tool for assessing genome editing results using NGS data.

    Science.gov (United States)

    Park, Jeongbin; Lim, Kayeong; Kim, Jin-Soo; Bae, Sangsu

    2017-01-15

    Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

  12. Using REDItools to Detect RNA Editing Events in NGS Datasets.

    Science.gov (United States)

    Picardi, Ernesto; D'Erchia, Anna Maria; Montalvo, Antonio; Pesole, Graziano

    2015-03-09

    RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.

  13. [Effectiveness of teaching gerontology and geriatrics in students of the 1st Faculty of Medicine, Charles University in Prague].

    Science.gov (United States)

    Mádlová, P; Neuwirth, J; Topinková, E

    2006-01-01

    Increasing number of seniors in the society requires more university-degree educated professionals--health care professionals, social care workers and managers with basic exposure to and knowledge of gerontology and geriatrics. The aim of our paper was to evaluate the effectiveness of undergraduate training of gerontology and geriatrics among students of the 1st Faculty of Medicine, Charles University in Prague. To get information about knowledge of medical students and students of ergotherapy and physiotherapy and about their attitudes towards senior citizens we conducted a survey using two anonymous questionnaires prepared in our department and piloted earlier. The survey ran during the academic year 2004/2005. Students completed identical questionnaires twice, first time before the start of the clinical rotation and second time after the training end (n=134). Evaluation of knowledge and attitudes confirmed that one to two weeks clinical rotation at Department of Geriatrics was effective and increased knowledge of students in the topic trained. The percentage of correct answers in all three evaluated training programmes increased after the completion of the clinical rotation and reached 83% and more. From 134 participating students, 54.5 % appreciated life experience and wisdom of seniors they met, 98.4 % of students were satisfied with the training programme and 67.2 % of students reported that after training they changed their attitude towards senior population. Our survey confirmed that clinical training in geriatric medicine at 1st Faculty of Medicine, Charles University in Prague, prepared in agreement with current European recommendations is sufficiently effective and well accepted by the students. Therefore we recommend introduction of formal geriatric training for students in all medical faculties in the Czech Republic.

  14. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

    Science.gov (United States)

    Li, Jing-Woei; Bolser, Dan; Manske, Magnus; Giorgi, Federico Manuel; Vyahhi, Nikolay; Usadel, Björn; Clavijo, Bernardo J; Chan, Ting-Fung; Wong, Nathalie; Zerbino, Daniel; Schneider, Maria Victoria

    2013-09-01

    Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

  15. HOW TO DERIVE KEYNESIAN RESULTS FROM 1ST PRINCIPLES - A SURVEY OF NEW-KEYNESIAN ECONOMICS

    NARCIS (Netherlands)

    VANEES, H; GARRETSEN, H

    1993-01-01

    In the 1980s theoretical research in macroeconomics was dominated by what has become known as new-Keynesian economics. The principal aim of new-Keynesian economics is to explain how Keynesian results can be reconciled with the neo-classical principles of utility and profit maximization. This paper

  16. "European Resuscitation Council 2015 burn 1st Aid recommendations-concerns and issues for first responders".

    Science.gov (United States)

    Goodwin, Nicholas S

    2016-08-01

    As the lead author of a recently published systematic review on hydrogel burn dressings in pre-hospital, I was alarmed to read the claim by the authors to the effect no one method of burn wound cooling was superior to any other; "There is no evidence to recommend a specific temperature or method of cooling". The reputation and prominence of the ERC within the circle of resuscitation councils now delving into 1st Aid recommendations leads to the conclusion that misguided recommendations may cause confusion amongst first responders, may falsely misdirect 1st Aid providers to unsupported practices or alternatively create a window of opportunity for marketers or sellers of alternative burn 1st Aid technologies to make unsupported claims in respect of comparable efficacy of their own product versus "traditional" methods.

  17. Excerpts from the 1st international NTNU symposium on current and future clinical biomarkers of cancer

    DEFF Research Database (Denmark)

    Robles, Ana I; Olsen, Karina Standahl; Tsui, Dana W T;

    2016-01-01

    The goal of biomarker research is to identify clinically valid markers. Despite decades of research there has been disappointingly few molecules or techniques that are in use today. The "1st International NTNU Symposium on Current and Future Clinical Biomarkers of Cancer: Innovation and Implement......The goal of biomarker research is to identify clinically valid markers. Despite decades of research there has been disappointingly few molecules or techniques that are in use today. The "1st International NTNU Symposium on Current and Future Clinical Biomarkers of Cancer: Innovation...

  18. 1st and 2nd Trimester Headsize in Fetuses with Congenital Heart Disease: A Cohort Study

    DEFF Research Database (Denmark)

    Lauridsen, Mette Høj; Petersen, Olav Bjørn; Vestergaard, Else Marie

    2014-01-01

    208 fetuses (75%) with presumed non-syndromic CHD were included, 85 (41%) with minor and 123 (59%) with major CHD. Z-scores for head size were analysed. Conclusions: Our preliminary results suggest that Bi-parietal-diameter in children with CHD is within the normal range in the 1st trimester...

  19. The Course of Psychological Disorders in the 1st Year After Cancer Diagnosis

    Science.gov (United States)

    Kangas, Maria; Henry, Jane L.; Bryant, Richard A.

    2005-01-01

    This study investigated the relationship between acute stress disorder (ASD) and posttraumatic stress disorder (PTSD) and comorbid anxiety, depressive, and substance use disorders over the first 12-month period following a cancer diagnosis. Individuals recently diagnosed with 1st onset head and neck or lung malignancy were assessed for ASD within…

  20. 1st ESMO Consensus Conference in lung cancer; Lugano 2010: small-cell lung cancer

    DEFF Research Database (Denmark)

    Stahel, R; Thatcher, N; Früh, M;

    2011-01-01

    The 1st ESMO Consensus Conference on lung cancer was held in Lugano, Switzerland on 21st and 22nd May 2010 with the participation of a multidisciplinary panel of leading professionals in pathology and molecular diagnostics and medical, surgical and radiation oncology. Before the conference, the e...

  1. Perspective through the 1st class innovation award-innovation in the key materials

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Directed by Prof.Litong Zhang (Member of CAS)from Northwestern Polytechnical University, the project on the topic of ceramic matrix composite, which sustains high temperature, resists oxidization, and has a long lifetime,achieved the 1st class National Technology Innovation Award in 2004.

  2. Complex brackets and balanced complex 1st-order difference polynomials in 4-dimensional Minkowski space

    Institute of Scientific and Technical Information of China (English)

    HUANG Lei; LI HongBo

    2008-01-01

    This paper investigates complex brackets and balanced complex 1st-order difference (BCD) polynomials. Then we propose an algorithm of O(nlog n) complexity to check the equality of brackets. It substitutes exponential algorithms before. Also, BCD polynomials have some usages in geometric calculation.

  3. Complex brackets and balanced complex 1st-order difference polynomials in 4-dimensional Minkowski space

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This paper investigates complex brackets and balanced complex 1st-order di?erence (BCD) polynomials. Then we propose an algorithm of O(n log n) complexity to check the equality of brackets. It substitutes exponential algorithms before. Also, BCD polynomials have some usages in geometric calculation.

  4. How Many Attempts Until Success in Some Core 1st. Year Disciplines?

    Science.gov (United States)

    Fernandes, Graça Leão; Andrade e Silva, João; Lopes, Margarida Chagas

    2012-01-01

    Due to a general development in education brought about by democracy, Portugal has witnessed tremendous development in Higher Education (HE) since the beginning of the 1980s. Nevertheless, the percentage of graduates among the Portuguese population still ranks far below most European countries. This is why academic performance in HE 1st cycle…

  5. Proceedings of the 1st Workshop on Technology Support for Self-Organized Learners

    NARCIS (Netherlands)

    Kalz, Marco; Koper, Rob; Hornung-Prähauser, Veronika; Luckmann, Michaela

    2008-01-01

    Kalz, M., Koper, R., Hornung-Prähauser, V., & Luckmann, M. (Eds.) (2008). Proceedings of the 1st Workshop on Technology Support for Self-Organized Learners. June, 2-3, 2008, Salzburg, Austria: CEUR Workshop Proceedings, ISSN 1613-0073. Available at http://ceur-ws.org/Vol-349.

  6. Proceedings of the 1st workshop on aspect reverse-engineering, Delft, 09.11.2004

    NARCIS (Netherlands)

    Tourwé, T.; Bruntink, M.; Marin, A.M.; Shepherd, D.

    2005-01-01

    This technical report contains the papers submitted to and presented at the 1st Workshop on Aspect Reverse-Engineering, held in conjunction with the 11th Working Conference on Reverse Engineering (WCRE), in Delft, The Netherlands. The aims of this workshop was to bring together researchers and pract

  7. Analysis of Historical Materiel Return Program (MRP) Credits at the 1st Marine Logistics Group Reparable Issue Point (RIP)

    Science.gov (United States)

    2011-12-01

    MATERIEL RETURN PROGRAM ( MRP ) CREDITS AT THE 1ST MARINE LOGISTICS GROUP REPARABLE ISSUE POINT (RIP) by Edward M. Caricato John D. Draper...Materiel Return Program ( MRP ) Credits at the 1st Marine Logistics Group Reparable Issue Point (RIP) 6. AUTHOR(S) Edward M. Caricato and John D. Draper...unlimited 12b. DISTRIBUTION CODE A 13. ABSTRACT (maximum 200 words) Materiel Returns Program ( MRP ) credits have increased 1st Marine

  8. QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.

    Science.gov (United States)

    Wagle, Prerana; Nikolić, Miloš; Frommolt, Peter

    2015-07-01

    Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive amounts of data remains challenging. Since multiple algorithmic approaches for the basic data analysis have been developed, there is now an increasing need to efficiently use these tools to obtain results in reasonable time. We have developed QuickNGS, a new workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. We demonstrate the efficiency of our new software by a comprehensive analysis of 10 RNA-Seq samples which we can finish in only a few minutes of hands-on time. The approach we have taken is suitable to process even much larger numbers of samples and multiple projects at a time. Our approach considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

  9. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11.

    Science.gov (United States)

    Castro-Fernández, Cristina; Arias, Manuel; Blanco-Arias, Patricia; Santomé-Collazo, Luis; Amigo, Jorge; Carracedo, Ángel; Sobrido, Maria-Jesús

    2015-06-01

    Next generation sequencing (NGS) is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  10. NGS-Trex: an automatic analysis workflow for RNA-Seq data.

    Science.gov (United States)

    Boria, Ilenia; Boatti, Lara; Saggese, Igor; Mignone, Flavio

    2015-01-01

    RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. Here we describe the complete analysis of sample data from raw sequences to data mining of results by using NGS-Trex platform, a low user interaction, fully automatic analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome of the samples identifying expressed genes, transcripts, and new and known splice variants. It also detects differentially expressed genes and transcripts across different experiments.

  11. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11

    Directory of Open Access Journals (Sweden)

    Cristina Castro-Fernández

    2015-06-01

    Full Text Available Next generation sequencing (NGS is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  12. KNIME4NGS: a comprehensive toolbox for Next Generation Sequencing analysis.

    Science.gov (United States)

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Werner Mewes, H-; Küffner, Robert

    2017-01-09

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME.

  13. 2014 NOAA NGS Topobathy Lidar: Post Sandy, Rhode Island

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  14. Airborne Gravity: NGS' Gravity Data for EN08 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Vermont, New Hampshire, Massachusettes, Maine, and Canada collected in 2013 over 1 survey. This data set is part of the Gravity...

  15. Airborne Gravity: NGS' Gravity Data for EN01 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Canada, and Lake Ontario collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  16. Airborne Gravity: NGS' Gravity Data for CS01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alabama and Florida collected in 2008 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical...

  17. Airborne Gravity: NGS' Gravity Data for CN02 (2013 & 2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Nebraska collected in 2013 & 2014 over 3 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical...

  18. 2014 NOAA NGS Lidar: Intracoastal Waterway, Florida Keys (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  19. Airborne Gravity: NGS' Gravity Data for CS03 (2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas and Louisiana collected in 2009 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical...

  20. 2013 NOAA NGS Topobathy Lidar: Great Egg (NJ)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  1. Airborne Gravity: NGS' Gravity Data for EN09 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Massachusetts, Connecticut, Rhode Island, New Hampshire, New York, and the Atlantic Ocean collected in 2012 over 1 survey. This data set is...

  2. Airborne Gravity: NGS' Gravity Data for TS01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Puerto Rico and the Virgin Islands collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  3. Airborne Gravity: NGS' Gravity Data for EN04 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Michigan and Lake Huron collected in 2012 over 1 survey. This data set is part of the Gravity for the Re-definition of the American...

  4. Airborne Gravity: NGS' Gravity Data for AN03 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  5. Airborne Gravity: NGS' Gravity Data for EN06 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine, Canada, and the Atlantic Ocean collected in 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the...

  6. Airborne Gravity: NGS' Gravity Data for EN05 (2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Minnesota, Wisconsin, and Michigan collected in 2012 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  7. Airborne Gravity: NGS' Gravity Data for EN10 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, New Jersey, Connecticut and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the...

  8. Airborne Gravity: NGS' Gravity Data for PN01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for California and Oregon collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical...

  9. Airborne Gravity: NGS' Gravity Data for ES01 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida, the Bahamas, and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of...

  10. Airborne Gravity: NGS' Gravity Data for CN03 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Nebraska collected in 2014 over one survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  11. 2014 NOAA NGS Topobathy Lidar: Post Sandy, Rhode Island

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  12. 2015 NOAA NGS Topobathy Lidar: Buzzards Bay (MA)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ880G system. The data...

  13. 2013 NOAA NGS Topobathy Lidar: Little Egg (NJ)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  14. Airborne Gravity: NGS' Gravity Data for ES03 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maryland, Pennsylvania, New Jersey, West Virginia, Virginia, Delaware, and the Atlantic Ocean collected in 2013 over 1 survey. This data...

  15. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    Directory of Open Access Journals (Sweden)

    Cañizares Joaquin

    2011-06-01

    Full Text Available Abstract Background The possibilities offered by next generation sequencing (NGS platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

  16. Genetic Architecture of Milk, Fat, Protein, Mastitis and Fertility Studied using NGS Data in Holstein Cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Janss, Luc; Guldbrandtsen, Bernt;

    cattle using NGS variants. The analysis was done using a linear mixed model (LMM) and a Bayesian mixture model (BMM). The top 10 QTL identified by LMM analyses explained 22.61, 23.86, 10.88, 18.58 and 14.83% of the total genetic variance for these traits respectively. Trait-specific sets of 4,964 SNPs...... from NGS variants (most ‘associated’ SNP for each 0.5 Mbp bin) explained 81.0, 81.6, 85.0, 60.4 and 70.9% of total genetic variance for milk, fat, protein, mastitis and fertility indices when analyzed simultaneously by BMM...

  17. Proceedings of the 1st Nordic Optimization Symposium - 10th Nordic MPS meeting, Copenhagen 2006

    DEFF Research Database (Denmark)

    Clausen, Jens; Jørgensen, Rene Munk; Kohl, Niklas;

    2006-01-01

    On behalf of the Technical University of Denmark, the Danish Operations Research Society and the Nordic Section of the Mathematical Programming Society we welcome you to Copenhagen and the 1st Nordic Optimization Symposium - the 10th meeting of the Nordic MPS. The meetings of the Nordic MPS have...... an enjoyable 1st Nordic Optimization Symposium (10th Nordic MPS meeting) in Copenhagen....... to add a new title, that reflects the much broader field that is our playground at these meetings. Still the odd trustworthy title “Meeting of the Nordic MPS” has been maintained to demonstrate the origin of the symposium. It is our hope that future Nordic MPS meetings will carry on using this “double...

  18. The 1st of April 2470 BC Total Solar Eclipse Seen by the Prophet Ibraheem

    Science.gov (United States)

    Yousef, S. M.

    The Holy Quran describes a phenomenon seen by young Abraham that can only fit a solar eclipse. Two criteria were given for this particular eclipse; first only one planet was seen as soon as it got dark and second no corona was seen. In order to justify the first selection rule, examinations of solar and planetary longitudes for total solar eclipses passing over Babel were carried out. Only the eclipse of the 1st of April 2470 BC meets this condition, as it was only Venus that was seen at that eclipse. The second selection rule was also naturally fulfilled, as Babel happened to be on the border of the totality zone hence no corona was seen, however all the time the moon glistened as Baily's beads. There is no doubt that the prophet Abraham witnessed the 1st of April total solar eclipse that passed over Babel. This will put him about 470 years backward than it was previously anticipated.

  19. Proceedings of the 1st CIRP Seminar on Micro and Nano Technology

    DEFF Research Database (Denmark)

    Hansen, Hans Nørgaard; Alting, Leo

    2003-01-01

    The present Proceedings of the 1st International CIRP Seminar on Micro and Nano Technology is the result of a CIRP initiative taken by the Working Group on Micro/Nano Technology established in 2002. The CIRP initiative is a recognition of the large potentials that micro/nano technology has...... in improving/enhancing many of the existing products and in forming the basis of a long range of new next generation of products. Micro and nano technology are common phrases used to describe phenomena, components, products etc. related to small dimensions, usually based on functioning principles...... accessible to a large group of customers. Therefore, product development and manufacture is very essential. Therefore this 1st CIRP Seminar represents an important milestone for design and industrial manufacture of products based on micro and nano technology. The Proceedings cover mostly new, interesting...

  20. Idaho National Laboratory Quarterly Performance Analysis - 1st Quarter FY2015

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Lisbeth A. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-03-01

    This report is published quarterly by the Idaho National Laboratory (INL) Quality and Performance Management Organization. The Department of Energy (DOE) Occurrence Reporting and Processing System (ORPS), as prescribed in DOE Order 232.2, “Occurrence Reporting and Processing of Operations Information,” requires a quarterly analysis of events, both reportable and not reportable, for the previous 12 months. This report is the analysis of 73 reportable events (27 from the 1St Qtr FY-15 and 46 from the prior three reporting quarters), as well as 38 other issue reports (including nine not reportable events and Significant Category A and B conditions reported during the1st Qtr FY-15) identified at INL during the past 12 months.

  1. A New Class of Group Field Theories for 1st Order Discrete Quantum Gravity

    CERN Document Server

    Oriti, Daniele

    2007-01-01

    Group Field Theories, a generalization of matrix models for 2d gravity, represent a 2nd quantization of both loop quantum gravity and simplicial quantum gravity. In this paper, we construct a new class of Group Field Theory models, for any choice of spacetime dimension and signature, whose Feynman amplitudes are given by path integrals for clearly identified discrete gravity actions, in 1st order variables. In the 3-dimensional case, the corresponding discrete action is that of 1st order Regge calculus for gravity (generalized to include higher order corrections), while in higher dimensions, they correspond to a discrete BF-theory (again, generalized to higher order) with an imposed orientation restriction on hinge volumes, similar to that characterizing discrete gravity. The new models shed also light on the large distance or semi-classical approximation of spin foam models. This new class of group field theories may represent a concrete unifying framework for loop quantum gravity and simplicial quantum grav...

  2. Development of repair mechanism of FSX-414 based 1st stage nozzle of gas turbine

    Science.gov (United States)

    Rahman, Md. Tawfiqur

    2017-06-01

    This paper describes the failure mechanism and repair technology of 1st stage nozzle or vane of industrial gas turbine which is made of cobalt based super alloy FSX-414. 1st stage nozzles or vanes are important stationery components of gas turbine based power plant. Those are the parts of hot gas path components of gas turbine and their manufacturing process is casting. At present, it is widely accepted that gas turbine based combined cycle power plant is the most efficient and cost effective solution to generate electricity. One of the factors of high efficiency of this type of gas turbine is the increase of its turbine inlet temperature. As an effect of this factor and in conjunction with some other factors, the 1st stage nozzle of gas turbine operates under extremely high temperature and thermal stresses. As a result, the design lifetime of these components becomes limited. Furthermore, attention on nozzles or vanes is required in order to achieve their design lifetime. However, due to unfriendly operational condition and environmental effect, anytime failure can occur on these heat resistant alloy based components which may lead to severe damage of gas turbine. To mitigate these adverse effects, schedule maintenance is performed on a predetermined time interval of hot gas path components of gas turbine based power plant. This paper addresses common failures in gas turbine's 1st stage nozzles or vanes. Usually these are repaired by using ADH process but for several reasons ADH process is not used here. Hence the challenging task is performed using gas tungsten arc welding which is presented in this article systematically.

  3. Aedes aegypti pharate 1st instar quiescence affects larval fitness and metal tolerance.

    Science.gov (United States)

    Perez, Mario H; Noriega, Fernando G

    2012-06-01

    The eggs of the mosquito Aedes aegypti possess the ability to undergo an extended quiescence hosting a fully developed 1st instar larvae within the chorion. As a result of this life history trait pharate larvae can withstand months of quiescence inside the egg where they depend on stored maternal reserves. A. aegypti mosquitoes are frequently associated with urban habitats that may contain significant metal pollution. Therefore, the duration of quiescence and extent of nutritional depletion may affect the physiology and survival of larvae that hatch in a suboptimal habitat. The aim of this study was to determine the effect of an extended quiescence on larval nutrient reserves and the subsequent effects of metal exposure on larval fitness, survival and development. We hypothesized that an extended quiescence would reduce nutritional reserves and alter the molecular response to metal exposure thereby reducing larval survival and altering larval development. As a molecular marker for metal stress responses, we evaluated transcriptional changes in the metallothionein gene (AaMtn) in response to quiescence and metal exposure. Extended 1st instar quiescence resulted in a significant decrease in lipid reserves and negatively affected larval fitness and development. AaMtn transcription and metal tolerance were compromised in first instars emerged from eggs that had undergone an extended quiescence. These findings suggest that newly emerged mosquito larvae that had survived a relatively long pharate 1st instar quiescence (as might occur during a dry season) are more vulnerable to environmental stress. Pharate 1st instar quiescence could have implications for vector control strategies. Newly emerged mosquito larvae at the end of the dry season or start of the wet season are physiologically compromised, and therefore potentially more susceptible to vector control strategies than mosquito larvae hatched subsequently throughout the wet season. Published by Elsevier Ltd.

  4. 1st Cavalry Division’s Effectiveness In Conducting Airmobile Operations During Operation Pegasus

    Science.gov (United States)

    2016-05-26

    assault, OH-6 Cayuse scout helicopters and AH­ 1G Cobra attack helicopters from the cavalry scoured the area at low altitude , collected intelligence...Lieutenant General John Tolson, the division commander, drew-up initial plans to relieve the Marines at Khe Sanh on January 25, 1968.13 When he briefed...Cavalry Division to relieve Khe Sanh. 64 The Rogers Board began the development of the aircraft that would make 1st Cavalry Division successful by

  5. Ruthenium indenylidene “1st generation” olefin metathesis catalysts containing triisopropyl phosphite

    Directory of Open Access Journals (Sweden)

    Stefano Guidone

    2015-09-01

    Full Text Available The reaction of triisopropyl phosphite with phosphine-based indenylidene pre-catalysts affords “1st generation” cis-complexes. These have been used in olefin metathesis reactions. The cis-Ru species exhibit noticeable differences with the trans-Ru parent complexes in terms of structure, thermal stability and reactivity. Experimental data underline the importance of synergistic effects between phosphites and L-type ligands.

  6. Ruthenium indenylidene "1(st) generation" olefin metathesis catalysts containing triisopropyl phosphite.

    Science.gov (United States)

    Guidone, Stefano; Nahra, Fady; Slawin, Alexandra M Z; Cazin, Catherine S J

    2015-01-01

    The reaction of triisopropyl phosphite with phosphine-based indenylidene pre-catalysts affords "1(st) generation" cis-complexes. These have been used in olefin metathesis reactions. The cis-Ru species exhibit noticeable differences with the trans-Ru parent complexes in terms of structure, thermal stability and reactivity. Experimental data underline the importance of synergistic effects between phosphites and L-type ligands.

  7. Ruthenium indenylidene “1st generation” olefin metathesis catalysts containing triisopropyl phosphite

    Science.gov (United States)

    Guidone, Stefano; Nahra, Fady; Slawin, Alexandra M Z

    2015-01-01

    Summary The reaction of triisopropyl phosphite with phosphine-based indenylidene pre-catalysts affords “1st generation” cis-complexes. These have been used in olefin metathesis reactions. The cis-Ru species exhibit noticeable differences with the trans-Ru parent complexes in terms of structure, thermal stability and reactivity. Experimental data underline the importance of synergistic effects between phosphites and L-type ligands. PMID:26425210

  8. Perception of 1 st year medical students towards career choices and specialty of psychiatry

    OpenAIRE

    Suneet Kumar Upadhyaya; Chintan M Raval

    2015-01-01

    Background: Shortage of psychiatrists is a worldwide phenomenon. If the factors that attract or repel students towards a specialty can be identified, it may be possible to encourage them towards it. Choice of specialty as a career depends on the complex interplay of experiences before, during or after exposure to the specialty. Objectives: The aim was to understand perceptions of 1 st year medical students regarding career choices and the specialty of psychiatry through a cross-sectional ...

  9. 1st Meeting of China-ROK Eligibility Assessment Subcommittee Held in Beijing

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ The 1st Meeting of China-ROK Eligibility Assessment Subcommittee was held in Beijing on May 27. Sun Dawei, Chief Chinese representative and Certification and Accreditation Administration of China (CNCA)Deputy Director of presided over the meeting and Hong Zong, Chief ROK representative and Director of Security Service Standard Department of Technology Standard Institute of the Ministry of Industrial Resources of the Republic of Korea led a delegation to Beijing for the meeting.

  10. Magnetic field induced 1st order transitions: Recent studies, and some new concepts

    Science.gov (United States)

    Chaddah, P.

    2015-05-01

    Phase transitions are caused by varying temperature, or pressure, or magnetic field. The observation of 1st order magneto-structural transitions has created application possibilities based on magnetoresistance, magnetocaloric effect, magnetic shape memory effect, and magneto-dielectric effect. Magnetic field induced transitions, and phase coexistence of competing magnetic phases down to the lowest temperature, gained prominence over a decade ago with theoretical models suggesting that the ground state is not homogeneous. Researchers at Indore pushed an alternative view that this phase coexistence could be due to glasslike "kinetic arrest" of a disorder-broadened first-order magnetic transition between two states with long-range magnetic order, resulting in phase coexistence down to the lowest temperatures. The CHUF (cooling and heating in unequal field) protocol created at Indore allows the observation of `devitrification', followed by `melting'. I show examples of measurements establishing kinetic arrest in various materials, emphasizing that glasslike arrest of 1st order magnetic transitions may be as ubiquitous as glass formation following the arrest of 1st order structural transitions.

  11. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    Science.gov (United States)

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  12. Airborne Gravity: NGS' Gravity Data for ES02 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida and the Gulf of Mexico collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of the American...

  13. Airborne Gravity: NGS' Gravity Data for AN05 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  14. Airborne Gravity: NGS' Gravity Data for CS04 (2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  15. Airborne Gravity: NGS' Gravity Data for AS02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  16. Airborne Gravity: NGS' Gravity Data for AN02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  17. Airborne Gravity: NGS' Gravity Data for AN06 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  18. Airborne Gravity: NGS' Gravity Data for AN04 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  19. Airborne Gravity: NGS' Gravity Data for CS05 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2014 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  20. Airborne Gravity: NGS' Gravity Data for AS01 (2008)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2008 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  1. Airborne Gravity: NGS' Gravity Data for CS08 (2015)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for CS08 collected in 2006 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  2. RepARK--de novo creation of repeat libraries from whole-genome NGS reads.

    Science.gov (United States)

    Koch, Philipp; Platzer, Matthias; Downie, Bryan R

    2014-05-01

    Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a de novo repeat assembly method--RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)--which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.

  3. Photometric calibration of NGS/POSS and ESO/SRC plates using the NOAO PDS measuring engine. I - Stellar photometry

    Science.gov (United States)

    Cutri, Roc M.; Low, Frank J.; Marvel, Kevin B.

    1992-01-01

    The PDS/Monet measuring engine at the National Optical Astronomy Observatory was used to obtain photometry of nearly 10,000 stars on the NGS/POSS and 2000 stars on the ESO/SRC Survey glass plates. These measurements have been used to show that global transformation functions exist that allow calibration of stellar photometry from any blue or red plate to equivalent Johnson B and Cousins R photoelectric magnitudes. The four transformation functions appropriate for the POSS O and E and ESO/SRC J and R plates were characterized, and it was found that, within the measurement uncertainties, they vary from plate to plate only by photometric zero-point offsets. A method is described to correct for the zero-point shifts and to obtain calibrated B and R photometry of stellar sources to an average accuracy of 0.3-0.4 mag within the range R between values of 8 and 19.5 for red plates in both surveys, B between values of 9 and 20.5 on POSS blue plates, and B between values of 10 and 20.5 on ESO/SRC blue plates. This calibration procedure makes it possible to obtain rapid photometry of very large numbers of stellar sources.

  4. Perception of 1 st year medical students towards career choices and specialty of psychiatry

    Directory of Open Access Journals (Sweden)

    Suneet Kumar Upadhyaya

    2015-01-01

    Full Text Available Background: Shortage of psychiatrists is a worldwide phenomenon. If the factors that attract or repel students towards a specialty can be identified, it may be possible to encourage them towards it. Choice of specialty as a career depends on the complex interplay of experiences before, during or after exposure to the specialty. Objectives: The aim was to understand perceptions of 1 st year medical students regarding career choices and the specialty of psychiatry through a cross-sectional questionnaire-based study. Materials and Methods: Perceptions of 137 1 st year medical students from the Government Medical College were recorded using a semi-structured questionnaire. Students provided their opinions about future career choices; perspective of these specialties in terms of financial reward, reputation, work-life balance, challenging aspect, ability to help patients effectively and emotional stability; their preferences in life and interaction with psychiatrist and its impact. Statistical Analysis Used: One-way analysis of variance (ANOVA with post-hoc analysis by Tukey-Kramer test. Results: Surgery was a high priority for 69 (50% while psychiatry was a high priority only for 11 (8%. Surgery was highest for financial reward and reputation, but lowest for work-life balance. Psychiatry had higher emotional stability, however, its the reputation was lower than surgery, medicine, obstetrics and gynaecology and paediatrics. Students preferred reputation (41% over social service opportunities (43%, work-life balance (16%, and high-income (11%. Interaction with psychiatrist increased inclination for psychiatry in 69% (9/13 students. Conclusions: Psychiatry is not a preferred specialty among 1 st year medical students due to its poor reputation.

  5. 1st ESMO Consensus Conference in lung cancer; Lugano 2010: small-cell lung cancer

    DEFF Research Database (Denmark)

    Stahel, R; Thatcher, N; Früh, M;

    2011-01-01

    , the expert panel prepared clinically relevant questions concerning five areas as follows: early and locally advanced non-small-cell lung cancer (NSCLC), first-line metastatic NSCLC, second-/third-line NSCLC, NSCLC pathology and molecular testing, and small-cell lung cancer (SCLC) to be addressed through......The 1st ESMO Consensus Conference on lung cancer was held in Lugano, Switzerland on 21st and 22nd May 2010 with the participation of a multidisciplinary panel of leading professionals in pathology and molecular diagnostics and medical, surgical and radiation oncology. Before the conference...

  6. 1st International Conference on Business Management - “New Challenges in Business Research”

    OpenAIRE

    Calafat Marzal, Maria Consuelo; Martí Selva, María Luisa

    2015-01-01

    We are glad to announce the 1st International Conference on Business Management “New Challenges in Business Research” that will be held in the Faculty of Business Management and Administration of the Universitat Politècnica de València (Valencia, Spain) on 2nd – 3rd of July, 2015. The aim of the conference is to give researchers the opportunity to get together and present unpublished and relevant research studies about different topics on business management and economics. We belie...

  7. 1st International Conference on Computer Science, Applied Mathematics and Applications (ICCSAMA 2013)

    CERN Document Server

    Do, Tien; Thi, Hoai; Advanced Computational Methods for Knowledge Engineering

    2013-01-01

    The book consists of 29 extended chapters which have been selected and invited from the submissions to the 1st International Conference on Computer Science, Applied Mathematics and Applications (ICCSAMA 2013) held on 9-10 May, 2013 in Warsaw, Poland. The book is organized into five parts, which are: Advanced Optimization Methods and Their Applications, Queueing Theory and Applications, Computational Methods for Knowledge Engineering, Knowledge Engineering with Cloud and Grid Computing, and Logic Based Methods for Decision Making and Data Mining, respectively. All chapters in the book discuss theoretical and practical issues connected with computational methods and optimization methods for knowledge engineering.

  8. Energy method for Stability of 1st Order CE with Variable Coefficients

    Institute of Scientific and Technical Information of China (English)

    LIU Ming

    2011-01-01

    It is well known that the Convection--diffusion e- quations arise in the fields of fluid mechanics and has been con- sidered extensively. The solving for these initial boundary value problems includes upwind difference scheme, Las- Friedrichs and Lax-- Wendroff difference schemes etc.. Methods such as Matrix method, the Hirt Heuristic Method and Fourier Method can be used to research the stability of the difference schemes. In the paper, using the 1st order convection equation(CE) with var- iable- coefficients as an example, the author gets the corre- sponding Lax--Wendroff difference scheme first, then Energy Method has been used to analyze the stability of the scheme.

  9. Introduction and application of South NGS - 200 type of GPS%南方NGS-2O0型GPS测量系统及其应用

    Institute of Scientific and Technical Information of China (English)

    郭胜利

    2002-01-01

    GPS(Global Positioning System)是全球卫星定位系统的缩写.南方NGS-200型GPS测量系统及其在永定河干堤加固工程中的应用表明,GPS测量相对传统的作业模式具有突破性的改变,这一新技术的应用使得广大测量工作者从繁重的外业劳动中解脱出来,并且工作效率有了根本性的提高.

  10. Developing a Personal-Learning-Portfolio (PLP) for 1st year students at Department of Psychology

    DEFF Research Database (Denmark)

    Johnsen, Anna Thit; Beck Hansen, Nina; Andersen, Mette Elmose

    Abstract title: Developing a Personal-Learning-Portfolio (PLP) for 1st year students at Department of Psychology Learning outcome of activity: B01 is the first module of the education in Psychology at University of Southern Denmark (SDU). The aim of B01 is to give the students a ‘map’ or a ‘schem......Abstract title: Developing a Personal-Learning-Portfolio (PLP) for 1st year students at Department of Psychology Learning outcome of activity: B01 is the first module of the education in Psychology at University of Southern Denmark (SDU). The aim of B01 is to give the students a ‘map......’ or a ‘schemata’ of psychology that they will later expand and modify throughout their education. This is done by introducing the students to the history of psychology, its theory of science and its different fields. However, feedback from our students told us that the risk of this objective is that the class...... be an inspiration to others who wish to develop and implements PLPs. Second, we will show the format of our particular Personal-Learning-Portfolio together with reflections on why it was developed in such a way. This includes the students’ opinions about the PLP and the results of the cognitive interviews....

  11. Functional genomics of tomato: Opportunities and challenges in post-genome NGS era

    Indian Academy of Sciences (India)

    Rahul Kumar; Ashima Khurana

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger’s and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-à-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other ‘omics’ tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  12. HLA-genotyping of clinical specimens using Ion Torrent-based NGS.

    Science.gov (United States)

    Barone, Jonathan C; Saito, Katsuyuki; Beutner, Karl; Campo, Maria; Dong, Wei; Goswami, Chirayu P; Johnson, Erica S; Wang, Zi-Xuan; Hsu, Susan

    2015-12-01

    We have evaluated and validated the NXType™ workflow (One Lambda, Inc.) and the accompanying TypeStream™ software on the Ion Torrent Next Generation Sequencing (NGS) platform using a comprehensive testing panel. The panel consisted of 285 genomic DNA (gDNA) samples derived from four major ethnic populations and contained 59 PT samples and 226 clinical specimens. The total number of alleles from the six loci interrogated by NGS was 3420. This validation panel provided a wide range of HLA sequence variations including many rare alleles, new variants and homozygous alleles. The NXType™ system (reagents and software) was able to correctly genotype the vast majority of these specimens. The concordance rate between SBT-derived genotypes and those generated by TypeStream™ auto-analysis ranged from 99.5% to 99.8% for the HLA-A, B, C, DRB1 and DQB1 loci, and was 98.9% for HLA-DPB1. A strategy for data review was developed that would allow correction of most of the few remaining typing errors. The entire NGS workflow from gDNA amplification to genotype assignment could be completed within 3 working days. Through this validation study, the limitations and shortcomings of the platform, specific assay system, and software algorithm were also revealed for further evaluation and improvement.

  13. The variation game: Cracking complex genetic disorders with NGS and omics data.

    Science.gov (United States)

    Cui, Hongzhu; Dhroso, Andi; Johnson, Nathan; Korkin, Dmitry

    2015-06-01

    Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.

  14. Development of a high-resolution NGS-based HLA-typing and analysis pipeline.

    Science.gov (United States)

    Wittig, Michael; Anmarkrud, Jarl A; Kässens, Jan C; Koch, Simon; Forster, Michael; Ellinghaus, Eva; Hov, Johannes R; Sauer, Sascha; Schimmler, Manfred; Ziemann, Malte; Görg, Siegfried; Jacob, Frank; Karlsen, Tom H; Franke, Andre

    2015-06-23

    The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.

  15. Parallel WGA and WTA for Comparative Genome and Transcriptome NGS Analysis Using Tiny Cell Numbers.

    Science.gov (United States)

    Korfhage, Christian; Fricke, Evelyn; Meier, Andreas

    2015-07-01

    Genomic DNA determines how and when the transcriptome is changed by a trigger or environmental change and how cellular metabolism is influenced. Comparative genome and transcriptome analysis of the same cell sample links a defined genome with all changes in the bases, structure, or numbers of the transcriptome. However, comparative genome and transcriptome analysis using next-generation sequencing (NGS) or real-time PCR is often limited by the small amount of sample available. In mammals, the amount of DNA and RNA in a single cell is ∼10 picograms, but deep analysis of the genome and transcriptome currently requires several hundred nanograms of nucleic acids for library preparation for NGS sequencing. Consequently, accurate whole-genome amplification (WGA) and whole-transcriptome amplification (WTA) is required for such quantitative analysis. This unit describes how the genome and the transcriptome of a tiny number of cells can be amplified in a highly parallel and comparable process. Protocols for quality control of amplified DNA and application of amplified DNA for NGS are included.

  16. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    Science.gov (United States)

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  17. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    Science.gov (United States)

    Russell, Joanne R; Hedley, Peter E; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.

  18. BAL31-NGS approach for identification of telomeres de novo in large genomes.

    Science.gov (United States)

    Peška, Vratislav; Sitová, Zdeňka; Fajkus, Petr; Fajkus, Jiří

    2017-02-01

    This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n=14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples.

  19. EDITORIAL: The 1st International Conference on Nanomanufacturing (NanoMan2008) The 1st International Conference on Nanomanufacturing (NanoMan2008)

    Science.gov (United States)

    Luo, Jack Jiqui; Fang, Fengzhou

    2009-05-01

    Nanomanufacturing is an emerging technology in the field of synthesis of nanomaterials, manufacture of nanodevices, nanosystems and the relevant characterization technologies, and will greatly impact our society and environment: speeding up scientific discovery, technological development, improving healthcare and living standards and slowing down the exhaustion of energy resources, to name but few. The 1st International Conference on Nanomanufacturing (NanoMan2008) was held on the 13-16 July 2008 in Singapore in conjunction with ThinFilm2008 (The 4th International Conference on Technological Advances of Thin Films & Surface Coatings). Approximately 140 delegates from all over the world have participated in the conference and presented their latest discoveries and technological developments. The main focuses of the conference were modern nanomanufacturing by laser machining, focused ion beam fabrication, nano/micro-molding/imprinting, nanomaterial synthesis and characterization, nanometrology and nano/microsystems fabrication and characterization. There was also great interest in applications of nanomanufacturing technologies in traditional areas such as free form machining, polishing and grinding with nano-scale precision and the smoothness of surfaces of objects, and applications in space exploration, military and medicine. This special issue is devoted to NanoMan2008 with a collection of 9 invited talks presented at the conference, covering all the topics of nanomanufacturing technology and development. These papers have been upgraded by the authors with new results and discoveries since the preparation of the conference manuscripts, hence presenting the latest developments. We would like to take this opportunity to thank all the delegates who attended the conference and made the conference successful, and to the authors who contributed papers to this special issue. Thanks also go to the conference committee for their efforts and devotion to the conference. We

  20. 1st International Symposium and 10th Balkan Conference on Operational Research

    CERN Document Server

    Sifaleras, Angelo; Georgiadis, Christos; Papathanasiou, Jason; Stiakakis, Emmanuil

    2013-01-01

    Over the past two decades, the Balkan Conference on Operational Research (BALCOR) has facilitated the exchange of scientific and technical information on the subject of Operations Research and related fields such as Mathematical Programming, Game Theory, Multiple Criteria Decision Analysis, Information Systems, Data Mining, and more, in order to promote international scientific cooperation.  The contributed papers contained in this volume consist of 25 selected research papers based on results presented at the 10th Balkan Conference & 1st International Symposium on Operational Research in Thessalonike, Greece. Subjects include, but do not restrict to, the development of theory and mathematical models for Operations Research, theory and applications of Combinatorial Optimization, Supply Chain Optimization, and Military Operations Research.  These carefully selected papers present important recent developments and modern applications, and will serve as excellent reference for students, researchers, and pr...

  1. Summary of the 1st International Workshop on Environmental, Safety and Economic Aspects of Fusion Power

    Science.gov (United States)

    Wu, Y.; Stevens, E.; Kim, K.; Maisonnier, D.; Kalashnikov, A.; Tobita, K.; Jackson, D.; Alejaldre, C.; Perrault, D.; Panayotov, D.; Merrill, B.; Grisolia, C.; Zucchetti, M.; Pinna, T.; van Houtte, D.; Konishi, S.; Kolbasov, B.

    2016-12-01

    The 1st International workshop on Environmental, Safety and Economic Aspects of Fusion Power (ESEFP) was held on 13 September 2015 at Jeju Island, South Korea. The workshop was initiated by the International Energy Agency Implementing Agreement on a Co-operative Program on ESEFP. The workshop was well attended with about forty participants representing twelve institutions in ten countries. The presentations covered safety issues and environmental impacts, availability improvement and risk control and socio-economic aspects of fusion power. Safety and licensing gaps between DEMO and ITER were discussed in depth with the consensus output presented as a plenary presentation at the 12th International Symposium on Fusion Nuclear Technology (ISFNT-12). The next workshop is planned to be held in conjunction with the ISFNT-13 in 2017.

  2. Idaho National Laboratory Quarterly Occurrence Analysis - 1st Quarter FY 2016

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Lisbeth Ann [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-03-01

    This report is published quarterly by the Idaho National Laboratory (INL) Quality and Performance Management Organization. The Department of Energy (DOE) Occurrence Reporting and Processing System (ORPS), as prescribed in DOE Order 232.2, “Occurrence Reporting and Processing of Operations Information,” requires a quarterly analysis of events, both reportable and not reportable, for the previous 12 months. This report is the analysis of 74 reportable events (16 from the 1st Qtr FY-16 and 58 from the prior three reporting quarters), as well as 35 other issue reports (including events found to be not reportable and Significant Category A and B conditions) identified at INL during the past 12 months (15 from this quarter and 20 from the prior three quarters).

  3. 1st European-Middle Asian Conference on Computer Modelling 2015

    CERN Document Server

    Kolosov, Dmitrii; Snášel, Václav; Karakeyev, Taalaybek; Abraham, Ajith

    2016-01-01

    This volume of Advances in Intelligent Systems and Computing contains papers presented at the 1st European-Middle Asian Conference on Computer Modelling, EMACOM 2015. This international conference was conceived as a brand new scientific and social event of mutual collaboration between the VSB - Technical University of Ostrava (Ostrava, Czech Republic) and the Kyrgyz National University named after J. Balasagyn (Bishkek, Kyrgyz Republic). The aim of EMACOM 2015 was to present the latest development in the field of computer-aided modelling as an essential aspect of research and development of innovative systems and their applications. The conference showed that together with simulations, various modeling techniques, enabled and encouraged by the rapid development of high-performance computing platforms, are crucial for cost-efficient design, verification, and prototyping of solutions in many diverse industrial fields spanning the whole range from manufacturing, mining, machinery, and automotive industries to in...

  4. 1st International Conference on Computational Advancement in Communication Circuits and Systems

    CERN Document Server

    Dalapati, Goutam; Banerjee, P; Mallick, Amiya; Mukherjee, Moumita

    2015-01-01

    This book comprises the proceedings of 1st International Conference on Computational Advancement in Communication Circuits and Systems (ICCACCS 2014) organized by Narula Institute of Technology under the patronage of JIS group, affiliated to West Bengal University of Technology. The conference was supported by Technical Education Quality Improvement Program (TEQIP), New Delhi, India and had technical collaboration with IEEE Kolkata Section, along with publication partner by Springer. The book contains 62 refereed papers that aim to highlight new theoretical and experimental findings in the field of Electronics and communication engineering including interdisciplinary fields like Advanced Computing, Pattern Recognition and Analysis, Signal and Image Processing. The proceedings cover the principles, techniques and applications in microwave & devices, communication & networking, signal & image processing, and computations & mathematics & control. The proceedings reflect the conference’s emp...

  5. The 1st Fermi LAT SNR Catalog: the Impact of Interstellar Emission Modeling

    CERN Document Server

    Brandt, T J; de Palma, F; Johannesson, G; Tibaldo, L

    2013-01-01

    Galactic interstellar emission contributes substantially to Fermi LAT observations in the Galactic plane, the location of the majority of supernova remnants (SNRs). To explore some systematic effects on SNRs' properties caused by interstellar emission modeling, we have developed a method comparing the official LAT interstellar emission model results to eight alternative models. We created the eight alternative Galactic interstellar models by varying a few input parameters to GALPROP, namely the height of the cosmic ray propagation halo, cosmic ray source distribution in the Galaxy, and atomic hydrogen spin temperature. We have analyzed eight representative SNRs chosen to encompass a range of Galactic locations, extensions, and spectral properties using the eight different interstellar emission models. We will present the results and method in detail and discuss the implications for studies such as the 1st Fermi LAT SNR Catalog.

  6. The new Facilities Management contract at CERN from 1st July 2002

    CERN Document Server

    Mauro Nonis

    2002-01-01

    Within the ST Division, all the Facilities Management activities have been under the ST/TFM group responsibility until the 30th June 2002, who has performed them using around 20 industrial support contracts. Starting from the 1st July 2002 a new unit, ST/FM, will take over these activities that will be unified into one single contract that has been adjudicated to the company Facilities Management Network SA. This contract will be in charge of the maintenance and minor works on tertiary installations (i.e. all structures and installations that have no direct relation to the running of the accelerators) for the following trades: - Technical: heating, ventilation, air conditioning, plumbing, electricity, civil engineering (painting, roofing, glazing, blinds, fencing, masonry etc.), passenger and goods lifts, automatic and powered doors, kitchen equipment, roads, signs, keys and locks, office furniture, - Services: waste collection, security, green areas, cleaning and sanitary supplies, disinfection, rodent cont...

  7. THE NEW FACILITIES MANAGEMENT CONTRACT AT CERN FROM 1st JULY 2002

    CERN Multimedia

    Mauro Nonis

    2002-01-01

    Within the ST Division, all the Facilities Management activities have been under the ST/TFM group responsibility until the 30th June 2002, who has performed them using around 20 industrial support contracts. Starting from the 1st July 2002 a new unit, ST/FM, will take over these activities that will be unified into one single contract that has been adjudicated to the company Facilities Management Network SA. This contract will be in charge of the maintenance and minor works on tertiary installations (i.e. all structures and installations that have no direct relation to the running of the accelerators) for the following trades: Technical: heating, ventilation, air conditioning, plumbing, electricity, civil engineering (painting, roofing, glazing, blinds, fencing, masonry etc.), passenger and goods lifts, automatic and powered doors, kitchen equipment, roads, signs, keys and locks, office furniture, Services: waste collection, security, green areas, cleaning and sanitary supplies, disinfection, rodent contro...

  8. Statistical Ring Opening Metathesis Copolymerization of Norbornene and Cyclopentene by Grubbs’ 1st-Generation Catalyst

    Directory of Open Access Journals (Sweden)

    Christiana Nikovia

    2015-08-01

    Full Text Available Statistical copolymers of norbornene (NBE with cyclopentene (CP were prepared by ring-opening metathesis polymerization, employing the 1st-generation Grubbs’ catalyst, in the presence or absence of triphenylphosphine, PPh3. The reactivity ratios were estimated using the Finemann-Ross, inverted Finemann-Ross, and Kelen-Tüdos graphical methods, along with the computer program COPOINT, which evaluates the parameters of binary copolymerizations from comonomer/copolymer composition data by integrating a given copolymerization equation in its differential form. Structural parameters of the copolymers were obtained by calculating the dyad sequence fractions and the mean sequence length, which were derived using the monomer reactivity ratios. The kinetics of thermal decomposition of the copolymers along with the respective homopolymers was studied by thermogravimetric analysis within the framework of the Ozawa-Flynn-Wall and Kissinger methodologies. Finally, the effect of triphenylphosphine on the kinetics of copolymerization, the reactivity ratios, and the kinetics of thermal decomposition were examined.

  9. Cancer incidence among 1st generation migrants compared to native Danes--a retrospective cohort study

    DEFF Research Database (Denmark)

    Nørredam, Marie Louise; Krasnik, A; Pipper, C

    2007-01-01

    had a significantly lower incidence. All migrants had a significantly lower incidence of breast and colorectal cancer but male migrants from East Europe had a significantly higher incidence of lung cancer. CONCLUSIONS: The overall cancer incidence among migrants was lower compared to native Danes......STUDY AIMS: To investigate the incidence of cancer among 1st generation migrants compared to native Danes, including time trends in the risk of cancer among migrants. METHODS: A retrospective cohort study design. Migrants were matched 1:4 on age and sex with a Danish born reference population....... The cohort was linked to the Danish Cancer Register and cancer cases among migrants (n=537) and native Danes (n=2829) were identified. RESULTS: The overall cancer incidence did not differ significantly between migrants from East Europe and native Danes; whereas migrants from the Middle East and North Africa...

  10. Challenges of changing a PBL-related curriculum for 1st year students

    DEFF Research Database (Denmark)

    Bruun-Pedersen, Jon Ram; Kofoed, Lise B.

    2011-01-01

    This paper discusses a transition related to a reformed study plan in the specific case of the Aalborg University education of Medialogy; a Bachelor and Master program with an average of 80 students starting 1st semester. Among other things, the change meant a new structure for preparation...... plan. The method used is based on an analysis of the students’ Process Analyses, a learning portfolio, where a project group of up to 7 students analyse and reflect on the CLP-related process of realizing their semester project. The theoretical background of the comparative analysis is based......, teaching and evaluation for the course: Cooperation, Learning and Project Management (CLP). This paper will discuss the implications, based on the students’understanding of the subject matter, the degree of practical use of the course curriculum in their project work, and compare it to the former study...

  11. Environmental engineering education - summary report of the 1st European Seminar

    DEFF Research Database (Denmark)

    Alha, K; Holliger, C.; Larsen, Bo Skjold;

    2000-01-01

    This paper summarizes the discussions of the 1st European Seminar on Environmental Engineering Education (E3), which was held at EAWAG, Zurich, Switzerland in August 1999. Although the emerging discipline of environmental engineering, which was once viewed as being a sub-set of civil or chemical...... engineering, has established a status in its own right, a definition of environmental engineering is still not agreed among European engineering educators. This report discusses the variation between European countries and the way in which higher education institutions in these countries address...... the educational needs of environmental engineers. A review of the acceptance of this new discipline by employers and the status of environmental engineering as a profession throughout Europe is presented. The question of how to achieve greater compatibility and comparability of the systems of environmental...

  12. Virtual Visit to the ATLAS Control Room by 1st and 3rd Lyceums in Chios

    CERN Multimedia

    2013-01-01

    High school students from the 1st and 3rd Lyceums of Chios, Greece, will be visiting the control room of ATLAS to discuss the latest results on the Higgs search, LHC’s first long shutdown and what the future holds for the ATLAS experiment. This visit takes place in the context of a Masterclass where students will learn how to analyse real events from the LHC with the use of the HYPATIA online applet based on educational scenarios from the Discover the COSMOS portal. This full-day activity is organized by the University of Athens, the University of the Aegean, Ellinogermaniki Agogi and the Chios Physical Society in the framework of the Open Discovery Space EU project.

  13. Proceedings of the 1st International Workshop on High-Speed and Intercity Railways

    CERN Document Server

    Ye, Xiao-Wei

    2012-01-01

    This book contains the papers included in the proceedings of the 1st International Workshop on High-speed and Intercity Railways (IWHIR 2011) held in Shenzhen and Hong Kong, China from July 19 to July 22, 2011, which is organized by The Hong Kong Polytechnic University, in collaboration with Southwest Jiaotong University, Beijing Jiaotong University, Dalian Jiaotong University, China Engineering Consultants, Inc., Zhejiang University, and Tsinghua University. Continuing the great initiatives and momentums of the rapid development in high-speed and intercity railways worldwide in recent years, IWHIR 2011 aims at providing a platform for academic scholars and practicing engineers to share knowledge and experience, to promote collaboration, and to strengthen R&D activities related to railway engineering. Engineers, scientists, professors, and students from universities, research institutes, and related industrial companies have been cordially invited to participate in the workshop. These papers have covered ...

  14. Idaho National Laboratory Quarterly Occurrence Analysis for the 1st Quarter FY2017

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Lisbeth Ann [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2017-01-01

    This report is published quarterly by the Idaho National Laboratory (INL) Quality and Performance Management Organization. The Department of Energy (DOE) Occurrence Reporting and Processing System (ORPS), as prescribed in DOE Order 232.2, “Occurrence Reporting and Processing of Operations Information,” requires a quarterly analysis of events, both reportable and not reportable, for the previous 12 months. This report is the analysis of 82 reportable events (13 from the 1st quarter (Qtr) of fiscal year (FY) 2017 and 68 from the prior three reporting quarters), as well as 31 other issue reports (including events found to be not reportable and Significant Category A and B conditions) identified at INL during the past 12 months (seven from this quarter and 24 from the prior three quarters).

  15. Proceedings of the 1st International Workshop on High-Speed and Intercity Railways

    CERN Document Server

    Ye, Xiao-Wei

    2012-01-01

    This book contains the papers included in the proceedings of the 1st International Workshop on High-speed and Intercity Railways (IWHIR 2011) held in Shenzhen and Hong Kong, China from July 19 to July 22, 2011, which is organized by The Hong Kong Polytechnic University, in collaboration with Southwest Jiaotong University, Beijing Jiaotong University, Dalian Jiaotong University, China Engineering Consultants, Inc., Zhejiang University, and Tsinghua University. Continuing the great initiatives and momentums of the rapid development in high-speed and intercity railways worldwide in recent years, IWHIR 2011 aims at providing a platform for academic scholars and practicing engineers to share knowledge and experience, to promote collaboration, and to strengthen R&D activities related to railway engineering. Engineers, scientists, professors, and students from universities, research institutes, and related industrial companies have been cordially invited to participate in the workshop. These papers have covered ...

  16. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

    Science.gov (United States)

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y-H; Thompson, Janelle R

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  17. The Aalborg Survey / Part 1 - Web Based Survey

    DEFF Research Database (Denmark)

    Harder, Henrik; Christensen, Cecilie Breinholm

    Background and purpose The Aalborg Survey consists of four independent parts: a web, GPS and an interview based survey and a literature study, which together form a consistent investigation and research into use of urban space, and specifically into young people’s use of urban space: what young......) and the research focus within the cluster of Mobility and Tracking Technologies (MoTT), AAU. Summary / Part 1 Web Base Survey The 1st part of the research project Diverse Urban Spaces (DUS) has been carried out during the period from December 1st 2007 to February 1st 2008 as a Web Based Survey of the 27.040 gross...... people do in urban spaces, where they are in the urban spaces and when the young people are in the urban spaces. The answers to these questions form the framework and enable further academic discussions and conclusions in relation to the overall research project Diverse Urban Spaces (DUS). The primary...

  18. 1st or 2nd generation bioethanol-impacts of technology integration & on feed production and land use

    DEFF Research Database (Denmark)

    Bentsen, Niclas Scott; Felby, Claus

    2009-01-01

    on agricultural land on a global scale, but increase the pressure on local/national scale. In contrast to that 2nd generation bioethanol based on wheat straw exhibits a poorer energy balance than 1st generation, but the induced imbalances on feed energy are smaller. Proteins are some of the plant components...... production comparable to gasoline production in terms of energy loss. Utilisation of biomass in the energy sector is inevitably linked to the utilisation of land. This is a key difference between fossil and bio based energy systems. Thus evaluations of bioethanol production based on energy balances alone...... are inadequate. 1st and 2nd generation bioethanol production exhibits major differences when evaluated on characteristics as feed energy and feed protein production and subsequently on land use changes. 1st generation bioethanol production based on wheat grain in Denmark may in fact reduce the pressure...

  19. DUSTiNGS. III. Distribution of Intermediate-age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    Science.gov (United States)

    McQuinn, Kristen B.; Boyer, Martha; DUSTiNGS Team

    2017-06-01

    As part of the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey, we have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group. We find intermediate age stars are well mixed with the older populations and extend to large radii, indicating that chemical enrichment from these dust-producing stars may occur in the outer regions of galaxies with some frequency. Theories of structure formation in dwarf galaxies must account for the lack of radial gradients in intermediate-age populations and the presence of these stars in the outer extremities of dwarfs. We also identify the tip of the red giant branch (TRGB) in Spitzer IRAC 3.6 μm photometry. Unlike the constant TRGB in the I band, at 3.6 μm, the TRGB magnitude varies by ˜0.7 mag and is not a metallicity independent distance indicator.

  20. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money.

    Science.gov (United States)

    Vincent, Antony T; Derome, Nicolas; Boyle, Brian; Culley, Alexander I; Charette, Steve J

    2017-07-01

    The Sanger sequencing method produces relatively long DNA sequences of unmatched quality and has been considered for long time as the gold standard for sequencing DNA. Many improvements of the Sanger method that culminated with fluorescent dyes coupled with automated capillary electrophoresis enabled the sequencing of the first genomes. Nevertheless, using this technology to sequence whole genomes was costly, laborious and time consuming even for genomes that are relatively small in size. A major technological advance was the introduction of next-generation sequencing (NGS) pioneered by 454 Life Sciences in the early part of the 21th century. NGS allowed scientists to sequence thousands to millions of DNA molecules in a single machine run. Since then, new NGS technologies have emerged and existing NGS platforms have been improved, enabling the production of genome sequences at an unprecedented rate as well as broadening the spectrum of NGS applications. The current affordability of generating genomic information, especially with microbial samples, has resulted in a false sense of simplicity that belies the fact that many researchers still consider these technologies a black box. In this review, our objective is to identify and discuss four steps that we consider crucial to the success of any NGS-related project. These steps are: (1) the definition of the research objectives beyond sequencing and appropriate experimental planning, (2) library preparation, (3) sequencing and (4) data analysis. The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research. Regardless of the evolution and improvement of the sequencing technologies, these four steps will remain relevant. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. PREFACE: 1st International Conference on Rheology and Modeling of Materials

    Science.gov (United States)

    Gömze, László A.

    2015-04-01

    Understanding the rheological properties of materials and their rheological behaviors during their manufacturing processes and in their applications in many cases can help to increase the efficiency and competitiveness not only of the finished goods and products but the organizations and societies also. The more scientific supported and prepared organizations develop more competitive products with better thermal, mechanical, physical, chemical and biological properties and the leading companies apply more competitive knowledge, materials, equipment and technology processes. The idea to organize in Hungary the 1st International Conference on Rheology and Modeling of Materials we have received from prospective scientists, physicists, chemists, mathematicians and engineers from Asia, Europe, North and South America including India, Korea, Russia, Turkey, Estonia, France, Italy, United Kingdom, Chile, Mexico and USA. The goals of ic-rmm1 the 1st International Conference on Rheology and Modeling of Materials are the following: • Promote new methods and results of scientific research in the fields of modeling and measurements of rheological properties and behavior of materials under processing and applications. • Change information between the theoretical and applied sciences as well as technical and technological implantations. • Promote the communication between the scientists of different disciplines, nations, countries and continents. The international conference ic-rmm1 provides a platform among the leading international scientists, researchers, PhD students and engineers for discussing recent achievements in measurement, modeling and application of rheology in materials technology and materials science of liquids, melts, solids, crystals and amorphous structures. Among the major fields of interest are the influences of material structures, mechanical stresses temperature and deformation speeds on rheological and physical properties, phase transformation of

  2. PREFACE: 1st European Conference on Gas Micro Flows (GasMems 2012)

    Science.gov (United States)

    Frijns, Arjan; Valougeorgis, Dimitris; Colin, Stéphane; Baldas, Lucien

    2012-05-01

    The aim of the 1st European Conference on Gas Micro Flows is to advance research in Europe and worldwide in the field of gas micro flows as well as to improve global fundamental knowledge and to enable technological applications. Gas flows in microsystems are of great importance and touch almost every industrial field (e.g. fluidic microactuators for active control of aerodynamic flows, vacuum generators for extracting biological samples, mass flow and temperature micro-sensors, pressure gauges, micro heat-exchangers for the cooling of electronic components or for chemical applications, and micro gas analyzers or separators). The main characteristic of gas microflows is their rarefaction, which for device design often requires modelling and simulation both by continuous and molecular approaches. In such flows various non-equilibrium transport phenomena appear, while the role played by the interaction between the gas and the solid device surfaces becomes essential. The proposed models of boundary conditions often need an empirical adjustment strongly dependent on the micro manufacturing technique. The 1st European Conference on Gas Micro Flows is organized under the umbrella of the recently established GASMEMS network (www.gasmems.eu/) consisting of 13 participants and six associate members. The main objectives of the network are to structure research and train researchers in the fields of micro gas dynamics, measurement techniques for gaseous flows in micro experimental setups, microstructure design and micro manufacturing with applications in lab and industry. The conference takes place on June 6-8 2012, at the Skiathos Palace Hotel, on the beautiful island of Skiathos, Greece. The conference has received funding from the European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement ITN GASMEMS no. 215504. It owes its success to many people. We would like to acknowledge the support of all members of the Scientific Committee and of all

  3. [Prevalence and causes of pain after cataract surgery: Comparison of 1st and 2nd eyes].

    Science.gov (United States)

    Gayadine-Harricham, Y; Amzallag, T

    2017-06-01

    In our practice, patients undergoing bilateral cataract surgery complain of more significant pain after the 2nd eye surgery. The goal of this study was to compare postoperative pain between the 1st and 2nd eyes with cataract surgery under topical anesthesia and to identify the causes of this pain. We conducted a prospective observational study between May and September 2015. We included 69 consecutive adults scheduled for bilateral cataract surgery under topical anesthesia within 2 months by the same surgeon. A self-assessment questionnaire of anxiety (the Amsterdam Preoperative Anxiety and Information Scale [APAIS]) was completed before each procedure. Postoperative pain was assessed by the visual analogue scale (VAS) in the recovery room. Among the 69 included patients (mean age: 70±1.3 years), 13 (19%) experienced more pain after the 2nd eye procedure. The median VAS was 0 (EI: 0-1) after the first eye versus 0 (EI: 0-2) after the second eye (P=0.836). The patients with the most pain after the second eye surgery had a median anxiety score of 5 (EI: 4 to 9.5), which was comparable to those without pain (P=0.589). On bivariate analysis, women had more pain after second eye surgery (27%) than men (4%) (P=0.026). However, this association lost its significance when the analysis was adjusted for the level of anxiety (adjusted OR 7.7, 95% CI [0.91; 64.6]). In fact, women were more anxious [median anxiety score of 6 (EI: 4 to 8.5)] before 2nd eye surgery than men [median score: 4 (EI: 4-6); P=0.013]. Pain levels appeared to be very moderate on both sides when measured postoperatively, as opposed to statements often made in the immediate postoperative period. There is a discrepancy with the literature data. However, each study had small sample sizes. We did not find any significant difference in pain between 1st and 2nd eye cataract surgery under topical local anesthesia. While postoperative pain appeared greater among women, we have noted the possible influence of

  4. Critical review of NGS analyses for de novo genotyping multigene families.

    Science.gov (United States)

    Lighten, Jackie; van Oosterhout, Cock; Bentzen, Paul

    2014-08-01

    The genotyping of highly polymorphic multigene families across many individuals used to be a particularly challenging task because of methodological limitations associated with traditional approaches. Next-generation sequencing (NGS) can overcome most of these limitations, and it is increasingly being applied in population genetic studies of multigene families. Here, we critically review NGS bioinformatic approaches that have been used to genotype the major histocompatibility complex (MHC) immune genes, and we discuss how the significant advances made in this field are applicable to population genetic studies of gene families. Increasingly, approaches are introduced that apply thresholds of sequencing depth and sequence similarity to separate alleles from methodological artefacts. We explain why these approaches are particularly sensitive to methodological biases by violating fundamental genotyping assumptions. An alternative strategy that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. Importantly, the 'degree of change' (DOC) method avoids using arbitrary cut-off thresholds by looking for statistical boundaries between the sequencing depth for alleles and artefacts, and hence, it is entirely repeatable across studies. Although the advances made in generating NGS data are still far ahead of our ability to perform reliable processing, analysis and interpretation, the community is developing statistically rigorous protocols that will allow us to address novel questions in evolution, ecology and genetics of multigene families. Future developments in third-generation single molecule sequencing may potentially help overcome problems that still persist in de novo multigene amplicon genotyping when using current second-generation sequencing approaches.

  5. Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Washington, A. L. II; Peters, T. B.

    2014-03-03

    This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or DCs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction DCs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.

  6. New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies.

    Science.gov (United States)

    Legati, Andrea; Reyes, Aurelio; Nasca, Alessia; Invernizzi, Federica; Lamantea, Eleonora; Tiranti, Valeria; Garavaglia, Barbara; Lamperti, Costanza; Ardissone, Anna; Moroni, Isabella; Robinson, Alan; Ghezzi, Daniele; Zeviani, Massimo

    2016-08-01

    Next Generation Sequencing (NGS) technologies are revolutionizing the diagnostic screening for rare disease entities, including primary mitochondrial disorders, particularly those caused by nuclear gene defects. NGS approaches are able to identify the causative gene defects in small families and even single individuals, unsuitable for investigation by traditional linkage analysis. These technologies are contributing to fill the gap between mitochondrial disease cases defined on the basis of clinical, neuroimaging and biochemical readouts, which still outnumber by approximately 50% the cases for which a molecular-genetic diagnosis is attained. We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. Not only this approach has allowed us to reach molecular diagnosis in a significant fraction (20%) of these difficult cases, but it has also revealed unexpected and conceptually new findings. These include the possibility of marked variable penetrance of recessive mutations, the identification of large-scale DNA rearrangements, which explain spuriously heterozygous cases, and the association of mutations in known genes with unusual, previously unreported clinical phenotypes. Importantly, WES on selected cases has unraveled the presence of pathogenic mutations in genes encoding non-mitochondrial proteins (e.g. the transcription factor E4F1), an observation that further expands the intricate genetics of mitochondrial disease and suggests a new area of investigation in mitochondrial medicine. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

  7. 77 FR 43063 - Affirmation of Vertical Datum for Surveying and Mapping Activities for the Territory of Puerto Rico

    Science.gov (United States)

    2012-07-23

    ... Activities for the Territory of Puerto Rico AGENCY: National Geodetic Survey (NGS), National Ocean Service... vertical datum for the Territory of Puerto Rico, which includes the islands of Puerto Rico,...

  8. Fast extraction from SPS LSS4 for the LHC and NGS projects

    CERN Document Server

    Goddard, B

    1998-01-01

    The proton and lead ion beams for the anti-clockwise ring of the LHC will be extracted from the SPS in LSS4 and transferred to LHC point 8 via the transfer line TT40-TI8. A conventional single turn 'fast' extraction will be used. The same extraction channel may be used to transfer protons to a neutrino target for the proposed long baseline Neutrino to Gran Sasso (NGS) project. The planned layout for the extraction channel in LSS4 now has the extraction septum in SPS half period 418, and is outlined for both fast-pulsed and DC septum designs.

  9. 1st paleomagnetic investigation of Nubia Sandstone at Kalabsha, south Western Desert of Egypt

    Science.gov (United States)

    Mostafa, R.; Khashaba, A.; El-Hemaly, I. A.; Takla, E. M.; Abdel Aal, E.; Odah, H.

    2016-06-01

    Two profiles have been sampled from the Nubia Sandstone at Aswan, south Western Desert: the 1st profile has been taken from Abu Aggag Formation and the 2nd one was from Sabaya Formation (23.25 °N, 32.75 °E). 136 oriented cores (from 9 sites) have been sampled. Abu Aggag Formation is of Late Cretaceous (Turonian) and Sabaya Formation is of early Cretaceous (Albian-Cenomanian). The studied rocks are subjected to rock magnetic measurements as well as demagnetization treatment. It has been found that hematite is the main magnetic mineral in both formations. Four profile sections from Abu Aggag Formation, yielded a magnetic component with D = 352.7°, I = 36.6° with α95 = 5.2° and the corresponding pole lies at Lat. = 82.8 °N and Long. = 283.1 °E. Five profile sections from Sabaya Formation, yielded a magnetic component with D = 348.6°, I = 33.3° with α95 = 5.8° and the corresponding pole lies at Lat. = 78.3 °N and Long. = 280.4 °E. The obtained paleopole for the two formations lies at Lat. = 80.5 °N and Long. = 281.7 °E. The obtaind magnetic components are considered primary and the corresponding paleopole reflects the age of Nubia Sandstone when compared with the previously obtained Cretaceous poles for Egypt.

  10. SEMANTICS POETIC STYLE IN THE ESTIMATES OF RUSSIAN CRITICISM 1st HALF OF THE XIX CENTURY

    Directory of Open Access Journals (Sweden)

    I. B. Serebrianaia

    2014-01-01

    Full Text Available The article is devoted to the analysis of the 19th century critical judgments about the language of poetic works. Such statements reflect current cultural and speech problems of the epoch, the difficulties of language standardization, linguistic habits and tastes and are very important for the linguistics. The analysis of Russian literary criticism of the 1st half of the 19th century brings one to the conclusion that the reviewers, exacting and very sensitive to lexical and semantic correctness of fiction, meticulously recorded inaccuracies in the use of poetic words, i. e. romantically colored, mostly archaic words having a symbolic function. Outdated tokens, such as chelo ‘ forehead ‘, sen’ ‘ cover ‘, kushcha ‘ hut ‘, etc., as a result of their intense poetic figurative-personalized use often lost their semantic clarity? Which disagreed with standard rules and caused an extremely negative and sometimes ironic reaction of critics. This article describes instances of reviewers’ negative reactions to the use of the archaism chelo in the meanings ‘ head, face ‘; sen’ in the meanings ‘mental tranquility, shelter ‘; kushcha ‘foliage, thicket’, etc. A good illustration of semantic “vagueness” of archaic Church Slavonic vocabulary is the discussion between A. S. Pushkin and M. A. Dmitriev concerning semantic content of the poetic word лоно ‘ depth’, or ‘surface, bosom’. Such phenomena manifest the tendency for losing semantic clarity and then rapid withdrawal of high frequency words to the periphery.

  11. The relation between 1st grade grey matter volume and 2nd grade math competence.

    Science.gov (United States)

    Price, Gavin R; Wilkey, Eric D; Yeo, Darren J; Cutting, Laurie E

    2016-01-01

    Mathematical and numerical competence is a critical foundation for individual success in modern society yet the neurobiological sources of individual differences in math competence are poorly understood. Neuroimaging research over the last decade suggests that neural mechanisms in the parietal lobe, particularly the intraparietal sulcus (IPS) are structurally aberrant in individuals with mathematical learning disabilities. However, whether those same brain regions underlie individual differences in math performance across the full range of math abilities is unknown. Furthermore, previous studies have been exclusively cross-sectional, making it unclear whether variations in the structure of the IPS are caused by or consequences of the development of math skills. The present study investigates the relation between grey matter volume across the whole brain and math competence longitudinally in a representative sample of 50 elementary school children. Results show that grey matter volume in the left IPS at the end of 1st grade relates to math competence a year later at the end of 2nd grade. Grey matter volume in this region did not change over that year, and was still correlated with math competence at the end of 2nd grade. These findings support the hypothesis that the IPS and its associated functions represent a critical foundation for the acquisition of mathematical competence.

  12. Calibration and commutability assessment of the 1st International Standard for Diphtheria Antitoxin Human.

    Science.gov (United States)

    Stickings, Paul; Rigsby, Peter; Coombes, Laura; von Hunolstein, Christina; Ralli, Luisa; Pinto, Antonella; Sesardic, Dorothea

    2013-11-01

    The 1st International Standard for Diphtheria Antitoxin Human (coded 10/262) was established by the World Health Organization Expert Committee on Biological Standardization in 2012. This paper describes the production, characterization and calibration of the new standard which is intended for use in the standardization of assays used to measure diphtheria antibody responses in human serum. The new standard was calibrated in terms of the International Standard for Diphtheria Antitoxin Equine in an international collaborative study. A total of 8 participants from 8 different countries performed in vivo and/or in vitro toxin neutralization tests and returned data that was used to assign units to the proposed new standard. The new standard has a diphtheria antitoxin potency of 2 IU/ampoule and is predicted to be stable. A follow up study was performed to assess commutability of the new standard. The follow up study was an existing external quality assessment, modified to include the new standard. Results obtained suggest that the new standard is commutable, showing comparable behaviour to native human serum samples in the majority of the assays compared, and is therefore suitable for use as a reference preparation in assays used to measure the level of anti-diphtheria antibodies in human serum.

  13. 1st Advanced Marine Renewable Energy Instrumentation Experts Workshop: April 5-7, 2011

    Energy Technology Data Exchange (ETDEWEB)

    2011-10-01

    The U.S. marine energy industry is actively pursuing development of offshore wind and marine hydrokinetic (MHK) energy systems. Experience in the wind energy sector demonstrates that new technology development requires thorough measurement and characterization of the environmental conditions prevalent at installation sites and of technology operating in the field. Presently, there are no turn-key instrumentation system solutions that meet the measurement needs of the marine energy industry. The 1st Advanced Marine Renewable Energy Instrumentation Experts Workshop brought together technical experts from government laboratories, academia, and industry representatives from marine energy, wind, offshore oil and gas, and instrumentation developers to present and discuss the instrumentation needs of the marine energy industry. The goals of the meeting were to: (1) Share the latest relevant knowledge among technical experts; (2) Review relevant state-of-the-art field measurement technologies and methods; (3) Review lessons learned from recent field deployments; (4) Identify synergies across different industries; (5) Identify gaps between existing and needed instrumentation capabilities; (6) Understand who are the leading experts; (7) Provide a forum where stakeholders from the marine energy industry could provide substantive input in the development of new marine energy field deployable instrumentation packages.

  14. A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform.

    Science.gov (United States)

    Lee, Howon; Kim, Hyoki; Kim, Sungsik; Ryu, Taehoon; Kim, Hwangbeom; Bang, Duhee; Kwon, Sunghoon

    2015-02-02

    Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.

  15. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses.

    Science.gov (United States)

    Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Nagarajan, Vijayaraj; Oler, Andrew J; Quiñones, Mariam; Hurt, Darrell; Fursov, Mikhail; Huyen, Yentram

    2014-01-01

    The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and re-run the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

  16. lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.

    Directory of Open Access Journals (Sweden)

    Sarah M Hird

    Full Text Available Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses - NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads. lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License.

  17. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    Science.gov (United States)

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  18. Italian research on Antarctic atmosphere: 1st workshop. Ricerche italiane sull'atmosfera antartica: 1o workshop

    Energy Technology Data Exchange (ETDEWEB)

    Colacino, M. (ed.); Giovannelli, G. (ed.); Stefanutti, L. (ed.)

    1989-01-01

    The papers and reports, presented at this 1st workshop on 'Italian research on antarctic atmosphere', deal with several main topics: meteorology and climatology, aerosol and tropospheric clouds, planetary boundary layer, chemical-physic stratospheric property, aeronomy. They define the stage of development of Italian research in this area after 3 years of activity in Antarctica.

  19. Sun-Earth Day:2008 Space Weather Around the World Total Solar Eclipse of 2008 August 1st in Siberia

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A very unique astronomical phenomenon will take place on the territory of Russia on the 1st August 2008.The total eclipse with a width of about 250 km will cross the Western Siberia from the north to the south,then will cross the Altai Mountains and will go further to the difficult to access regions of China and Mongolia.

  20. Addressing learning difficulties in Newtons 1st and 3rd Laws through problem based inquiry using Easy Java Simulation

    CERN Document Server

    Goh, Khoon Song Aloysius; Yip, Kim Wah; Toh, Ping Yong Jeffrey; Lye, Sze Yee

    2013-01-01

    We develop an Easy Java Simulation (EJS) model for students to visualize Newtons 1st and 3rd laws, using frictionless constant motion equation and a spring collision equation during impact. Using Physics by Inquiry instructional (PbI) strategy, the simulation and its problem based inquiry worksheet aim to enhance learning of these two Newtonian concepts. We report results from Experimental (N=62 students) and Control (N=67) Groups in 11 multiple choice questions pre and post tests, conducted by three teachers in the school. Results suggest, at 95 percent confidence level, significant improvement for concept of Newtons 1st Law while not so for Newtons 3rd Law. A Focus Group Discussion revealed students confirming the usefulness of the EJS model in visualizing the 1st Law while not so much for the 3rd Law. We speculate the design ideas for constant velocity motion in the computer model coupled with the PbI worksheet did allow for making sense and experiencing of the 1st Law, where traditional pen-paper represen...

  1. Aquaporin-2 excretion and renal function during the 1st week of life in preterm newborn infants.

    NARCIS (Netherlands)

    Iacobelli, S.; Addabbo, F.; Bonsante, F.; Procino, G.; Tamma, G.; Acito, A.; Esposito, L.; Svelto, M.; Valenti, G.

    2006-01-01

    In many preterm infants, a characteristic pattern of fluid and electrolyte homeostasis occurs during the 1st week of life, consisting of three phases: prediuretic, diuretic, and postdiuretic. In this study, we evaluated the possible role of aquaporin-2 (AQP2) in renal concentrating ability and corre

  2. Jordanian Kindergarten and 1st-Grade Teachers' Beliefs about Child-Based Dimensions of School Readiness

    Science.gov (United States)

    Fayez, Merfat; Ahmad, Jamal Fathi; Oliemat, Enass

    2016-01-01

    The purpose of this study was to explore the beliefs of Jordanian kindergarten and 1st-grade teachers regarding six child-based dimensions of school readiness: academic knowledge, basic thinking skills, socioemotional maturity, physical well-being and motor development, self-discipline, and communication skills. Questionnaires were used to collect…

  3. The 1st Kalmyk Regiment Formation and Its Military Experience in the War of 1812–1814

    Directory of Open Access Journals (Sweden)

    Utash B. Ochirov

    2012-11-01

    Full Text Available The war of 1812–1814 has become a challenge for the Russian Empire. To meet the attack of “The Grand Armee”, great forces were called up, including the regiments, formed from non-Russian ethnic groups. The 1st Kalmyk Regiment (Commander – Captain Dzhamba-taysha Tundutov was one of these regiments. It should be noted that the historiography of Napoleonic Wars starting from the XIX century was interested in irregular regiments far less than in the regular ones, that is why their history abounded with unexplored facts. Stavropol, 1st and 2nd Kalmyk Regiments went through a glorious way in the war of 1812–1814, but, unfortunately, for a number of reasons it was misrepresented in the history of the XХ century. The 1st Kalmyk Regiment was the most unlucky, as its military experience was far from being true due to the mistakes, made by the researchers. The article is focused on the history of the 1st Kalmyk Regiment formation and its military experience in the war of 1812–1814. The work is chiefly based on the Russian State Military History Archive data.

  4. Chairs' Introduction to APOS2008——The 1st Asia-Pacific Optical Fiber Sensors Conference

    Institute of Scientific and Technical Information of China (English)

    Yun-Jiang Rao

    2008-01-01

    @@ This special issue in the Journal of Electronic Science & Technology of China (JESTC) contains the selected papers presented at the 1st Asia-Pacific Optical Fiber Sensors Conference (APOS2008) organized by University of Electronic Science and Technology of China and Chongqing University, China.

  5. NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine.

    Science.gov (United States)

    Abulí, Anna; Boada, Montserrat; Rodríguez-Santiago, Benjamín; Coroleu, Buenaventura; Veiga, Anna; Armengol, Lluís; Barri, Pedro N; Pérez-Jurado, Luis A; Estivill, Xavier

    2016-06-01

    Next-generation sequencing (NGS) has the capacity of carrier screening in gamete donation (GD) programs. We have developed and validated an NGS carrier-screening test (qCarrier test) that includes 200 genes associated with 368 disorders (277 autosomal recessive and 37 X-linked). Carrier screening is performed on oocyte donation candidates and the male partner of oocyte recipient. Carriers of X-linked conditions are excluded from the GD program, whereas donors are chosen who do not carry mutations for the same gene/disease as the recipients. The validation phase showed a high sensitivity (>99% sensitivity) detecting all single-nucleotide variants, 13 indels, and 25 copy-number variants included in the validation set. A total of 1,301 individuals were analysed with the qCarrier test, including 483 candidate oocyte donors and 635 receptor couples, 105 females receiving sperm donation, and 39 couples seeking pregnancy. We identified 56% of individuals who are carriers for at least one genetic condition and 1.7% of female donors who were excluded from the program due to a carrier state of X-linked conditions. Globally, 3% of a priori assigned donations had a high reproductive risk that could be minimized after testing. Genetic counselling at different stages is essential for helping to facilitate a successful and healthy pregnancy.

  6. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.

    Science.gov (United States)

    Bianchi, Valerio; Ceol, Arnaud; Ogier, Alessandro G E; de Pretis, Stefano; Galeota, Eugenia; Kishore, Kamal; Bora, Pranami; Croci, Ottavio; Campaner, Stefano; Amati, Bruno; Morelli, Marco J; Pelizzola, Mattia

    2016-01-01

    Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: (1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; (2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; (3) ensuring complete traceability of the analysis performed; (4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; (5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  7. Integrated systems for NGS data management and analysis: open issues and available solutions

    Directory of Open Access Journals (Sweden)

    Valerio eBianchi

    2016-05-01

    Full Text Available Next-generation sequencing (NGS technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: 1 adopting a laboratory management system (LIMS and safeguard the resulting raw data structure in downstream analyses; 2 monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; 3 ensuring complete traceability of the analysis performed; 4 enabling non-experienced users to run analyses through a graphical user interface (GUI acting as a front-end for the pipelines; 5 relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system (WMS conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  8. CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS).

    Science.gov (United States)

    El-Husny, Antonette; Raiol-Moraes, Milene; Amador, Marcos; Ribeiro-Dos-Santos, André M; Montagnini, André; Barbosa, Silvanira; Silva, Artur; Assumpção, Paulo; Ishak, Geraldo; Santos, Sidney; Pinto, Pablo; Cruz, Aline; Ribeiro-Dos-Santos, Ândrea

    2016-05-13

    Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform.

  9. Assessment of the latest NGS enrichment capture methods in clinical context.

    Science.gov (United States)

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  10. Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa.

    Science.gov (United States)

    Perez-Carro, Raquel; Corton, Marta; Sánchez-Navarro, Iker; Zurita, Olga; Sanchez-Bolivar, Noelia; Sánchez-Alcudia, Rocío; Lelieveld, Stefan H; Aller, Elena; Lopez-Martinez, Miguel Angel; López-Molina, Ma Isabel; Fernandez-San Jose, Patricia; Blanco-Kelly, Fiona; Riveiro-Alvarez, Rosa; Gilissen, Christian; Millan, Jose M; Avila-Fernandez, Almudena; Ayuso, Carmen

    2016-01-25

    Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) characterized by photoreceptor degeneration. RP is highly heterogeneous both clinically and genetically, which complicates the identification of causative genes and mutations. Targeted next-generation sequencing (NGS) has been demonstrated to be an effective strategy for the detection of mutations in RP. In our study, an in-house gene panel comprising 75 known RP genes was used to analyze a cohort of 47 unrelated Spanish families pre-classified as autosomal recessive or isolated RP. Disease-causing mutations were found in 27 out of 47 cases achieving a mutation detection rate of 57.4%. In total, 33 pathogenic mutations were identified, 20 of which were novel mutations (60.6%). Furthermore, not only single nucleotide variations but also copy-number variations, including three large deletions in the USH2A and EYS genes, were identified. Finally seven out of 27 families, displaying mutations in the ABCA4, RP1, RP2 and USH2A genes, could be genetically or clinically reclassified. These results demonstrate the potential of our panel-based NGS strategy in RP diagnosis.

  11. NGS-based Molecular diagnosis of 105 eyeGENE(®) probands with Retinitis Pigmentosa.

    Science.gov (United States)

    Ge, Zhongqi; Bowles, Kristen; Goetz, Kerry; Scholl, Hendrik P N; Wang, Feng; Wang, Xinjing; Xu, Shan; Wang, Keqing; Wang, Hui; Chen, Rui

    2015-12-15

    The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE(®)) was established in an effort to facilitate basic and clinical research of human inherited eye disease. In order to provide high quality genetic testing to eyeGENE(®)'s enrolled patients which potentially aids clinical diagnosis and disease treatment, we carried out a pilot study and performed Next-generation sequencing (NGS) based molecular diagnosis for 105 Retinitis Pigmentosa (RP) patients randomly selected from the network. A custom capture panel was designed, which incorporated 195 known retinal disease genes, including 61 known RP genes. As a result, disease-causing mutations were identified in 52 out of 105 probands (solving rate of 49.5%). A total of 82 mutations were identified, and 48 of them were novel. Interestingly, for three probands the molecular diagnosis was inconsistent with the initial clinical diagnosis, while for five probands the molecular information suggested a different inheritance model other than that assigned by the physician. In conclusion, our study demonstrated that NGS target sequencing is efficient and sufficiently precise for molecular diagnosis of a highly heterogeneous patient cohort from eyeGENE(®).

  12. Specialty preferences of 1st year medical students in a Saudi Medical School – Factors affecting these choices and the influence of gender

    Science.gov (United States)

    Kaliyadan, Feroze; Amin, Tarek Tawfik; Qureshi, Habib; Al Wadani, Fahad

    2015-01-01

    Background and Aims: In recent years there has been a growing appreciation of the issues of career preference in medicine as it affects student learning and academic performance. Various factors influence the specialty choices of medical students. Some specialties tend to attract students more than others. One possible consequence of this would be a mismatch between health needs and specialist numbers in the region. This study investigated the career preferences of 1st year medical students in a Saudi medical school and to assess factors affecting these choices. Materials and Methods: The study was a cross-sectional survey carried out on the 1st year undergraduate students in the college of medicine, King Faisal University, Saudi Arabia. A total of 109 students (57 female and 52 males) responded to the questionnaire which was initially administered to all the students of the 1st year – A total of 120 students (response rate was 90.8%). A mixed method approach was used and qualitative data from open-ended questions were analyzed based on thematic analysis. Results: The top choices were general surgery, internal medicine, and pediatrics. Among female students; the top specialty choices were: General surgery (23%), pediatrics (18%), and dermatology (15%). Among the male students; the top choices were: General surgery (54%) and internal medicine (23%). Of the total, 57% of the students agreed or strongly agreed that primary aptitude was the main factor affecting the choice. Only 31% felt that there was a significant influence of role model, 48% felt that the advice of others – peers and family, would be a factor influencing their choices, and 53% agreed that specialty choice would influence their future learning patterns. Males were more likely to choose a specialty based on actual aptitude for the specialty, financial rewards, and scope for research; and this gender difference was statistically significant. Conclusion: Surgery was the top-choice in both genders

  13. Next generation sequencing (NGS database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Directory of Open Access Journals (Sweden)

    Chinta Someswara Rao

    2016-03-01

    Full Text Available Next generation sequencing (NGS technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  14. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S. Viswanadha

    2016-01-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching. PMID:26981434

  15. A case study for cloud based high throughput analysis of NGS data using the globus genomics system.

    Science.gov (United States)

    Bhuvaneshwar, Krithika; Sulakhe, Dinanath; Gauba, Robinder; Rodriguez, Alex; Madduri, Ravi; Dave, Utpal; Lacinski, Lukasz; Foster, Ian; Gusev, Yuriy; Madhavan, Subha

    2015-01-01

    Next generation sequencing (NGS) technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the "Globus Genomics" system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon 's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  16. Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string matching.

    Science.gov (United States)

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research in recent years. To provide the comprehensive NGS resource for the research, in this paper , we have considered 10 loci/codi/repeats TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA. Then we developed the NGS Tandem Repeat Database (TandemRepeatDB) for all the chromosomes of Homo sapiens, Callithrix jacchus, Chlorocebus sabaeus, Gorilla gorilla, Macaca fascicularis, Macaca mulatta, Nomascus leucogenys, Pan troglodytes, Papio anubis and Pongo abelii genome data sets for all those locis. We find the successive occurence frequency for all the above 10 SSR (simple sequence repeats) in the above genome data sets on a chromosome-by-chromosome basis with multiple pattern 2° shaft multicore string matching.

  17. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    Directory of Open Access Journals (Sweden)

    Krithika Bhuvaneshwar

    2015-01-01

    Full Text Available Next generation sequencing (NGS technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  18. Creating Research-Rich Learning Experiences and Quantitative Skills in a 1st Year Earth Systems Course

    Science.gov (United States)

    King, P. L.; Eggins, S.; Jones, S.

    2014-12-01

    We are creating a 1st year Earth Systems course at the Australian National University that is built around research-rich learning experiences and quantitative skills. The course has top students including ≤20% indigenous/foreign students; nonetheless, students' backgrounds in math and science vary considerably posing challenges for learning. We are addressing this issue and aiming to improve knowledge retention and deep learning by changing our teaching approach. In 2013-2014, we modified the weekly course structure to a 1hr lecture; a 2hr workshop with hands-on activities; a 2hr lab; an assessment piece covering all face-to-face activities; and a 1hr tutorial. Our new approach was aimed at: 1) building student confidence with data analysis and quantitative skills through increasingly difficult tasks in science, math, physics, chemistry, climate science and biology; 2) creating effective learning groups using name tags and a classroom with 8-person tiered tables; 3) requiring students to apply new knowledge to new situations in group activities, two 1-day field trips and assessment items; 4) using pre-lab and pre-workshop exercises to promote prior engagement with key concepts; 5) adding open-ended experiments to foster structured 'scientific play' or enquiry and creativity; and 6) aligning the assessment with the learning outcomes and ensuring that it contains authentic and challenging southern hemisphere problems. Students were asked to design their own ocean current experiment in the lab and we were astounded by their ingenuity: they simulated the ocean currents off Antarctica; varied water density to verify an equation; and examined the effect of wind and seafloor topography on currents. To evaluate changes in student learning, we conducted surveys in 2013 and 2014. In 2014, we found higher levels of student engagement with the course: >~80% attendance rates and >~70% satisfaction (20% neutral). The 2014 cohort felt that they were more competent in writing

  19. 1st paleomagnetic investigation of Nubia Sandstone at Kalabsha, south Western Desert of Egypt

    Directory of Open Access Journals (Sweden)

    R. Mostafa

    2016-06-01

    Full Text Available Two profiles have been sampled from the Nubia Sandstone at Aswan, south Western Desert: the 1st profile has been taken from Abu Aggag Formation and the 2nd one was from Sabaya Formation (23.25 °N, 32.75 °E. 136 oriented cores (from 9 sites have been sampled. Abu Aggag Formation is of Late Cretaceous (Turonian and Sabaya Formation is of early Cretaceous (Albian–Cenomanian. The studied rocks are subjected to rock magnetic measurements as well as demagnetization treatment. It has been found that hematite is the main magnetic mineral in both formations. Four profile sections from Abu Aggag Formation, yielded a magnetic component with D = 352.7°, I = 36.6° with α95 = 5.2° and the corresponding pole lies at Lat. = 82.8 °N and Long. = 283.1 °E. Five profile sections from Sabaya Formation, yielded a magnetic component with D = 348.6°, I = 33.3° with α95 = 5.8° and the corresponding pole lies at Lat. = 78.3 °N and Long. = 280.4 °E. The obtained paleopole for the two formations lies at Lat. = 80.5 °N and Long. = 281.7 °E. The obtaind magnetic components are considered primary and the corresponding paleopole reflects the age of Nubia Sandstone when compared with the previously obtained Cretaceous poles for Egypt.

  20. Patterns of Irregular Burials in Western Europe (1st-5th Century A.D.)

    Science.gov (United States)

    Milella, Marco; Mariotti, Valentina; Belcastro, Maria Giovanna; Knüsel, Christopher J.

    2015-01-01

    Background Irregular burials (IB—burials showing features that contrast with the majority of others in their geographic and chronological context) have been the focus of archaeological study because of their relative rarity and enigmatic appearance. Interpretations of IB often refer to supposed fear of the dead or to social processes taking place in time-specific contexts. However, a comprehensive and quantitative analysis of IB for various geographical contexts is still lacking, a fact that hampers any discussion of these burials on a larger scale. Methods Here, we collected a bibliographic dataset of 375 IB from both Britain and Continental Europe, altogether spanning a time period from the 1st to the 5th century AD. Each burial has been coded according to ten dichotomous variables, further analyzed by means of chi-squared tests on absolute frequencies, non-metric multidimensional scaling, and cluster analysis. Results Even acknowledging the limits of this study, and in particular the bias represented by the available literature, our results point to interesting patterns. Geographically, IB show a contrast between Britain and Continental Europe, possibly related to historical processes specific to these regions. Different types of IB (especially prone depositions and depositions with the cephalic extremity displaced) present a series of characteristics and associations between features that permit a more detailed conceptualization of these occurrences from a socio-cultural perspective that aids to elucidate their funerary meaning. Conclusions and Significance Altogether, the present work stresses the variability of IB, and the need to contextualize them in a proper archaeological and historical context. It contributes to the discussion of IB by providing a specific geographic and chronological frame of reference that supports a series of hypotheses about the cultural processes possibly underlying their occurrence. PMID:26115408

  1. After Meeting: The 1st Maritime Pilotage/Towage Services and Technologies Congress

    Directory of Open Access Journals (Sweden)

    Adnan PARLAK

    2016-03-01

    Full Text Available The 1st Maritime Pilotage/Towage Services and Technologies Congress has been organized by UCTEA Chambers of Marine Engineers, UCTEA the Chamber of Turkish Naval Architects & Marine Engineers and Turkish Maritime Pilots’ Association at 23 October 2015, Hilton Hotel, İzmir. In the opening ceremony, two distinguished keynote speakers have presented their presentations. Captain Stein Inge DAHN who is the president of European Maritime Pilots’ Association(EMPA has given a fulfilling speech on switching to hand steering by giving an example from the automation in the Aviation Industry. The second keynote speaker Robert G. Allan, who is the Executive Chairman of Robert Allan Ltd., has given a leading speech under the title of “The State of the Art in Escort Tug Technology -2015”. Five key points have come into prominence during the symposium. To summarize: • To prevent ships and cargos which are exposed to damages, • To prevent marine and coastal environments against pollution due to collisions, • To establish fast, secure and well organized sea traffic • To develop new escort tug technologies and pilotage softwares in the national level which is open to competitions in the international markets. • Opening maritime pilotage into the competitions in the areas which needs special expertize. In my opinion, the topics discussed in the symposium have the attendants won a wide horizon in the field. However, the presentations related to Escort Tug Technologies were insufficient from the standpoint of both quality and numbers of the manuscripts presented. Due to importance of Maritime Pilotage/Towage Services and Technologies, much more attentions must be taken in the national and international levels and sustainability of the symposium must be provided .

  2. Prevalence of injuries in Wushu competition during the 1st Asian Martial Arts Games 2009.

    Science.gov (United States)

    Yiemsiri, Pichet; Wanawan, Amarin

    2014-02-01

    To determine the prevalence and characteristic of injuries in Wushu Competition during the IP' Asian MartialArts Games 2009. Sixty international athletes (38 males) participating in Wushu Competition during the 1st Asian Martial Arts Games 2009. Injuries were recorded on injury report forms to document any injuries seen and treatment provided by tournament physician during competitions. The injury forms described the athlete s causes, type, site, and severity of the injuries. There were 60 international athletes the average age were 22.49 +/- 3.75 years. The prevalence ofinjuries was 228.07/ 1000 athlete exposure (AE). The prevalence in males andfemales was 161.76/1000 AE and 326.09/1000 AE, respectively. The most common injured body parts in males were lower extremities 102.94/1000 AE, followed by head and face injuries 58.82/1000 AE. The most common injured body parts in females were lower extremities 282.61/1000 AE. The most common types of injuries in males were contusions 58.82/1000 AE, concussion 29.41/1000 AE and strain-sprain 29.41/1000 AE. In females the most common type of injury were contusion 195.65/1000 AEfollowed by strain-sprain 130.43/1000 AE. The most common mechanism of injury in males werereceiving a punch 58.82/1000 AE, receiving a kick 44.12/1000 AE and delivering a kick 44.12/1000 AE. Meanwhile, in females common mechanisms were receiving a kick 152.17/1000 AE followed by delivering a kick 130.43/1000 AE. High prevalence of injuries in Wushu competition during the 1" Asian MartialArts Games 2009 revealedfemale injuries were higher than male and had a higher prevalence compared with Muay Thai or Taekwondo competitions.

  3. Meteorological features associated with unprecedented precipitation over India during 1st week of March 2015

    Indian Academy of Sciences (India)

    Naresh Kumar; M Mohapatra; A K Jaswal

    2017-07-01

    Unprecedented precipitation along with heavy falls occurred over many parts of India from 28th February to 2nd March 2015. Many of the stations of northwest and central India received an all time high 24 hr cumulative precipitation of March during this period. Even the national capital, New Delhi, broke all the previous historical 24 hr rainfall records of the last 100 years to the rainfall record in March 2015. Due to this event, huge loss to agricultural and horticultural crops occurred in several parts of India. In the present study, an attempt is made to understand the various meteorological features associated with this unprecedented precipitation event over India. It occurred due to the presence of an intense western disturbance (WD) over Afghanistan and neighbouring areas in the form of north–south oriented deep trough in westerlies in middle and upper tropospheric levels with its southern end deep in the Arabian Sea, which pumped huge moisture feed over Indian region. Also, there was a jet stream with core wind speed up to 160 knots that generated high positive divergence at upper tropospheric level over Indian region; along with this there was high magnitude of negative vertical velocity and velocity convergence were there at middle tropospheric level. It caused intense upward motion and forced lower levels air to rise and strengthen the lower levels cyclonic circulations (CCs)/Lows. Moreover, the induced CCs/Lows at lower tropospheric levels associated with WD were more towards south of its normal position. Additionally, there was wind confluence over central parts of India due to westerlies in association with WD and easterlies from anticyclone over north Bay of Bengal. Thus, intense WD along with wind confluence between westerlies and easterlies caused unprecedented precipitation over India during the 1st week of March 2015.

  4. A simple design rule for 1st order form-closure of underactuated hands

    Directory of Open Access Journals (Sweden)

    S. Krut

    2011-02-01

    Full Text Available The property of form-closure of a grasp, as generally defined in the literature, is based on the assumption that contact points between the hand and the object are fixed in space. However, this assumption is false when considering a grasp exerted by an underactuated hand, since in this case, it is not possible to control the position of each phalanx independently. In spite of researchers' interest in studying form-closure, none of the available published work on this subject takes into consideration the particular kinematics of underactuated hands. Actually, there are few available tools to qualify or quantify the stability of a grasp exerted by an underactuated hand, thus the design of underactuated hands mostly results from an intuitive approach. This paper aims to reduce this gap.

    A classification of underactuated hands is proposed, based on the expression of contact forces. This highlights the influence of non-backdrivable mechanisms introduced in the transmission of the closing motion of the hand on the stability of the grasp. The way to extend the original definition of form-closure to underactuated grasps is illustrated. A more general definition is formulated, which checks the stability of the set "object + hand". Using this new definition, a simple rule is proposed for designing a hand capable of achieving 1st order form-closed grasps.

    This paper was presented at the IFToMM/ASME International Workshop on Underactuated Grasping (UG2010, 19 August 2010, Montréal, Canada.

  5. PREFACE: 1st Conference on Light and Particle Beams in Materials Science 2013 (LPBMS2013)

    Science.gov (United States)

    Kumai, Reiji; Murakami, Youichi

    2014-04-01

    From 29-31 August 2013, the 1st International Conference on Light and Particle Beams in Materials Science, LPBMS 2013, took place in the Tsukuba International Congress Center in the city of Tsukuba, Japan. The conference was a continuation of the international series Synchrotron Radiation in Materials Science (SRMS), which started in 1994. The last one, SRMS-7, was held in Oxford UK 11-14 July 2010, where the International Advisory Committee (IAC) recommended the conference be enlarged to incorporate Materials Research from Neutron, Muon, and Slow Positron Sources, as well as the science emerging from Synchrotron Light Sources. The conference brought together contributions from academics and industrial researchers with a diverse background and experience from the physics, chemistry and engineering communities. The topics covered in the LPBMS2013 include strongly correlated electron systems, magnetism and magnetic materials, soft matter, interface and surface defects, catalysts, biomaterials, and ceramics. In the 3-day scientific program, the conference consisted of 9 plenary talks, 33 invited talks, 20 oral presentations, and 126 poster presentations. We are pleased to publish the proceedings of the LPBMS2013 in this volume of Journal of Physics: Conference Series. This volume contains 58 papers representing the work that was presented and discussed at the conference. We hope that this volume will promote further development of this interdisciplinary materials research emerging from synchrotron light, neutron, muon, and slow positron sciences. Finally, we would like to thank the International Advisory Committee (Chair: Professor G N Greaves), sponsors, all the participants and contributors for making possible this international meeting of researchers. Reiji Kumai & Youichi Murakami Conference photograph Details of the program and organizing committees are available in the pdf

  6. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

    Science.gov (United States)

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

  7. Next-generation sequencing (NGS for assessment of microbial water quality: current progress, challenges, and future opportunities

    Directory of Open Access Journals (Sweden)

    BoonFei eTan

    2015-09-01

    Full Text Available Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  8. SURVEY

    DEFF Research Database (Denmark)

    SURVEY er en udbredt metode og benyttes inden for bl.a. samfundsvidenskab, humaniora, psykologi og sundhedsforskning. Også uden for forskningsverdenen er der mange organisationer som f.eks. konsulentfirmaer og offentlige institutioner samt marketingsafdelinger i private virksomheder, der arbejder...... med surveys. Denne bog gennemgår alle surveyarbejdets faser og giver en praktisk indføring i: • design af undersøgelsen og udvælgelse af stikprøver, • formulering af spørgeskemaer samt indsamling og kodning af data, • metoder til at analysere resultaterne...

  9. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients.

    Science.gov (United States)

    Pulsipher, Michael A; Carlson, Chris; Langholz, Bryan; Wall, Donna A; Schultz, Kirk R; Bunin, Nancy; Kirsch, Ilan; Gastier-Foster, Julie M; Borowitz, Michael; Desmarais, Cindy; Williamson, David; Kalos, Michael; Grupp, Stephan A

    2015-05-28

    Positive detection of minimal residual disease (MRD) by multichannel flow cytometry (MFC) prior to hematopoietic cell transplantation (HCT) of patients with acute lymphoblastic leukemia (ALL) identifies patients at high risk for relapse, but many pre-HCT MFC-MRD negative patients also relapse, and the predictive power MFC-MRD early post-HCT is poor. To test whether the increased sensitivity of next-generation sequencing (NGS)-MRD better identifies pre- and post-HCT relapse risk, we performed immunoglobulin heavy chain (IgH) variable, diversity, and joining (V[D]J) DNA sequences J NGS-MRD on 56 patients with B-cell ALL enrolled in Children's Oncology Group trial ASCT0431. NGS-MRD predicted relapse and survival more accurately than MFC-MRD (P NGS-MRD detection was better at predicting relapse than MFC-MRD (P NGS-MRD positive relapse rate, 67%; P = .004). Any post-HCT NGS positivity resulted in an increase in relapse risk by multivariate analysis (hazard ratio, 7.7; P = .05). Absence of detectable IgH-V(D)J NGS-MRD pre-HCT defines good-risk patients potentially eligible for less intense treatment approaches. Post-HCT NGS-MRD is highly predictive of relapse and survival, suggesting a role for this technique in defining patients early who would be eligible for post-HCT interventions. The trial was registered at www.clinicaltrials.gov as #NCT00382109.

  10. SU-E-T-188: Commission of World 1st Commercial Compact PBS Proton System

    Energy Technology Data Exchange (ETDEWEB)

    Ding, X; Patel, B; Song, X; Syh, J; Syh, J; Zhang, J; Freund, D; Rosen, L; Wu, H [Willis-Knighton Medical Center, Shreveport, LA (United States)

    2015-06-15

    Purpose: ProteusONE is the 1st commercial compact PBS proton system with an upstream scanning gantry and C230 cyclotron. We commissioned XiO and Raystation TPS simultaneously. This is a summary of beam data collection, modeling, and verification and comparison without range shiter for this unique system with both TPS. Methods: Both Raystation and XiO requires the same measurements data: (i) integral depth dose(IDDs) of single central spot measured in water tank; (ii) absolute dose calibration measured at 2cm depth of water with mono-energetic 10×10 cm2 field with spot spacing 4mm, 1MU per spot; and (iii) beam spot characteristics in air at 0cm and ± 20cm away from ISO. To verify the beam model for both TPS, same 15 cube plans were created to simulate different treatment sites, target volumes and positions. PDDs of each plan were measured using a Multi-layer Ionization Chamber(MLIC), absolute point dose verification were measured using PPC05 in water tank and patient-specific QA were measured using MatriXX PT, a 2D ion chamber array. Results: All the point dose measurements at midSOBP were within 2% for both XiO and Raystation. However, up to 5% deviations were observed in XiO’s plans at shallow depth while within 2% in Raystation plans. 100% of the ranges measured were within 1 mm with maximum deviation of 0.5 mm. 20 patient specific plan were generated and measured in 3 planes (distal, proximal and midSOBP) in Raystation. The average of gamma index is 98.7%±3% with minimum 94% Conclusions: Both TPS were successfully commissioned and can be safely deployed for clinical use for ProteusONE. Based on our clinical experience in PBS planning, user interface, function and workflow, we preferably use Raystation as our main clinical TPS. Gamma Index >95% at 3%/3 mm criteria is our institution action level for patient specific plan QAs.

  11. PREFACE: 1st International Conference on Sensing for Industry, Control, Communication & Security Technologies

    Science.gov (United States)

    Shuja Syed, Ahmed

    2013-12-01

    The 1st International Conference on Sensing for Industry, Control, Communication & Security Technologies (ICSICCST-2013), took place in Karachi, Pakistan, from 24-26 June 2013. It was organized by Indus University, Karachi, in collaboration with HEJ Research Institute of Chemistry, University of Karachi, Karachi. More than 80 abstracts were submitted to the conference and were double blind-reviewed by an international scientific committee. The topics of the Conference were: Video, Image & Voice Sensing Sensing for Industry, Environment, and Health Automation and Controls Laser Sensors and Systems Displays for Innovative Applications Emerging Technologies Unmanned, Robotic, and Layered Systems Sensing for Defense, Homeland Security, and Law Enforcement The title of the conference, 'Sensing for Industry, Control, Communication & Security Technologies' is very apt in capturing the main issues facing the industry of Pakistan and the world. We believe the sensing industry, particularly in Pakistan, is currently at a critical juncture of its development. The future of the industry will depend on how the industry players choose to respond to the challenge of global competition and opportunities arising from strong growth in the Asian region for which we are pleased to note that the conference covered a comprehensive spectrum of issues with an international perspective. This will certainly assist industry players to make informed decisions in shaping the future of the industry. The conference gathered qualified researchers from developed countries like USA, UK, Sweden, Saudi Arabia, China, South Korea and Malaysia etc whose expertise resulting from the research can be drawn upon to build an exploitable area of new technology that has potential Defense, Homeland Security, and Military applicability. More than 250 researchers/students attended the event and made the event great success as the turnout was 100%. An exceptional line-up of speakers spoke at the occasion. We want

  12. PREFACE: 1st International Conference on Mechanical Engineering Research 2011 (ICMER2011)

    Science.gov (United States)

    Abu Bakar, Rosli

    2012-09-01

    The year 2010 represented a significant milestone in the history of the Mechanical Engineering community with the organization of the first and second national level conferences (National Conference in Mechanical Engineering for Research, 1st and 2nd NCMER) at Universiti Malaysia Pahang on 26-27 May and 3-4 December 2010. The conferences attracted a large number of delegates from different premier academic and research institutions in the country to participate and share their research experiences at the conference. The International Conference on Mechanical Engineering Research (ICMER 2011) followed on from the first and second conferences due to good support from researchers. The ICMER 2011 is a good platform for researchers and postgraduate students to present their latest finding in research. The conference covers a wide range of topics including the internal combustion engine, machining processes, heat and mass transfer, fuel, biomechanical analysis, aerodynamic analysis, thermal comfort, computational techniques, design and simulation, automotive transmission, optimization techniques, hybrid electric vehicles, engine vibration, heat exchangers, finite element analysis, computational fluid dynamics, green energy, vehicle dynamics renewable energy, combustion, design, product development, advanced experimentation techniques, to name but a few. The international conference has helped to bridge the gap between researchers working at different institutions and in different countries to share their knowledge and has helped to motivate young scientists with their research. This has also given some clear direction for further research from the deliberations of the conference. Several people have contributed in different ways to the success of the conference. We thank the keynote speakers and all authors of the contributed papers, for the cooperation rendered to us in the publication of the CD conference proceedings. In particular, we would like to place on record our

  13. [Molecular-genetic analysis of DNA pol and TK of HSV-1 population using NGS technology].

    Science.gov (United States)

    Gus'kova, A A; Skoblov, M Iu; Lavrov, A V; Zubtsov, D A; Andronova, V L; Gol'dshteĭn, D V; Galegov, G A; Skoblov, Iu S

    2013-01-01

    It was determined the ratio of viral DNA and DNA from Vero cells using the polymerase chain reaction in real time in Vero cell lysate, infected with L2 strain of the herpes simplex virus type 1. Copy number of the virus reached a maximum after 24 hours of incubation of infection. Total DNA was isolated and sequenced using NGS technology by Ion Torrent device. Nucleotide sequences of the thymidine kinase gene (UL23) and DNA polymerase (UL30) were determined for a population of HSV-1 strain L2. Comparison of the primary structure of these genes with the corresponding nucleotide sequences of known strains of HSV-1 KOS and 17 was conducted. Differences in the structure of genes UL23 and UL30 between strain L2 and reference strains KOS and 17 are not important, because changes are found in non-conservative regions.

  14. ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.

    Science.gov (United States)

    Raine, Keiran M; Van Loo, Peter; Wedge, David C; Jones, David; Menzies, Andrew; Butler, Adam P; Teague, Jon W; Tarpey, Patrick; Nik-Zainal, Serena; Campbell, Peter J

    2016-12-08

    We have developed ascatNgs to aid researchers in carrying out Allele-Specific Copy number Analysis of Tumours (ASCAT). ASCAT is capable of detecting DNA copy number changes affecting a tumor genome when comparing to a matched normal sample. Additionally, the algorithm estimates the amount of tumor DNA in the sample, known as Aberrant Cell Fraction (ACF). ASCAT itself is an R-package which requires the generation of many file types. Here, we present a suite of tools to help handle this for the user. Our code is available on our GitHub site (https://github.com/cancerit). This unit describes both 'one-shot' execution and approaches more suitable for large-scale compute farms. © 2016 by John Wiley & Sons, Inc.

  15. [Fe II] 1.64 um Imaging Observations of the Outflow Features around Ultracompact H II Regions in the 1st Galactic Quadrant

    CERN Document Server

    Shinn, Jong-Ho; Lee, Jae-Joon; Lee, Yong-Hyun; Kim, Hyun-Jeong; Pyo, Tae-Soo; Koo, Bon-Chul; Kyeong, Jaemann; Hwang, Narae; Park, Byeong-Gon

    2014-01-01

    We present [Fe II] 1.644 um features around ultracompact H II regions (UCHIIs) found on a quest for the "footprint" outflow features of UCHIIs---the feature produced by the outflowing materials ejected during the earlier, active accretion phase of massive young stellar objects (MYSOs). We surveyed 237 UCHIIs in the 1st Galactic quadrant, employing the CORNISH UCHII catalog and UWIFE data which is an imaging survey in [Fe II] 1.644 um performed with UKIRT-WFCAM under ~ 0.8" seeing condition. The [Fe II] features were found around five UCHIIs, one of which is of low plausibility. We interpret that the [Fe II] features are shock-excited by outflows from YSOs, and estimate the outflow mass loss rates from the [Fe II] flux, which are ~ 1 x 10^-6 - 4 x 10^-5 Ms yr^-1. We propose that the [Fe II] features might be the "footprint" outflow features, but more studies are required to clarify it. This is based on the morphological relation between the [Fe II] and 5 GHz radio features, the outflow mass loss rate, the trav...

  16. The August 1st, 2014 ( M w 5.3) Moderate Earthquake: Evidence for an Active Thrust Fault in the Bay of Algiers (Algeria)

    Science.gov (United States)

    Benfedda, A.; Abbes, K.; Bouziane, D.; Bouhadad, Y.; Slimani, A.; Larbes, S.; Haddouche, D.; Bezzeghoud, M.

    2017-03-01

    On August 1st, 2014, a moderate-sized earthquake struck the capital city of Algiers at 05:11:17.6 (GMT+1). The earthquake caused the death of six peoples and injured 420, mainly following a panic movement among the population. Following the main shock, we surveyed the aftershock activity using a portable seismological network (short period), installed from August 2nd, 2014 to August 21st, 2015. In this work, first, we determined the main shock epicenter using the accelerograms recorded by the Algerian accelerograph network (under the coordination of the National Center of Applied Research in Earthquake Engineering-CGS). We calculated the focal mechanism of the main shock, using the inversion of the accelerograph waveforms in displacement that provides a reverse fault with a slight right-lateral component of slip and a compression axis striking NNW-SSE. The obtained scalar seismic moment ( M o = 1.25 × 1017 Nm) corresponds to a moment magnitude of M w = 5.3. Second, the analysis of the obtained aftershock swarm, of the survey, suggests an offshore ENE-WSW, trending and NNW dipping, causative active fault in the bay of Algiers, which may likely correspond to an offshore unknown segment of the Sahel active fault.

  17. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling.

    Science.gov (United States)

    Rovigatti, Ugo

    2015-11-01

    It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.

  18. Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case

    Directory of Open Access Journals (Sweden)

    Adam G. Marsh

    2016-11-01

    Full Text Available Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS data using methyl-sensitive restriction endonucleases (MSRE. An integrated pipeline efficiently incorporates raw NGS metrics into a statistical discrimination platform to identify functional linkages between shifts in epigenetic DNA methylation and disease phenotypes in samples being analyzed. In this pilot proof-of-concept study we quantify and compare DNA methylation in blood serum of individuals with Parkinson's Disease relative to matched healthy blood profiles. Even with a small study of only six samples, a high degree of statistical discrimination was achieved based on CpG methylation profiles between groups, with 1,008 statistically different CpG sites (p textless 0.0025, after false discovery rate correction. A methylation load calculation was used to assess higher order impacts of methylation shifts on genes and pathways and most notably identified FGF3, FGF8, HTT, KMTA5, MIR8073, and YWHAG as differentially methylated genes with high relevance to Parkinson's Disease and neurodegeneration (based on PubMed literature citations. Of these, KMTA5 is a histone methyl-transferase gene and HTT is Huntington Disease Protein or Huntingtin, for which there are well established neurodegenerative impacts. The future need for precision diagnostics now requires more tools for exploring epigenetic processes that may be linked to cellular dysfunction and subsequent disease progression.

  19. Determining performance characteristics of an NGS-based HLA typing method for clinical applications.

    Science.gov (United States)

    Duke, J L; Lind, C; Mackiewicz, K; Ferriola, D; Papazoglou, A; Gasiewski, A; Heron, S; Huynh, A; McLaughlin, L; Rogers, M; Slavich, L; Walker, R; Monos, D S

    2016-03-01

    This study presents performance specifications of an in-house developed human leukocyte antigen (HLA) typing assay using next-generation sequencing (NGS) on the Illumina MiSeq platform. A total of 253 samples, previously characterized for HLA-A, -B, -C, -DRB1 and -DQB1 were included in this study, which were typed at high-resolution using a combination of Sanger sequencing, sequence-specific primer (SSP) and sequence-specific oligonucleotide probe (SSOP) technologies and recorded at the two-field level. Samples were selected with alleles that cover a high percentage of HLA specificities in each of five different race/ethnic groups: European, African-American, Asian Pacific Islander, Hispanic and Native American. Sequencing data were analyzed by two software programs, Omixon's target and GenDx's NGSengine. A number of metrics including allele balance, sensitivity, specificity, precision, accuracy and remaining ambiguity were assessed. Data analyzed by the two software systems are shown independently. The majority of alleles were identical in the exonic sequences (third field) with both programs for HLA-A, -B, -C and -DQB1 in 97.7% of allele determinations. Among the remaining discrepant genotype calls at least one of the analysis programs agreed with the reference typing. Upon additional manual analysis 100% of the 2530 alleles were concordant with the reference HLA genotypes; the remaining ambiguities did not exceed 0.8%. The results demonstrate the feasibility and significant benefit of HLA typing by NGS as this technology is highly accurate, eliminates virtually all ambiguities, provides complete sequencing information for the length of the HLA gene and forms the basis for utilizing a single methodology for HLA typing in the immunogenetics labs.

  20. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

    Science.gov (United States)

    D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

    2015-01-01

    The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

  1. DEVELOPMENT OF ANALYTICAL METHODS FOR DETERMINING SUPPRESSOR CONCENTRATION IN THE MCU NEXT GENERATION SOLVENT (NGS)

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K.; Fondeur, F.; White, T.; Diprete, D.; Milliken, C.

    2013-07-31

    Savannah River National Laboratory (SRNL) was tasked with identifying and developing at least one, but preferably two methods for quantifying the suppressor in the Next Generation Solvent (NGS) system. The suppressor is a guanidine derivative, N,N',N"-tris(3,7-dimethyloctyl)guanidine (TiDG). A list of 10 possible methods was generated, and screening experiments were performed for 8 of the 10 methods. After completion of the screening experiments, the non-aqueous acid-base titration was determined to be the most promising, and was selected for further development as the primary method. {sup 1}H NMR also showed promising results from the screening experiments, and this method was selected for further development as the secondary method. Other methods, including {sup 36}Cl radiocounting and ion chromatography, also showed promise; however, due to the similarity to the primary method (titration) and the inability to differentiate between TiDG and TOA (tri-n-ocytlamine) in the blended solvent, {sup 1}H NMR was selected over these methods. Analysis of radioactive samples obtained from real waste ESS (extraction, scrub, strip) testing using the titration method showed good results. Based on these results, the titration method was selected as the method of choice for TiDG measurement. {sup 1}H NMR has been selected as the secondary (back-up) method, and additional work is planned to further develop this method and to verify the method using radioactive samples. Procedures for analyzing radioactive samples of both pure NGS and blended solvent were developed and issued for the both methods.

  2. Coronal MR imaging of the normal 3rd, 4th, and 5th lumbar and 1st sacral nerve roots

    Energy Technology Data Exchange (ETDEWEB)

    Hald, J.K.; Nakstad, P.H.; Hauglum, B.E. (National Hospital, Oslo (Norway). Dept. of Radiology)

    1991-05-01

    Seven healthy volunteers underwent coronal MR imaging at 1.5 tesla of the normal 3rd, 4th, and 5th lumbar, and 1st sacral nerve roots. Coronal slices, 3-mm-thick with a 0.3-mm gap between the slices were obtained (TR/TE 600/22) through the lumbar spinal canal. All the nerve roots were visible on at least one image. One can routinely expect to demonstrate the 3rd, 4th, and 5th lumbar, and 1st sacral nerve roots on T1-weighted, 3-mm-thick coronal MR scans. We found no correlation between the degree of lumbar lordosis and the lengths of the visible nerve roots. Five patients with one of the following spinal problems: anomaly, tumor, disk herniation, and failed back surgery syndrome were examined according to our protocol. In all these cases coronal MR imaging gave the correct diagnosis. (orig.).

  3. MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

    Science.gov (United States)

    Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2016-01-01

    Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

  4. NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.

    Science.gov (United States)

    Mendoza-Parra, Marco Antonio; Saleem, Mohamed-Ashick M; Blum, Matthias; Cholley, Pierre-Etienne; Gronemeyer, Hinrich

    2016-01-01

    The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.

  5. ngs (notochord granular surface) gene encodes a novel type of intermediate filament family protein essential for notochord maintenance in zebrafish.

    Science.gov (United States)

    Tong, Xiangjun; Xia, Zhidan; Zu, Yao; Telfer, Helena; Hu, Jing; Yu, Jingyi; Liu, Huan; Zhang, Quan; Sodmergen; Lin, Shuo; Zhang, Bo

    2013-01-25

    The notochord is an important organ involved in embryonic patterning and locomotion. In zebrafish, the mature notochord consists of a single stack of fully differentiated, large vacuolated cells called chordocytes, surrounded by a single layer of less differentiated notochordal epithelial cells called chordoblasts. Through genetic analysis of zebrafish lines carrying pseudo-typed retroviral insertions, a mutant exhibiting a defective notochord with a granular appearance was isolated, and the corresponding gene was identified as ngs (notochord granular surface), which was specifically expressed in the notochord. In the mutants, the notochord started to degenerate from 32 hours post-fertilization, and the chordocytes were then gradually replaced by smaller cells derived from chordoblasts. The granular notochord phenotype was alleviated by anesthetizing the mutant embryos with tricaine to prevent muscle contraction and locomotion. Phylogenetic analysis showed that ngs encodes a new type of intermediate filament (IF) family protein, which we named chordostatin based on its function. Under the transmission electron microcopy, bundles of 10-nm-thick IF-like filaments were enriched in the chordocytes of wild-type zebrafish embryos, whereas the chordocytes in ngs mutants lacked IF-like structures. Furthermore, chordostatin-enhanced GFP (EGFP) fusion protein assembled into a filamentous network specifically in chordocytes. Taken together, our work demonstrates that ngs encodes a novel type of IF protein and functions to maintain notochord integrity for larval development and locomotion. Our work sheds light on the mechanisms of notochord structural maintenance, as well as the evolution and biological function of IF family proteins.

  6. Haydn, by Villa-Lobos: an analysis of 1st movement of Villa-Lobos's String Quartet #7

    OpenAIRE

    2012-01-01

    Este estudo analisa o 1º movimento do Quarteto de Cordas nº 7 de Villa-Lobos e investiga possíveis referências aos quartetos de cordas compostos por Franz Haydn, como Villa-Lobos sugeriu a Arnaldo Estrella.This article analyses the 1st movement of Villa-Lobos' String Quartet nº 7 and search for possible references to Franz Haydn's string quartets, as suggested by Villa-Lobos in conversations with Arnaldo Estrella.

  7. Uncertainty Requirement Analysis for the Orbit, Attitude, and Burn Performance of the 1st Lunar Orbit Insertion Maneuver

    Science.gov (United States)

    Song, Young-Joo; Bae, Jonghee; Kim, Young-Rok; Kim, Bang-Yeop

    2016-12-01

    In this study, the uncertainty requirements for orbit, attitude, and burn performance were estimated and analyzed for the execution of the 1st lunar orbit insertion (LOI) maneuver of the Korea Pathfinder Lunar Orbiter (KPLO) mission. During the early design phase of the system, associate analysis is an essential design factor as the 1st LOI maneuver is the largest burn that utilizes the onboard propulsion system; the success of the lunar capture is directly affected by the performance achieved. For the analysis, the spacecraft is assumed to have already approached the periselene with a hyperbolic arrival trajectory around the moon. In addition, diverse arrival conditions and mission constraints were considered, such as varying periselene approach velocity, altitude, and orbital period of the capture orbit after execution of the 1st LOI maneuver. The current analysis assumed an impulsive LOI maneuver, and two-body equations of motion were adapted to simplify the problem for a preliminary analysis. Monte Carlo simulations were performed for the statistical analysis to analyze diverse uncertainties that might arise at the moment when the maneuver is executed. As a result, three major requirements were analyzed and estimated for the early design phase. First, the minimum requirements were estimated for the burn performance to be captured around the moon. Second, the requirements for orbit, attitude, and maneuver burn performances were simultaneously estimated and analyzed to maintain the 1st elliptical orbit achieved around the moon within the specified orbital period. Finally, the dispersion requirements on the B-plane aiming at target points to meet the target insertion goal were analyzed and can be utilized as reference target guidelines for a mid-course correction (MCC) maneuver during the transfer. More detailed system requirements for the KPLO mission, particularly for the spacecraft bus itself and for the flight dynamics subsystem at the ground control center

  8. Draft Genome Sequences of Staphylococcus aureus AMRF1 (ST22) and AMRF2 (ST672), Ocular Methicillin-Resistant Isolates

    KAUST Repository

    Velusamy, Nithya

    2014-03-20

    Sequence type 22 (ST22) and ST672 are the two major emerging clones of community-acquired methicillin-resistant Staphylococcus aureus in India. ST672 strains were found to cause severe ocular infections. We report the draft genome sequences of two emerging strains of methicillin-resistant S. aureus, AMRF1 (ST22) and AMRF2 (ST672), isolated from patients with ocular infections.

  9. Addressing learning difficulties in Newtons 1st and 3rd Laws through problem based inquiry using Easy Java Simulation

    OpenAIRE

    Goh, Khoon Song Aloysius; Wee, Loo Kang; Yip, Kim Wah; Toh, Ping Yong Jeffrey; Lye, Sze Yee

    2013-01-01

    We develop an Easy Java Simulation (EJS) model for students to visualize Newtons 1st and 3rd laws, using frictionless constant motion equation and a spring collision equation during impact. Using Physics by Inquiry instructional (PbI) strategy, the simulation and its problem based inquiry worksheet aim to enhance learning of these two Newtonian concepts. We report results from Experimental (N=62 students) and Control (N=67) Groups in 11 multiple choice questions pre and post tests, conducted ...

  10. The Viability of Phantom Dark Energy as a Quantum Field in 1st-Order FLRW Space

    Science.gov (United States)

    Ludwick, Kevin

    2017-01-01

    In the standard cosmological framework of the 0th-order FLRW metric and the use of perfect fluids in the stress-energy tensor, dark energy with an equation-of-state parameter w - 1) do not necessarily have positive kinetic energy categorically. We then investigate the same question treating dark energy as a quantum field in 1st-order FLRW space-time and examining the expectation value of the stress-energy tensor for w < - 1 using adiabatic expansion.

  11. Educational impact of a clinical anatomy workshop on 1st-year orthopedic and rheumatology fellows in Mexico City.

    Science.gov (United States)

    Saavedra, M A; Villaseñor-Ovies, P; Harfush, L A; Navarro-Zarza, J E; Canoso, J J; Cruz-Domínguez, P; Vargas, A; Hernández-Díaz, C; Chiapas-Gasca, K; Camacho-Galindo, J; Alvarez-Nemegyei, J; Kalish, R A

    2016-05-01

    We aim to study the educational impact of a clinical anatomy workshop in 1st-year orthopedic and rheumatology fellows. First-year rheumatology fellows (N = 17) and a convenience sample of 1st-year orthopedic fellows (N = 14) from Mexico City in the 9th month of training participated in the study. The pre- and the post- workshop tests included the same 20 questions that had to be answered by identification or demonstration of relevant anatomical items. The questions, arranged by anatomical regions, were asked in five dynamic stations. Overall, the 31 participants showed an increase of correct answers, from a median of 6 (range 1 to 12) in the pre-workshop test, to a median of 14 (range 7 to 19) in the post-workshop test. In the pre-workshop test, the correct median answers were 7 (range 2 to 12) in the orthopedic fellows and 5 (range 1 to 10) in the rheumatology fellows (p = 0.297). Corresponding scores in the post-workshop were 15 (range 10 to 19) and 12 (range 7 to 18) (p = 0.026) showing a significant difference favoring the orthopedic group. Our clinical anatomy workshop was efficacious, in the short term, as a teaching instrument for 1st-year orthopedic and rheumatology fellows. The post-workshop scores, although significantly improved in both groups, particularly in the orthopedic fellows, were still suboptimal. Further refinements of our workshop might yield better results.

  12. When should orthostatic blood pressure changes be evaluated in elderly: 1st, 3rd or 5th minute?

    Science.gov (United States)

    Soysal, Pinar; Aydin, Ali Ekrem; Koc Okudur, Saadet; Isik, Ahmet Turan

    2016-01-01

    Detection of orthostatic hypotension (OH) is very important in geriatric practice, since OH is associated with mortality, ischemic stroke, falls, cognitive failure and depression. It was aimed to determine the most appropriate time for measuring blood pressure in transition from supine to upright position in order to diagnose OH in elderly. Comprehensive geriatric assessment (CGA) including Head up Tilt Table (HUT) test was performed in 407 geriatric patients. Orthostatic changes were assessed separately for the 1st, 3rd and 5th minutes (HUT1, HUT3 and HUT5, respectively) taking the data in supine position as the basis. The mean age, recurrent falls, presence of dementia and Parkinson's disease, number of drugs, alpha-blocker and anti-dementia drug use, and fasting blood glucose levels were significantly higher in the patients with versus without OH; whereas, albumin and 25-hydroxy vitamin D levels were significantly lower (pfasting blood glucose level was prominent in HUT1 as compared to HUT3 (p<0.01, p<0.05). Comparison of the patients that had OH only in HUT1, HUT3or HUT5 revealed no difference in terms of CGA parameters. These results suggests that orthostatic blood pressure changes determined at the 1st minute might be more important for geriatric practice. Moreover, 1st minute measurement might be more convenient in the elderly as it requires shorter time in practice.

  13. Genotype-phenotype correlation in a cohort of Portuguese patients comprising the entire spectrum of VWD types: impact of NGS.

    Science.gov (United States)

    Fidalgo, Teresa; Salvado, Ramon; Corrales, Irene; Pinto, Silva Catarina; Borràs, Nina; Oliveira, Ana; Martinho, Patricia; Ferreira, Gisela; Almeida, Helena; Oliveira, Cristina; Marques, Dalila; Gonçalves, Elsa; Diniz, MJoão; Antunes, Margarida; Tavares, Alice; Caetano, Gonçalo; Kjöllerström, Paula; Maia, Raquel; Sevivas, Teresa S; Vidal, Francisco; Ribeiro, Leticia

    2016-07-01

    The diagnosis of von Willebrand disease (VWD), the most common inherited bleeding disorder, is characterised by a variable bleeding tendency and heterogeneous laboratory phenotype. The sequencing of the entire VWF coding region has not yet become a routine practice in diagnostic laboratories owing to its high costs. Nevertheless, next-generation sequencing (NGS) has emerged as an alternative to overcome this limitation. We aimed to determine the correlation of genotype and phenotype in 92 Portuguese individuals from 60 unrelated families with VWD; therefore, we directly sequenced VWF. We compared the classical Sanger sequencing approach and NGS to assess the value-added effect on the analysis of the mutation distribution in different types of VWD. Sixty-two different VWF mutations were identified, 27 of which had not been previously described. NGS detected 26 additional mutations, contributing to a broad overview of the mutant alleles present in each VWD type. Twenty-nine probands (48.3 %) had two or more mutations; in addition, mutations with pleiotropic effects were detected, and NGS allowed an appropriate classification for seven of them. Furthermore, the differential diagnosis between VWD 2B and platelet type VWD (n = 1), Bernard-Soulier syndrome and VWD 2B (n = 1), and mild haemophilia A and VWD 2N (n = 2) was possible. NGS provided an efficient laboratory workflow for analysing VWF. These findings in our cohort of Portuguese patients support the proposal that improving VWD diagnosis strategies will enhance clinical and laboratory approaches, allowing to establish the most appropriate treatment for each patient.

  14. Preoperative and Postoperative (1st and 3rd Month Metabolic Data of Patients Who Underwent Bariatric Surgery

    Directory of Open Access Journals (Sweden)

    Nilüfer Özdemir Kutbay

    2015-03-01

    Full Text Available Purpose: The growing prevalence of obesity has become a major concern. The efficacy of medical treatment, diet and behavior therapy in morbidly obese patients is limited. Obesity surgery is a treatment option for selected morbidly obese patients. Material and Method: Data of 47 patients (n=39 women, 8 men who underwent bariatric surgery were investigated. Results: Out of 47 patients, 20 underwent Roux-en-Y gastric bypass (RYGB (43% and 27 had sleeve gastrectomy (SG (57%. The mean age of the patients was 37±9.5 (19-59 years. 17% of patients were men and 83% were women. In the analysis of data on weight that could be found for 31 out of 47 patients, we detected preoperative and postoperative (1st and 3rd month mean weight values as 125.4±15.9 kg, 112.7±13.2 kg (p<0.001 and 100.9±17.5 kg (p<0.001, respectively. In addition, the analysis of the data on mean fasting plasma glucose (FPG levels which could be found for 23 out of 47 patients, showed us that preoperative and postoperative (1st and 3rd month FPG levels were 100.9±17.5 mg/dL, 91.6±10.9 mg/dL (p=0.03 and 87.3±2.0 mg/dL, respectively. Only 1 patient had diabetes before the surgery. In the RYGB group, the mean change in weight was 12.4±5.5 kg in the 1st month and 22.2±8.6 kg in the 3rd month (compared to the weights in the preoperative period. Moreover, in the SG group, the mean change in weight was 13.7±4.5 kg in the 1st month and 23.4±5.8 kg in the 3rd month. No statistically significant difference was found between the weight changes in the 1st and the 3rd month as for surgery types. Discussion: After bariatric surgery, significant loss in weight and reduction in FPG occurred in short-term.

  15. An Infrared Census of DUST in Nearby Galaxies with Spitzer (DUSTiNGS), II. Discovery of Metal-poor Dusty AGB Stars

    CERN Document Server

    Boyer, Martha L; Barmby, P; Bonanos, A Z; Gehrz, R D; Gordon, K D; Groenewegen, M A T; Lagadec, E; Lennon, D; Marengo, M; McDonald, I; Meixner, M; Skillman, E; Sloan, G C; Sonneborn, G; van Loon, J Th; Zijlstra, A

    2014-01-01

    The DUSTiNGS survey (DUST in Nearby Galaxies with Spitzer) is a 3.6 and 4.5 micron imaging survey of 50 nearby dwarf galaxies designed to identify dust-producing Asymptotic Giant Branch (AGB) stars and massive stars. Using two epochs, spaced approximately six months apart, we identify a total of 526 dusty variable AGB stars (sometimes called "extreme" or x-AGB stars; [3.6]-[4.5]>0.1 mag). Of these, 111 are in galaxies with [Fe/H] < -1.5 and 12 are in galaxies with [Fe/H] < -2.0, making them the most metal-poor dust-producing AGB stars known. We compare these identifications to those in the literature and find that most are newly discovered large-amplitude variables, with the exception of approximately 30 stars in NGC 185 and NGC 147, one star in IC 1613, and one star in Phoenix. The chemical abundances of the x-AGB variables are unknown, but the low metallicities suggest that they are more likely to be carbon-rich than oxygen-rich and comparisons with existing optical and near-IR photometry confirms tha...

  16. Project of new 1st order gravimetric network of the Republic of Slovenia

    OpenAIRE

    Koler, Božo; Medved, Klemen; Kuhar, Miran

    2006-01-01

    The project of a new gravimetric network of Slovenia is presented. It resulted from the needs for the new gravimetric and height systems of Slovenia, all parts of the new national coordinate system. The project of the gravimetric network is based on analyses of old gravimetric network and surveys carried out at the territory of the Republic of Slovenia. Besides, the geological assessment of suitability of the preserved and new planned gravimetric stations was completed.

  17. PREFACE: PAGES 1st Young Scientists Meeting (YSM) - 'Retrospective views on our planet's future'

    Science.gov (United States)

    Margrethe Basse, Ellen

    2010-03-01

    more recent pollution. The concept and format of the 1st PAGES YSM worked very well, and created a high degree of enthusiasm and stimulation among the participants (as is demonstrated by this special issue). The 2nd YSM is therefore firmly planned to take place in 2013, back-to-back with the 4th PAGES OSM. Crucial and gratefully acknowledged contributions to the success of the YSM were made by the numerous co-sponsors (see logos below), who provided the financial basis for the YSM and supported the attendance of many early-career researchers from various parts of the world. Furthermore, we cordially thank all reviewers for shaping this proceeding issue with their insightful and helpful reviews. Conference photograph

  18. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    Science.gov (United States)

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  19. NGS-200型GPS测量系统在建立三维控制网中的应用%Application of NGS-200 GPS in Establishment of Three-Dimensional Control Network

    Institute of Scientific and Technical Information of China (English)

    赵俊兰; 冯建秋

    2001-01-01

    介绍了NGS-200GPS测量系统的组成及原理,阐述了利用该系统在北京八大处公园建立测区首级平面控制网的具体做法,对布网方案、数据处理、平差计算和测量结果可靠性进行了分析.实践表明NGS-200GPS在八大处公园山地地形复杂,树木覆盖较密的情况下 ,其性能仍然比较稳定,所取得的测量结果达到了国家有关规范要求.该系统替代常规测量技术是经济、合理可靠的.

  20. Report on: "The 1st Workshop on National Immunization Programs and Vaccine Coverage in ASEAN Countries, April 30, 2015, Pattaya, Thailand".

    Science.gov (United States)

    Hattasingh, Weerawan; Pengsaa, Krisana; Thisyakorn, Usa

    2016-03-04

    The 1st Workshop on National Immunization Programs and Vaccine Coverage in Association of Southeast Asian Nations (ASEAN) Countries Group (WNIPVC-ASEAN) held a meeting on April 30, 2015, Pattaya, Thailand under the auspices of the Pediatric Infectious Diseases Society and the World Health Organization (WHO). Reports on the current status and initiatives of the national immunization program (NIP) in each ASEAN countries that attended were presented. These reports along with survey data collected from ministries of health in ASEAN countries NIPs demonstrate that good progress has been made toward the goal of the Global Vaccine Action Plan (GVAP). However, some ASEAN countries have fragile health care systems that still have insufficient vaccine coverage of some basic EPI antigens. Most ASEAN countries still do not have national coverage of some new and underused vaccines, and raising funds for the expansion of NIPs is challenging. Also, there is insufficient research into disease burden of vaccine preventable diseases and surveillance. Health care workers must advocate NIPs to government policy makers and other stakeholders as well as improve research and surveillance to achieve the goals of the GVAP.

  1. PECULIAR FEATURES CONCERNING 1-ST-YEAR STUDENT ADAPTATION TO LIFE-ACTIVITY AT ENGINEERING HIGHER EDUCATIONAL INSTITUTION

    Directory of Open Access Journals (Sweden)

    V. A. Klimenko

    2008-01-01

    Full Text Available The paper contains an analysis of peculiar features concerning a 1-st-year student adaptation to new conditions of life-activity  on the basis of self-evaluation made by 212 persons.  In order to obtain the data a methodology for diagnostics of social and psychological adaptation developed by K.Rodgers and R.Diamond has been applied with the purpose to study such integral indices as adaptivity, emotional comfort, friendly attitude, internality, tolerance and domination symptom.

  2. Chondrosarcoma of right 1st rib presenting as neurogenic thoracic outlet syndrome; A 13th case report in world literature

    Directory of Open Access Journals (Sweden)

    Ravisagar Patel

    2016-07-01

    Full Text Available Thoracic outlet syndrome [TOS] caused by a tumor of the rib is rare and has been reported only 12 times in the literature over the past one and one-half centuries, with the majority of cases due to osteochondroma. We report a case of chondrosarcoma of right 1st rib causing neurogenic TOS that was resected via posterolateral thoracotomy and biopsy confirmed a grade I chondrosarcoma. In the treatment of chondrosarcoma, chemotherapy and radiotherapy are less effective, and appropriate surgery is needed.

  3. Lectures given at the 1st Session of the Centro Internazionale Matematico Estivo (C.I.M.E.)

    CERN Document Server

    1990-01-01

    The courses given at the 1st C.I.M.E. Summer School of 1988 dealt with the main areas on the borderline between applied logic and theoretical computer science. These courses are recorded here in five expository papers: S. Homer: The Isomorphism Conjecture and its Generalization.- A. Nerode: Some Lectures on Intuitionistic Logic.- R.A. Platek: Making Computers Safe for the World. An Introduction to Proofs of Programs. Part I. - G.E. Sacks: Prolog Programming.- A. Scedrov: A Guide to Polymorphic Types.

  4. NGS-based identification of druggable alterations and signaling pathways – hepatocellular carcinoma case report

    Directory of Open Access Journals (Sweden)

    Kotelnikova E. A.

    2015-12-01

    Full Text Available Aim. To identify potential cancer driving or clinically relevant molecular events for a patient with hepatocellular carcinoma. Methods. In order to achieve this goal, we performed RNA-seq and exome sequencing for the tumor tissue and its matched control. We annotated the alterations found using several publicly available databases and bioinformatics tools. Results. We identified several differentially expressed genes linked to the classical sorafenib treatment as well as additional pathways potentially druggable by therapies studied in clinical trials (Erlotinib, Lapatinib and Temsirolimus. Several germline mutations, found in XRCC1, TP53 and DPYD, according to the data from other clinical trials, could be related to the increased sensitivity to platinum therapies and reduced sensitivity to 5-Fluorouracil. We also identified several potentially driving mutations that could not be currently linked to therapies, like deletion in CIRBP, SNVs in BTG1, ERBB3, TCF7L2 et al. Conclusions. The presented study shows the potential usefulness of the integrated approach to the NGS data analysis, including the analysis of germline mutations and transcriptome in addition to the cancer panel or the exome sequencing data.

  5. Tratamento de dados de NGS para pesquisa de novas mutações associadas à miocardiopatia hipertrófica

    OpenAIRE

    2012-01-01

    Tese de mestrado em Bioestatística, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2012 A Sequenciação de Nova Geração (NGS - Next Generation Sequencing) está a revolucionar a investigação na área da biomédica, contribuindo significativamente para o avanço da medicina personalizada. A NGS, apoiando-se nos conhecimentos da Estatística Bayesiana e da Bioinformática para a análise e tratamento dos dados que esta técnica origina, torna-se num excelente exemplo dos novo...

  6. Improvement of PCR-free NGS Library Preparation to Obtain Uniform Read Coverage of Genome with Extremely High AT Content

    OpenAIRE

    Williams, A.; Storton, D.; Buckles, J.; Llinas, M.; Wang, Wei

    2012-01-01

    PCR amplification is commonly used in generating libraries for Next-Generation Sequencing (NGS) to efficiently enrich and amplify sequenceable DNA fragments. However, it introduces bias in the representation of the original complex template DNA. Such artifact has devastating effects in sequencing genomes with highly unbalanced base composition: regions of extremely high or low GC content, which are a substantial fraction of such genomes, are often covered with zero or near-zero read depth. PC...

  7. Comparable Research of Energy and Ecology Parameters of 1st, 2nd and 3rd Generation Biofuels for Compression Ignition Engines

    National Research Council Canada - National Science Library

    Justas Zaglinskis

    2015-01-01

    .... Main attention focused on energy and environmental characteristics of diesel engine performance using 1st, 2nd and 3rd generation alcohol, fatty acid methyl and butyl esters blends with conventional diesel fuel (EN 590...

  8. Coal mining situation in the Federal Republic of Germany. The 1st quarter 2017; Zur Lage des Kohlenbergbaus in der Bundesrepublik Deutschland. 1. Vierteljahr 2017

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2017-06-14

    The paper reports on the coal mining in the Federal Republic of Germany in the 1st quarter of 2017. Statistical data are presented for mining, exports and imports of hard coal and lignite and for employees.

  9. Coal mining situation in the Federal Republic of Germany. The 1st quarter 2016; Zur Lage des Kohlenbergbaus in der Bundesrepublik Deutschland. 1. Vierteljahr 2016

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2016-06-06

    The paper reports on the coal mining in the Federal Republic of Germany in the 1st quarter of 2016. Statistical data are presented for mining, exports and imports of hard coal and lignite and for employees.

  10. An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.

    Science.gov (United States)

    Xiong, Yun; Guo, Yufeng; Xiao, Weidi; Cao, Qichen; Li, Shanshan; Qi, Xianni; Zhang, Zhidan; Wang, Qinhong; Shui, Wenqing

    2016-03-01

    Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs.

  11. Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

    Science.gov (United States)

    Scarcelli, N; Mariac, C; Couvreur, T L P; Faye, A; Richard, D; Sabot, F; Berthouly-Salazar, C; Vigouroux, Y

    2016-03-01

    Next-generation sequencing allows access to a large quantity of genomic data. In plants, several studies used whole chloroplast genome sequences for inferring phylogeography or phylogeny. Even though the chloroplast is a haploid organelle, NGS plastome data identified a nonnegligible number of intra-individual polymorphic SNPs. Such observations could have several causes such as sequencing errors, the presence of heteroplasmy or transfer of chloroplast sequences in the nuclear and mitochondrial genomes. The occurrence of allelic diversity has practical important impacts on the identification of diversity, the analysis of the chloroplast data and beyond that, significant evolutionary questions. In this study, we show that the observed intra-individual polymorphism of chloroplast sequence data is probably the result of plastid DNA transferred into the mitochondrial and/or the nuclear genomes. We further assess nine different bioinformatics pipelines' error rates for SNP and genotypes calling using SNPs identified in Sanger sequencing. Specific pipelines are adequate to deal with this issue, optimizing both specificity and sensitivity. Our results will allow a proper use of whole chloroplast NGS sequence and will allow a better handling of NGS chloroplast sequence diversity.

  12. COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists.

    Science.gov (United States)

    Monot, Marc; Orgeur, Mickael; Camiade, Emilie; Brehier, Clément; Dupuy, Bruno

    2014-03-01

    COV2HTML is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. To demonstrate the scope of COV2HTML, the program was tested with data from two published studies. The first data were from RNA-seq analysis of Campylobacter jejuni, based on comparison of two conditions with two replicates. We were able to recover 26 out of 27 genes highlighted in the publication using COV2HTML. The second data comprised of stranded TSS and RNA-seq data sets on the Archaea Sulfolobus solfataricus. COV2HTML was able to highlight most of the TSSs from the article and allows biologists to visualize both TSS and RNA-seq on the same screen. The strength of the COV2HTML interface is making possible NGS data analysis without software installation, login, or a long training period. A web version is accessible at https://mmonot.eu/COV2HTML/ . This website is free and open to users without any login requirement.

  13. RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.

    Directory of Open Access Journals (Sweden)

    Cheng Yuan

    Full Text Available The number of transcriptomic sequencing projects of various non-model organisms is still accumulating rapidly. As non-coding RNAs (ncRNAs are highly abundant in living organism and play important roles in many biological processes, identifying fragmentary members of ncRNAs in small RNA-seq data is an important step in post-NGS analysis. However, the state-of-the-art ncRNA search tools are not optimized for next-generation sequencing (NGS data, especially for very short reads. In this work, we propose and implement a comprehensive ncRNA classification tool (RNA-CODE for very short reads. RNA-CODE is specifically designed for ncRNA identification in NGS data that lack quality reference genomes. Given a set of short reads, our tool classifies the reads into different types of ncRNA families. The classification results can be used to quantify the expression levels of different types of ncRNAs in RNA-seq data and ncRNA composition profiles in metagenomic data, respectively. The experimental results of applying RNA-CODE to RNA-seq of Arabidopsis and a metagenomic data set sampled from human guts demonstrate that RNA-CODE competes favorably in both sensitivity and specificity with other tools. The source codes of RNA-CODE can be downloaded at http://www.cse.msu.edu/~chengy/RNA_CODE.

  14. A new method to prevent carry-over contaminations in two-step PCR NGS library preparations.

    Science.gov (United States)

    Seitz, Volkhard; Schaper, Sigrid; Dröge, Anja; Lenze, Dido; Hummel, Michael; Hennig, Steffen

    2015-11-16

    Two-step PCR procedures are an efficient and well established way to generate amplicon libraries for NGS sequencing. However, there is a high risk of cross-contamination by carry-over of amplicons from first to second amplification rounds, potentially leading to severe misinterpretation of results. Here we describe a new method able to prevent and/or to identify carry-over contaminations by introducing the K-box, a series of three synergistically acting short sequence elements. Our K-boxes are composed of (i) K1 sequences for suppression of contaminations, (ii) K2 sequences for detection of possible residual contaminations and (iii) S sequences acting as separators to avoid amplification bias. In order to demonstrate the effectiveness of our method we analyzed two-step PCR NGS libraries derived from a multiplex PCR system for detection of T-cell receptor beta gene rearrangements. We used this system since it is of high clinical relevance and may be affected by very low amounts of contaminations. Spike-in contaminations are effectively blocked by the K-box even at high rates as demonstrated by ultra-deep sequencing of the amplicons. Thus, we recommend implementation of the K-box in two-step PCR-based NGS systems for research and diagnostic applications demanding high sensitivity and accuracy.

  15. Body conceptions of 1st and 8th semesters students from two Goiás Universities.

    Directory of Open Access Journals (Sweden)

    Terita Michele da Silva Ferreira

    2013-12-01

    Full Text Available To understand physical education student’s body conceptions is important to analyze how their formation and social determinations is influencing their way of thinking, which can impact on theirs posterior professional intervention. This way, the scientific question of this text is to know if: “Does exist differences between body conceptions of academic students of 1st and 8th period of two graduation courses?”. The general objective is to identify and compare the body conceptions of 1st and 8th period of physical education graduation courses (licensure of two teaching institutions of Goiás. This descriptive research with qualitative analyzes was made by a questionnaire specially elaborated to this research that it was applied with 143 students of Physical Education Licensure of the two Universities. The results show that the body conceptions are near the hegemonic paradigms, directed to an understanding of instrumental body, showing that is necessary a better discussion in the academic environment.

  16. Chinese Commission of Science Technology and Industry for National Defense Senior Vice Minister CHEN Qiufa visiting ALICE experiment on 1st November 2007 with CERN Director-General R. Aymar and Adviser J.-P. Revol. Thursday, 1st and Friday, 2nd November 2007

    CERN Multimedia

    Maximilien Brice

    2007-01-01

    Chinese Commission of Science Technology and Industry for National Defense Senior Vice Minister CHEN Qiufa visiting ALICE experiment on 1st November 2007 with CERN Director-General R. Aymar and Adviser J.-P. Revol. Thursday, 1st and Friday, 2nd November 2007

  17. DUSTiNGS III: Distribution of Intermediate-Age and Old Stellar Populations in Disks and Outer Extremities of Dwarf Galaxies

    CERN Document Server

    McQuinn, Kristen B W; Mitchell, Mallory B; Skillman, Evan D; Gehrz, R D; Groenewegen, Martin A T; McDonald, Iain; Sloan, G C; van Loon, Jacco Th; Whitelock, Patricia A; Zijlstra, Albert A

    2016-01-01

    We have traced the spatial distributions of intermediate-age and old stars in nine dwarf galaxies in the distant parts of the Local Group, using multi-epoch 3.6 and 4.5 micron data from the DUST in Nearby Galaxies with Spitzer (DUSTiNGS) survey. Using complementary optical imaging from the Hubble Space Telescope, we identify the tip of the red giant branch (TRGB) in the 3.6 micron photometry, separating thermally-pulsating asymptotic giant branch (TP-AGB) stars from the larger red giant branch (RGB) populations. Unlike the constant TRGB in the I-band, at 3.6 micron the TRGB magnitude varies by ~0.7 mag, making it unreliable as a distance indicator. The intermediate-age and old stars are well mixed in two-thirds of the sample with no evidence of a gradient in the ratio of the intermediate-age to old stellar populations outside the central ~1-2'. Variable AGB stars are detected in the outer extremities of the galaxies, indicating that chemical enrichment from these dust-producing stars may occur in the outer re...

  18. AG-NGS: a powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms.

    Science.gov (United States)

    Callejas, Sergio; Álvarez, Rebeca; Benguria, Alberto; Dopazo, Ana

    2014-01-01

    Next-generation sequencing (NGS) is becoming one of the most widely used technologies in the field of genomics. Library preparation is one of the most critical, hands-on, and time-consuming steps in the NGS workflow. Each library must be prepared in an independent well, increasing the number of hours required for a sequencing run and the risk of human-introduced error. Automation of library preparation is the best option to avoid these problems. With this in mind, we have developed automatic genomics NGS (AG-NGS), a computing application that allows an open liquid handling platform to be transformed into a library preparation station without losing the potential of an open platform. Implementation of AG-NGS does not require programming experience, and the application has also been designed to minimize implementation costs. Automated library preparation with AG-NGS generated high-quality libraries from different samples, demonstrating its efficiency, and all quality control parameters fell within the range of optimal values.

  19. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads.

    Science.gov (United States)

    Suez, Marie; Behdenna, Abdelkader; Brouillet, Sophie; Graça, Paula; Higuet, Dominique; Achaz, Guillaume

    2016-03-01

    Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.

  20. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Birdwell, Jr, Joseph F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Delmau, Laetitia Helene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duncan, Nathan C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ensor, Dale [Tennessee Technological Univ., Cookeville, TN (United States); Hill, Talon G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Denise L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rajbanshi, Arbin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roach, Benjamin D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Szczygiel, Patricia L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stoner, Erica L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Neil J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  1. Optimizing information in Next-Generation-Sequencing (NGS) reads for improving de novo genome assembly.

    Science.gov (United States)

    Liu, Tsunglin; Tsai, Cheng-Hung; Lee, Wen-Bin; Chiang, Jung-Hsien

    2013-01-01

    Next-Generation-Sequencing is advantageous because of its much higher data throughput and much lower cost compared with the traditional Sanger method. However, NGS reads are shorter than Sanger reads, making de novo genome assembly very challenging. Because genome assembly is essential for all downstream biological studies, great efforts have been made to enhance the completeness of genome assembly, which requires the presence of long reads or long distance information. To improve de novo genome assembly, we develop a computational program, ARF-PE, to increase the length of Illumina reads. ARF-PE takes as input Illumina paired-end (PE) reads and recovers the original DNA fragments from which two ends the paired reads are obtained. On the PE data of four bacteria, ARF-PE recovered >87% of the DNA fragments and achieved >98% of perfect DNA fragment recovery. Using Velvet, SOAPdenovo, Newbler, and CABOG, we evaluated the benefits of recovered DNA fragments to genome assembly. For all four bacteria, the recovered DNA fragments increased the assembly contiguity. For example, the N50 lengths of the P. brasiliensis contigs assembled by SOAPdenovo and Newbler increased from 80,524 bp to 166,573 bp and from 80,655 bp to 193,388 bp, respectively. ARF-PE also increased assembly accuracy in many cases. On the PE data of two fungi and a human chromosome, ARF-PE doubled and tripled the N50 length. However, the assembly accuracies dropped, but still remained >91%. In general, ARF-PE can increase both assembly contiguity and accuracy for bacterial genomes. For complex eukaryotic genomes, ARF-PE is promising because it raises assembly contiguity. But future error correction is needed for ARF-PE to also increase the assembly accuracy. ARF-PE is freely available at http://140.116.235.124/~tliu/arf-pe/.

  2. Impact of volcanic eruptions on the climate of the 1st millennium AD in a comprehensive climate simulation

    Science.gov (United States)

    Wagner, Sebastian; Zorita, Eduardo

    2015-04-01

    The climate of the 1st millennium AD shows some remarkable differences compared to the last millennium concerning variation in external forcings. Together with an orbitally induced increased solar insolation during the northern hemisphere summer season and a general lack of strong solar minima, the frequency and intensity of large tropical and extratropical eruptions is decreased. Here we present results of a new climate simulation carried out with the comprehensive Earth System Model MPI-ESM-P forced with variations in orbital, solar, volcanic and greenhouse gas variations and land use changes for the last 2,100 years. The atmospheric model has a horizontal resolution of T63 (approx. 125x125 km) and therefore also allows investigations of regional-to-continental scale climatic phenomena. The volcanic forcing was reconstructed based on a publication by Sigl et al. (2013) using the sulfate records of the NEEM and WAIS ice cores. To obtain information on the aerosol optical depth (AOD) these sulfate records were scaled to an established reconstruction from Crowley and Unterman (2010), which is also a standard forcing in the framework of CMIP5/PMIP3. A comparison between the newly created data set with the Crowley and Unterman dataset reveals that the new reconstruction shows in general weaker intensities, especially of the large tropical outbreaks and fewer northern hemispheric small-to-medium scale eruptions. However, the general pattern in the overlapping period is similar. A hypothesis that can be tested with the simulation is whether the reduced volcanic intensity of the 1st millennium AD contributed to the elevated temperature levels over Europe, evident within a new proxy-based reconstruction. On the other hand, the few but large volcanic eruptions, e.g. the 528 AD event, also induced negative decadal-scale temperature anomalies. Another interesting result of the simulation relates to the 79 AD eruption of the Vesuvius, which caused the collapse of the city of

  3. Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS.

    Science.gov (United States)

    Tuononen, Katja; Mäki-Nevala, Satu; Sarhadi, Virinder Kaur; Wirtanen, Aino; Rönty, Mikko; Salmenkivi, Kaisa; Andrews, Jenny M; Telaranta-Keerie, Aino I; Hannula, Sari; Lagström, Sonja; Ellonen, Pekka; Knuuttila, Aija; Knuutila, Sakari

    2013-05-01

    The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next-generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real-time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens from 81 non-small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real-time PCR. Moreover, targeted NGS revealed seven nonsynonymous single-nucleotide variations and one insertion-deletion variation in EGFR not detectable by the real-time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material.

  4. Levels of innate immune factors in preterm and term mothers' breast milk during the 1st month postpartum.

    Science.gov (United States)

    Trend, Stephanie; Strunk, Tobias; Lloyd, Megan L; Kok, Chooi Heen; Metcalfe, Jessica; Geddes, Donna T; Lai, Ching Tat; Richmond, Peter; Doherty, Dorota A; Simmer, Karen; Currie, Andrew

    2016-04-14

    There is a paucity of data on the effect of preterm birth on the immunological composition of breast milk throughout the different stages of lactation. We aimed to characterise the effects of preterm birth on the levels of immune factors in milk during the 1st month postpartum, to determine whether preterm milk is deficient in antimicrobial factors. Colostrum (days 2-5 postpartum), transitional milk (days 8-12) and mature milk (days 26-30) were collected from mothers of extremely preterm (preterm (28-preterm (32-preterm mothers had significantly higher concentrations of HBD1 and TGF-β2 in colostrum than term mothers did. After controlling for other variables in regression analyses, preterm birth was associated with higher concentrations of HBD1, LZ and sCD14 in milk samples. In conclusion, preterm breast milk contains significantly higher concentrations of some immune proteins than term breast milk.

  5. Plasma properties from the multi-wavelength analysis of the November 1st 2003 CME/shock event

    CERN Document Server

    Benna, Carlo; Giordano, Silvio; Gioannini, Lorenzo

    2012-01-01

    The analysis of the spectral properties and dynamic evolution of a CME/shock event observed on November 1st 2003 in white-light by the LASCO coronagraph and in the ultraviolet by the UVCS instrument operating aboard SOHO, has been performed to compute the properties of some important plasma parameters in the middle corona below about 2 solar radii. Simultaneous observations obtained with the MLSO/Mk4 white-light coronagraph, providing both the early evolution of the CME expansion in the corona and the pre-shock electron density profile along the CME front, were also used to study this event. By combining the above information with the analysis of the metric type II radio emission detected by ground-based radio spectrographs, we finally derive estimates of the values of the local Alfv\\'en speed and magnetic field strength in the solar corona.

  6. Proceedings of the 1st International Operational Modal Analysis Conference, April 26-27, 2005, Copenhagen, Denmark

    DEFF Research Database (Denmark)

    /S and the Department of Building Technology and Structural Engineering at Aalborg University. It is the first conference ever to focus solely on experimental modal analysis for cases where only the responses are measured. It was decided to hold the conference to generate interest in operational modal analysis (also......These proceedings contain approximately 100 papers presented at the 1st International Operational Modal Conference, Copenhagen, Denmark, April 26 - 27, 2005. The conference is jointly organised by Structural Vibration Systems (SVS), Aalborg, Brüel & Kjær Sound and Vibration Measurement A...... known as ambient modal analysis, output-only modal analysis and natural input modal analysis) which has been around since the beginning of the development of traditional modal analysis in the early seventies. From the beginning, these techniques proved to have several advantages, due to less testing...

  7. LARGE BOULDERS ALONG THE RABAT COAST (MOROCCO; POSSIBLE EMPLACEMENT BY THE NOVEMBER, 1st, 1755 A.D. TSUNAMI

    Directory of Open Access Journals (Sweden)

    Nadia Mhammdi, Fida Medina

    2008-01-01

    Full Text Available The rocky coastline south of Rabat (Morocco shows a large number of boulders lying upon the lithified dune system. The boulders, of 4-100 tons, may be single, in imbricated sets, or forming clusters and ridges. Several of the boulders were lifted and overturned, thus showing pool apertures downwards. Transport distance is generally decametric because of the surface roughness, but it can reach 300 m in flat areas. All boulders have been detached from their initial position at the fractured front of the active cliff. Quantification with the help wave hydrodynamics and rock displacement mechanics shows that dislodgement and transport of these boulders were accomplished rather by tsunami than by storm waves. Although no dating was attempted, post- emplacement bio-erosion by littorinids and the absence of any erosional features below the boulders suggests that they were emplaced during the 1st November 1755 AD Lisbon tsunami.

  8. 1st or 2nd generation bioethanol-impacts of technology integration & on feed production and land use

    DEFF Research Database (Denmark)

    Bentsen, Niclas Scott; Felby, Claus

    2009-01-01

    with the poorest bio synthesis efficiency and as such the area demand for their production is relatively high. Preservation of the proteins in the biomass such as in feed by-products from bioethanol production is of paramount importance in developing sustainable utilisation of biomass in the energy sector......."1st or 2nd generation bioethanol-impacts of technology integration & on feed production and land use" Liquid bio fuels are perceived as a means of mitigating CO2 emissions from transport and thus climate change, but much concern has been raised to the energy consumption from refining biomass...... to liquid fuels. Integrating technologies such that waste stream can be used will reduce energy consumption in the production of bioethanol from wheat. We show that the integration of bio refining and combined heat an power generation reduces process energy requirements with 30-40 % and makes bioethanol...

  9. Report about the 1st De Frutos - Universidad Miguel Hernández Judo Scientific Congress with Training Camp

    Directory of Open Access Journals (Sweden)

    Juan José Pulido González

    2013-12-01

    Full Text Available The current report resumes the 1st De Frutos-Universidad Miguel Hernández Judo Scientific Congress, held in San Juan de Alicante (Spain from the 27th to the 30th of June in 2013. Three plenary sessions in classroom, 12 oral communications, a round – table, 2 theoretical – practical workshops on tatami, and 3 randori sessions were developed. This congress was a new event where judo personalities at the international level as well as scientists from the whole Spanish geography interested in this field assisted. The event complied the aim to approach the science to judo professionals and vice versa. A total amount of 112 participants were in the congress.

  10. AN INFRARED CENSUS OF DUST IN NEARBY GALAXIES WITH SPITZER (DUSTiNGS). II. DISCOVERY OF METAL-POOR DUSTY AGB STARS

    Energy Technology Data Exchange (ETDEWEB)

    Boyer, Martha L.; Sonneborn, George [Observational Cosmology Lab, Code 665, NASA Goddard Space Flight Center, Greenbelt, MD 20771 (United States); McQuinn, Kristen B. W.; Gehrz, Robert D.; Skillman, Evan [Minnesota Institute for Astrophysics, School of Physics and Astronomy, 116 Church Street SE, University of Minnesota, Minneapolis, MN 55455 (United States); Barmby, Pauline [Department of Physics and Astronomy, University of Western Ontario, London, ON N6A 3K7 (Canada); Bonanos, Alceste Z. [IAASARS, National Observatory of Athens, GR-15236 Penteli (Greece); Gordon, Karl D.; Meixner, Margaret [STScI, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Groenewegen, M. A. T. [Royal Observatory of Belgium, Ringlaan 3, B-1180 Brussels (Belgium); Lagadec, Eric [Laboratoire Lagrange, UMR7293, Univ. Nice Sophia-Antipolis, CNRS, Observatoire de la Côte d' Azur, F-06300 Nice (France); Lennon, Daniel [ESA-European Space Astronomy Centre, Apdo. de Correo 78, E-28691 Villanueva de la Cañada, Madrid (Spain); Marengo, Massimo [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); McDonald, Iain; Zijlstra, Albert [Jodrell Bank Centre for Astrophysics, Alan Turing Building, University of Manchester, Manchester M13 9PL (United Kingdom); Sloan, G. C. [Astronomy Department, Cornell University, Ithaca, NY 14853-6801 (United States); Van Loon, Jacco Th., E-mail: martha.boyer@nasa.gov [Astrophysics Group, Lennard-Jones Laboratories, Keele University, Staffordshire ST5 5BG (United Kingdom)

    2015-02-10

    The DUSTiNGS survey (DUST in Nearby Galaxies with Spitzer) is a 3.6 and 4.5 μm imaging survey of 50 nearby dwarf galaxies designed to identify dust-producing asymptotic giant branch (AGB) stars and massive stars. Using two epochs, spaced approximately six months apart, we identify a total of 526 dusty variable AGB stars (sometimes called ''extreme'' or x-AGB stars; [3.6]-[4.5] > 0.1 mag). Of these, 111 are in galaxies with [Fe/H] < –1.5 and 12 are in galaxies with [Fe/H] < –2.0, making them the most metal-poor dust-producing AGB stars known. We compare these identifications to those in the literature and find that most are newly discovered large-amplitude variables, with the exception of ≈30 stars in NGC 185 and NGC 147, 1 star in IC 1613, and 1 star in Phoenix. The chemical abundances of the x-AGB variables are unknown, but the low metallicities suggest that they are more likely to be carbon-rich than oxygen-rich and comparisons with existing optical and near-IR photometry confirm that 70 of the x-AGB variables are confirmed or likely carbon stars. We see an increase in the pulsation amplitude with increased dust production, supporting previous studies suggesting that dust production and pulsation are linked. We find no strong evidence linking dust production with metallicity, indicating that dust can form in very metal-poor environments.

  11. On the recent large EQ of Karpathos, Greece (April 1st, 2011, Ms = 6.7R) and its similarities to the large EQ of the January 1st, 2006 (Ms = 6.9R) at East of Kythira, Greece

    CERN Document Server

    Thanassoulas, C; Verveniotis, G; Zymaris, N

    2011-01-01

    The recent large EQ that occurred in Greece (April 1st, 2011, Ms = 6.7R) is investigated as far as it concerns regional geophysical features of the Greek territory. In particular, the EQ location is compared to the deep lithospheric fracture zones and faults, derived from the analysis of the corresponding earth's gravity field; to the current seismic potential map determined from the study of the past seismicity, while its time of occurrence is compared to the peaks of the M1 and diurnal tidal waves. The detailed investigation of the earth's electric field that was recorded by the ATH monitoring site, located in Athens, revealed the presence of short train like pulses type electric seismic precursory signals which were generated short (1 - 2 days) before the EQ occurrence time. Moreover, the analysis (for T = 1 day) of the earth's oscillating electric field, that was simultaneously recorded at PYR and ATH monitoring sites, revealed that the "strange attractor like" seismic electric precursor preceded for 1 - ...

  12. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs

    DEFF Research Database (Denmark)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter

    2016-01-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the......This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report...

  13. U.S. Army Chemical Corps Historical Studies, Gas Warfare in World War I: The 1st Division in the Meuse-Argonne 1-12 October 1918

    Science.gov (United States)

    1957-08-01

    October, instead of 30 September-I October 0 On the night of the relief the .Jnemy began shelling at 10s00 porn October 1st and continued until 4s00... Juvin and Landre, out off the Argoure front, and attack in rear of the Brunhild position to effect decisive action on the Group -Argonnej." 8 7 At...attack, fired on the Son’.erance area and north of St Georges et Landres, Juvin , Marcq, and Champigxeulle. 93 Company C, 1st Gas Regiment, was ordered

  14. CFD analysis of the impingement cooling effect of the coolant jet caused by the T56 1st stage disc metering hole

    CSIR Research Space (South Africa)

    Snedden, Glen C

    2003-09-01

    Full Text Available OF THE IMPINGEMENT COOLING EFFECT OF THE COOLANT JET CAUSED BY THE T56 1ST STAGE DISC METERING HOLE ISABE-2003-1065 Glen C. Snedden CSIR, Defencetek, P O Box 395 Pretoria, 0001, South Africa Tony Lambert Rolls-Royce Indianapolis, Indiana, USA Abstract... the cavities via metering holes drilled through the curvic-coupling web. As a result of physical restrictions during the manufacturing process these holes are angled toward the face of the disc and result in flow impinging on the rear surface of the 1st...

  15. Invasive pneumococcal disease in healthy adults: increase of empyema associated with the clonal-type Sweden(1-ST306.

    Directory of Open Access Journals (Sweden)

    Imma Grau

    Full Text Available BACKGROUND: Adult invasive pneumococcal disease (IPD occurs mainly in the elderly and patients with co-morbidities. Little is known about the clinical characteristics, serotypes and genotypes causing IPD in healthy adults. METHODS: We studied 745 culture-proven cases of IPD in adult patients aged 18-64 years (1996-2010. Patients were included in two groups: 1. adults with co-morbidities, and 2. healthy adults, who had no prior or coincident diagnosis of a chronic or immunosuppressive underlying disease. Microbiological studies included pneumococcal serotyping and genotyping. RESULTS: Of 745 IPD episodes, 525 (70% occurred in patients with co-morbidities and 220 (30% in healthy adults. The healthy adults with IPD were often smokers (56% or alcohol abusers (18%. As compared to patients with co-morbidities, the healthy adults had (P<0.05: younger age (43.5+/-13.1 vs. 48.7+/-11.3 years; higher proportions of women (45% vs. 24%, pneumonia with empyema (15% vs. 7% and infection with non-PCV7 serotypes including serotypes 1 (25% vs. 5%, 7F (13% vs. 4%, and 5 (7% vs. 2%; and lower mortality (5% vs. 20%. Empyema was more frequently caused by serotype 1. No death occurred among 79 patients with serotype 1 IPD. There was an emergence of virulent clonal-types Sweden(1-ST306 and Netherlands(7F-ST191. The vaccine serotype coverage with the PCV13 was higher in healthy adults than in patients with co-morbidities: 82% and 56%, respectively, P<0.001. CONCLUSION: In this clinical study, one-third of adults with IPD had no underlying chronic or immunosuppressive diseases (healthy adults. They were often smokers and alcohol abusers, and frequently presents with pneumonia and empyema caused by virulent clones of non-PCV7 serotypes such as the Sweden(1-ST306. Thus, implementing tobacco and alcohol abuse-cessation measures and a proper pneumococcal vaccination, such as PCV13 policy, in active smokers and alcohol abusers may diminish the burden of IPD in adults.

  16. 1st EUCOMAS conference

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2008-07-01

    The following topics were dealt with: CFC Infusion Technology - the Future for Commercial CFC Fuselages? Structural Optimization of Composite Aircraft Panels with Large Cut-Outs. Design and Analysis of Advanced Composite Load Introduction Structures for High Lift Devices. A new highly formable quasi-isotropic prepreg for complex shape parts - HexMC, a unique composite technology for new aerospace needs. Ultra Thick Laminates for Highly Loaded Main Landing Gear Fittings - Development of a main landing gear fitting in carbon fibre reinforced plastics. ''ScaLA'' -2nd generation of AlMgSc materials dedicated for short manufacturing chains in the aerospace industry. Latest generation of Al-Li alloys developed by Alcan Aerospace. Aleris' Advanced Aluminium Sheet and Plate Products for High-Performance Aircraft Applications. Mechanical and environmental validation of a spherical multipurpose inflatable structure. Design, Analysis and Manufacturing of a Thermoplastic Slat. Novel load-introduction systems for lightweight aircraft components in composite-metal-hybrid design - Multi-Materials Design for lightweight hydraulic actuators. SiC-fibre reinforced titanium shafts under multiaxial loading - Tests and numerical simulations for torsion and tension loading. New Design Philosophy for Improvement of Damage Tolerance of Welded Airframe Structure. New Approaches for the Flexible Manufacturing of Helicopter FRP-structures. Development of an innovative process for the manufacture of composite components. Thermoplastic Technologies - An Alternative for Aircraft Structures. New Prepreg Materials for Crushed Core Technology - Influence of Cure Cycle on Flammability and Fracture Toughness. Influence of Heat Treatment on Mechanical Properties of Ti-5Al-5V-5Mo-3Cr. Manufacturing and Properties of Induction Welded Metal/Composite Joints. Multi-Physics Modelling of Bobbin-Tool Friction Stir Welding - Applications to a latest generation aluminium Alloy - A simple numerical model supports the development of FSW technology. ABiTAS - Advanced Bonding Technologies for Aircraft Structures. Individual Laser Cladding for High Pressure Turbine Blades. Advanced high temperature repair brazing for single crystal and directionally solidified turbine components. Thermoplastic Tape Placement - Challenging the Autoclave Process. Modern Methods of Preforming Titanium Alloys for Forging Aero Engine Vanes. Ultrasonic Shot Peening for Ti-6Al-4V Aero-Engine Components. Stiffening spherical panels by means of modern braiding processes. Potential and Challenges of Fibre Reinforced Ceramics in Gas Turbines. Development of a nickel alloy for disc applications. Application of Thermal Barrier Coatings on Intermetallic Turbine Blade Materials. Development and Validation of A Dual Titanium Alloy Dual-Microstructure BLISK. PTAH-Socar Fuel-Cooled Composite Materials Structure. Manufacturing Methods and Typical Applications of C/C-SiC Materials Based on the Liquid Silicon Infiltration Process (LSI) - Non brittle C/C-SiC materials based on filament winding. Dilution phenomenon during coating of titanium alloys by Plasma Transferred Arc (PTA) process. Tools, processes and examples of Space Structures Optimisation. Topology Optimisation in the Design Process of Light Weight Structural Components for Aeroengines. Residual strength prediction of integral structures using numerical crack extension analyses. Finite element based optimization of a novel metal-composite-joint. Investigations on the pulsed MIG/MAG welding of dissimilar austenitic-ferritic steels (W7335-X10CrNiTi18.9). Isothermal Oxidation Behaviour and Microstructure of the single crystal superalloy PWA 1483 at 950 C. The Use of Fluorine for the Protection of TiAl-Components against High-Temperature Oxidation. Stability Estimation for Stiffened Structures Considering Laser Beam Welded Stringers - comparision of methods to estimate fuselage buckling behaviour. New design concept for integral manufacturing of high performance composite parts. Structural Adhesives with Debonding Ability for R

  17. Using GC-FID to Quantify the Removal of 4-sec-Butylphenol from NGS Solvent by NaOH

    Energy Technology Data Exchange (ETDEWEB)

    Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-12-01

    A caustic wash of the solvent used in the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process was found to remove the modifier breakdown product 4-sec-butylphenol (SBP) with varying efficiency depending on the aqueous NaOH concentration. Recent efforts at ORNL have aimed at characterizing the flowsheet chemistry and reducing the technical uncertainties of the NG-CSSX process. One technical uncertainty has been the efficacy of caustic washing of the solvent for the removal of lipophilic anions, in particular, the efficient removal of SBP, an important degradation product of the solvent modifier, Cs-7SB. In order to make this determination, it was necessary to develop a sensitive and reliable analytical technique for the detection and quantitation of SBP. This report recounts the development of a GC-FID-based (Gas Chromatography Flame Ionization Detection) technique for analyzing SBP and the utilization of the technique to subsequently confirm the ability of the caustic wash to efficiently remove SBP from the Next Generation Solvent (NGS) used in NG-CSSX. In particular, the developed technique was used to monitor the amount of SBP removed from a simple solvent and the full NGS by contact with sodium hydroxide wash solutions over a range of concentrations. The results show that caustic washing removes SBP with effectively the same efficiency as it did in the original Caustic-Side Solvent Extraction (CSSX) process.

  18. The 1st Euro-Mediterranean Workshop: Natural Products in Health and Diseases: Cairo, Egypt, March 2, 2015

    Directory of Open Access Journals (Sweden)

    Kamal D. Moudgil

    2016-04-01

    Full Text Available Natural plant products have been used for centuries for health maintenance and treatment of a variety of diseases in various traditional systems of medicine in Egypt and other African countries, India, China, and other countries around the world. Over the past several decades, the popularity of herbal and other natural products has gradually increased in many western countries. Despite the increasing popularity of natural products, both the public and the professionals are skeptical about the use of these products. Reasons for this skepticism include, but are not limited to, the lack of proper documentation about the source and formulations used; standardization of the composition, batch-to-batch consistency, documented safety of herbal products; and information about the mechanisms of action of these products. The 1st Euro-Mediterranean Workshop: Natural Products in Health and Diseases was organized by the Euro-Mediterranean Association of Life Sciences (EMALS and various other local organizations to review and discuss the above-mentioned strengths and limitations of the use of natural products. The aim of this workshop was to share best practices and expertise about natural products, and to identify opportunities for collaboration among researchers, health professionals, and business personnel in a productive atmosphere.

  19. Grammar Instruction in the 1st Grade of Senior High School: a Comparative Study of two Methods

    Directory of Open Access Journals (Sweden)

    Argyro Vagiatidou

    2010-02-01

    Full Text Available The present dissertation endeavours to investigate the effectiveness of two opposing grammar teaching approaches on students’ performance in the 1st grade of a Greek State Senior High School. This study, in particular, compares the learning outcomes of the meaning-focused grammar teaching approach, based on a communication-based perspective of language against the outcomes of traditional, structure-based teaching. For the collection of data, a pretest-posttest experiment was conducted, involving the teaching of the Reported speech grammar form to two groups of randomly selected students in a Greek Senior High School. One group of students attended a series of lessons on the Reported Speech through the structure-based approach, while the other one was presented with the same structure in a meaning-focused way. The study has found significant statistical differences in favour of the meaning-focused teaching approach, as it was demonstrated by the outcome that the students of the relevant group were far more successful when compared to their schoolmates of the other group in their attempts to form Reported Speech promptly and accurately as well as use it in a quite fluent way to accomplish relevant contextualised tasks.

  20. 1st World Congress on Electroporation and Pulsed Electric Fields in Biology, Medicine and Food & Environmental Technologies

    CERN Document Server

    Kramar, Peter

    2016-01-01

    This volume presents the proceedings of the 1st World Congress on Electroporation and Pulsed Electric Fields in Biology, Medicine and Food & Environmental Technologies (WC2015). The congress took place in Portorož, Slovenia, during the week of September 6th to 10th, 2015. The scientific part of the Congress covered different aspects of electroporation and related technologies and included the following main topics:   ·         Application of pulsed electric fields technology in food: challenges and opportunities ·         Electrical impedance measurement for assessment of electroporation yield ·         Electrochemistry and electroporation ·         Electroporation meets electrostimulation ·         Electrotechnologies for food and biomass treatment ·         Food and biotechnology applications ·         In vitro electroporation - basic mechanisms ·         Interfacial behaviour of lipid-assemblies, membranes and cells in electric f...

  1. Synthesis of nanomagnetic fluids and their UV spectrophotometric response with aliphatic organic acids and 1st tier dendrimers

    Science.gov (United States)

    Pandya, Shivani R.; Singh, Man

    2016-04-01

    Synthesis of Magnetic nanoparticles were made using coprecipitation method on mixing Fe+3 and Fe+2 in 2:1 ratio with aqueous 8M NaOH which on heating at 90°C for 2 h has yielded 85% magnetic (Fe3O4) nanoparticles (MNPs), characterized by XRD, VSM, SEM, and HR-TEM. The formic acid (FA), oxalic acid (OA) and citric acid (CA), the series of aliphatic organic acids along with Trimesoyl 1, 3, 5 tridimethyl malonate (TTDMM), trimesoyl 1, 3, 5 tridiethyl malonate (TTDEM), trimesoyl 1, 3, 5 tridipropyl malonate (TTDPM), trimesoyl 1, 3, 5 tridibutyl malonate (TTDBM) and trimesoyl 1, 3, 5 tridihexyl malonate (TTDHM) 1st tier dendrimers were used separately for preparing nanomagnetic fluid. From 25 to 150 µM MNPs at an interval of 25 µM were dispersed in 150 µM of acids and dendrimers separately with DMSO. UV-VIS spectrophotometry showed a maximum MNPs dispersion with TTDMM against others and found to be most stable nanomagnetic fluid on account of capping type mechanism of acids.

  2. Child gender and weight status moderate the relation of maternal feeding practices to body esteem in 1st grade children.

    Science.gov (United States)

    Shriver, Lenka H; Hubbs-Tait, Laura; Harrist, Amanda W; Topham, Glade; Page, Melanie

    2015-06-01

    Prevention of body dissatisfaction development is critical for minimizing adverse effects of poor body esteem on eating behaviors, self-esteem, and overall health. Research has examined body esteem and its correlates largely in pre-adolescents and adolescents; however, important questions remain about factors influencing body esteem of younger children. The main purpose of this study was to test moderation by children's gender and weight status of the relation of maternal controlling feeding practices to 1st graders' body esteem. The Body Esteem Scale (BES) and anthropometric measurements were completed during one-on-one child interviews at school. Mothers completed the Child Feeding Questionnaire (restriction, monitoring, concern, self-assessed maternal weight). A total of 410 mother/child dyads (202 girls) participated. Percent of children classified as overweight (BMI-for-age ≥85th) was: girls - 29%; boys - 27%. Gender moderated the relation between restriction and body esteem (β = -.140, p = .05), with maternal restriction predicting body esteem in girls but not boys. The hypothesized three-way interaction among gender, child weight status, and monitoring was confirmed. Monitoring was significantly inversely related to body esteem only for overweight/obese girls (b = -1.630). The moderating influence of gender or gender and weight status on the link between maternal feeding practices and body esteem suggests the importance of body esteem interventions for girls as early as first grade.

  3. Palaeopathology of human remains of the 1st century BC–3rd century AD from Armenia (Beniamin, Shirakavan I

    Directory of Open Access Journals (Sweden)

    Khudaverdyan Anahit Yu.

    2015-06-01

    Full Text Available The aim of this article was to document the pathology of the individuals from the archeological sites of Beniamin and Shirakavan I, Armenia, dated on the 1st century BC - 3rd century AD. The findings revealed that two groups differed in mean age at death of adults. At Beniamin it was 24 years, 40.8 years for males and 30.9 years for females, whereas at Shirakavanit it was 29.3 years, 29.6 years for males and 35.8 years for females. The greatest mortality appeared to have occurred when the children reached the age of one year (Beniamin. The population had high number of young-adult females with a cause of death associated with child-bearing. Very few females survived to old age. Traumatic conditions (63.64% and enamel hypoplasias (57.2% have a high frequency in the skeletal material from Shirakavan. The volume of selection of Shirakavan does not allow itself to so big discussion as it was possible with the Beniamin site. Fewer hypoplasias in Beniamin group indicate that food resources were more abundant and more easily exploited. The small frequency of a periodontal disorder indicates that dental hygiene was good during the Antiquity period. We here report a case of possible pituitary dwarfism and a case of decapitation.

  4. 1st Quarter Transportation Report FY 2015: Radioactive Waste Shipments to and from the Nevada National Security Site (NNSS)

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, Louis [National Security Technologies, LLC, Las Vegas, NV (United States)

    2015-02-20

    This report satisfies the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) commitment to prepare a quarterly summary report of radioactive waste shipments to and from the Nevada National Security Site (NNSS) Radioactive Waste Management Complex (RWMC) at Area 5. There were no shipments sent for offsite treatment and returned to the NNSS this quarter. This report summarizes the 1st quarter of Fiscal Year (FY) 2015 low-level radioactive waste (LLW) and mixed low-level radioactive waste (MLLW) shipments. Tabular summaries are provided which include the following: Sources of and carriers for LLW and MLLW shipments to and from the NNSS; Number and external volume of LLW and MLLW shipments; Highway routes used by carriers; and Incident/accident data applicable to LLW and MLLW shipments. In this report shipments are accounted for upon arrival at the NNSS, while disposal volumes are accounted for upon waste burial. The disposal volumes presented in this report include minor volumes of non-radioactive classified waste/material that were approved for disposal (non-radioactive classified or nonradioactive classified hazardous). Volume reports showing cubic feet generated using the Low-Level Waste Information System may vary slightly due to rounding conventions for volumetric conversions from cubic meters to cubic feet.

  5. Airborne Gravity: NGS' Airborne Gravity Data for AN01 (2009-2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2009-2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  6. Airborne Gravity: NGS' Gravity Data for EN03 (2011-2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Michigan, Wisconsin, Illinois, Indiana, and Lake Michigan collected in 2011 to 2013 over 3 surveys. This data set is part of the Gravity...

  7. Airborne Gravity: NGS' Gravity Data for EN02 (2011-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, Ohio, Michigan, Canada and Lake Erie collected in 2011 and 2012 over 3 surveys. This data set is part of the...

  8. Airborne Gravity: NGS' Gravity Data for ES04 (2013-2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for North Carolina, South Carolina, Virginia, and the Atlantic Ocean collected in 2013 and 2014 over two surveys. This data set is part of the...

  9. 2008 NOAA/NGS Integrated Ocean and Coastal Mapping (IOCM) LIDAR: Kenai Peninsula Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using an OPTECH ALTM system. The data...

  10. High Accuracy Reference Network (HARN), Points generated from coordinates supplied by NGS, Published in 1993, MARIS.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This High Accuracy Reference Network (HARN) dataset, was produced all or in part from Field Survey/GPS information as of 1993. It is described as 'Points generated...

  11. Geodetic Networks, geodetic control points within the National Spatial Reference System, Published in unknown, NGS.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Geodetic Networks dataset, was produced all or in part from Field Survey/GPS information as of unknown. It is described as 'geodetic control points within the...

  12. Airborne Gravity: NGS' Gravity Data for AS03 (2010-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  13. Airborne Gravity: NGS' Gravity Data for CS02 (2008-2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Louisana and Mississippi collected in 2008-2009 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  14. Airborne Gravity: NGS' Gravity Data for EN07 (2012-2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine and Canada collected in 2012 and 2013 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  15. 2008 NOAA/NGS Integrated Ocean and Coastal Mapping (IOCM) LIDAR: Kenai Peninsula Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using an OPTECH ALTM system. The data...

  16. 2014 NOAA NGS Topobathy Lidar: Key West National Wildlife Refuge (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ880G system. The data...

  17. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

    Science.gov (United States)

    Katta, Mohan A. V. S. K.; Khan, Aamir W.; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K.

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data. PMID:26460497

  18. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

    Science.gov (United States)

    Katta, Mohan A V S K; Khan, Aamir W; Doddamani, Dadakhalandar; Thudi, Mahendar; Varshney, Rajeev K

    2015-01-01

    Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

  19. NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina Data.

    Directory of Open Access Journals (Sweden)

    Mohan A V S K Katta

    Full Text Available Rapid popularity and adaptation of next generation sequencing (NGS approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1 (http://htslib.org, for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2, SNP calling (SAMtools and other utilities (bedtools towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina data.

  20. Experimental observations on the response of 1(st) and 2(nd) order fibre optic long period grating coupling bands to the deposition of nanostructured coatings.

    Science.gov (United States)

    James, Stephen W; Cheung, C S; Tatam, Ralph P

    2007-10-01

    The sensitivity of attenuation bands corresponding to the 2(nd) order coupling to cladding modes by a fibre optic long period grating (LPG) to the deposition of nanostructured coatings is investigated and compared with that of the 1(st) order coupling. The experimental observations support previously reported theoretical descriptions of LPGs with nanoscale coatings.

  1. Hybrid distributed Raman amplification combining random fiber laser based 2nd-order and low-noise LD based 1st-order pumping.

    Science.gov (United States)

    Jia, Xin-Hong; Rao, Yun-Jiang; Yuan, Cheng-Xu; Li, Jin; Yan, Xiao-Dong; Wang, Zi-Nan; Zhang, Wei-Li; Wu, Han; Zhu, Ye-Yu; Peng, Fei

    2013-10-21

    A configuration of hybrid distributed Raman amplification (H-DRA), that is formed by incorporating a random fiber laser (RFL) based 2nd-order pump and a low-noise laser-diode (LD) based 1st-order pump, is proposed in this paper. In comparison to conventional bi-directional 1st-order DRA, the effective noise figure (ENF) is found to be lower by amount of 0 to 4 dB due to the RFL-based 2nd-order pump, depending on the on-off gain, while the low-noise 1st-order Raman pump is used for compensating the worsened signal-to-noise ratio (SNR) in the vicinity towards the far end of the fiber and avoiding the potential nonlinear impact induced by excess injection of pump power and suppressing the pump-signal relative intensity noise (RIN) transfer. As a result, the gain distribution can be optimized along ultra-long fiber link, due to combination of the 2nd-order RFL and low-noise 1st-order pumping, making the transmission distance be extended significantly. We utilized such a configuration to achieve ultra-long-distance distributed sensing based on Brillouin optical time-domain analysis (BOTDA). A repeater-less sensing distance record of up to 154.4 km with 5 m spatial resolution and ~ ± 1.4 °C temperature uncertainty is successfully demonstrated.

  2. Moving beyond the Lone Scientist: Helping 1st-Grade Students Appreciate the Social Context of Scientific Work Using Stories about Scientists

    Science.gov (United States)

    Sharkawy, Azza

    2009-01-01

    While several studies have documented young children's (K-2) stereotypic views of scientists and scientific work, few have examined students' views of the social nature of scientific work and the strategies effective in broadening these views. The purpose of this study is to examine how stories about scientists influence 1st-grade students' views…

  3. Pre-Proceedings of the 1st International Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07)

    NARCIS (Netherlands)

    Reichert, M.U.; Peleg, M.; Lenz, R.

    2007-01-01

    These pre-proceedings contain the presentations given at the 1st Int'l Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07). Formal proceedings will be published in Springer's LNCS series. Process-oriented information systems have been demanded for more than 20 years and t

  4. Pre-Proceedings of the 1st International Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07)

    NARCIS (Netherlands)

    Reichert, M.U.; Peleg, M.; Lenz, R.

    2007-01-01

    These pre-proceedings contain the presentations given at the 1st Int'l Workshop on Process-oriented Information Systems in Healthcare (ProHealth'07). Formal proceedings will be published in Springer's LNCS series. Process-oriented information systems have been demanded for more than 20 years and ter

  5. Validation of the Edinburgh Claudication Questionnaire in 1st generation Black African-Caribbean and South Asian UK migrants: A sub-study to the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES) study

    Science.gov (United States)

    2011-01-01

    Background We determined the diagnostic accuracy of the Edinburgh Claudication Questionnaire (ECQ) in 1st generation Black African-Caribbean UK migrants as previous diagnostic questionnaires have been found to be less accurate in this population. We also determined the diagnostic accuracy of translated versions of the ECQ in 1st generation South Asian UK migrants, as this has not been investigated before. Methods Subjects were recruited from the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES) study, a community based screening survey for heart failure in minority ethnic groups. Translated versions of the ECQ were prepared following a recognised protocol. All participants attending screening between October 2007 and February 2009 were asked to complete the ECQ in the language of their choice (English, Punjabi, Bengali, Urdu, Hindi or Gujarati). Subjects answering positively to experiencing leg pain or discomfort on walking were asked to return to have Ankle Brachial Pressure Index (ABPI) measured. Results 154 out of 2831 subjects participating in E-ECHOES (5.4%) were eligible to participate in this sub-study, for which 74.3% returned for ABPI assessment. Non-responders were younger than participants (59[9] vs. 65[11] years; p = 0.015). Punjabi, English and Bengali questionnaires identified participants with Intermittent Claudication, so these questionnaires were assessed. The sensitivities (SN), specificities (SP), positive (PPV) and negative (NPV) predictive values were calculated. English: SN: 50%; SP: 68%; PPV: 43%; NPV: 74%. Punjabi: SN: 50%; SP: 87%; PPV: 43%; NPV: 90%. Bengali: SN: 33%; SP: 50%; PPV: 13%; NPV: 73%. There were significant differences in diagnostic accuracy between the 3 versions (Punjabi: 83.8%; Bengali: 45%; English: 62.2%; p < 0.0001). No significant differences were found in sensitivity and specificity between illiterate and literate participants in any of the questionnaires and there was no significant different difference

  6. Validation of the Edinburgh Claudication Questionnaire in 1st generation Black African-Caribbean and South Asian UK migrants: A sub-study to the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES study

    Directory of Open Access Journals (Sweden)

    Silverman Stanley

    2011-06-01

    Full Text Available Abstract Background We determined the diagnostic accuracy of the Edinburgh Claudication Questionnaire (ECQ in 1st generation Black African-Caribbean UK migrants as previous diagnostic questionnaires have been found to be less accurate in this population. We also determined the diagnostic accuracy of translated versions of the ECQ in 1st generation South Asian UK migrants, as this has not been investigated before. Methods Subjects were recruited from the Ethnic-Echocardiographic Heart of England Screening (E-ECHOES study, a community based screening survey for heart failure in minority ethnic groups. Translated versions of the ECQ were prepared following a recognised protocol. All participants attending screening between October 2007 and February 2009 were asked to complete the ECQ in the language of their choice (English, Punjabi, Bengali, Urdu, Hindi or Gujarati. Subjects answering positively to experiencing leg pain or discomfort on walking were asked to return to have Ankle Brachial Pressure Index (ABPI measured. Results 154 out of 2831 subjects participating in E-ECHOES (5.4% were eligible to participate in this sub-study, for which 74.3% returned for ABPI assessment. Non-responders were younger than participants (59[9] vs. 65[11] years; p = 0.015. Punjabi, English and Bengali questionnaires identified participants with Intermittent Claudication, so these questionnaires were assessed. The sensitivities (SN, specificities (SP, positive (PPV and negative (NPV predictive values were calculated. English: SN: 50%; SP: 68%; PPV: 43%; NPV: 74%. Punjabi: SN: 50%; SP: 87%; PPV: 43%; NPV: 90%. Bengali: SN: 33%; SP: 50%; PPV: 13%; NPV: 73%. There were significant differences in diagnostic accuracy between the 3 versions (Punjabi: 83.8%; Bengali: 45%; English: 62.2%; p Conclusions Our findings suggest that the ECQ is not as sensitive or specific a diagnostic tool in 1st generation Black African-Caribbean and South Asian UK migrants than in the Edinburgh

  7. Evaluation of neutron irradiation embrittlement in the Korean reactor pressure vessel steels(I) (1st progress report)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Jun Hwa; Lee, Bong Sang; Park, Duck Gun; Byun, Tak Sang; Kim, Joo Hag; Oh, Yong Jun; Yoon, Ji Hyun; Chi, Sei Hwan; Kuk, Il Hyun [Korea Atomic Energy Research Institute, Taejon (Korea)

    1998-10-01

    The SA508-3 reactor pressure vessel materials degrade due to the application at high temperature, high pressure, and neutron irradiation. In the present study it is planned to examine the effects of neutron irradiation on the properties for assessing the integrity of domestic reactors. The key tests are the Charpy impact test, tensile test, static and dynamic fracture toughness test, J-R test. The additional tests for obtaining basic material properties, such as micro-hardness, microstructural properties, small punch energy etc., are also performed. The irradiation tests are being performed at HANARO of KAERI through the instrumented capsules designed by KAERI and the post-irradiation tests are being performed at IMEF(Irradiated Material Evaluation Facility) of material (UCN-4), Si+Al (YGN-5), UCN-4 weld metal, and UCN-4 HAZ. In the irradiation test the temperature should be controlled in the range of 290 {+-} 10 deg C and the test materials would be irradiated to 2 to 3 neutron fluence levels including the end-of-life fluence. The status of performing this project is that (1) the key data on mechanical properties, mainly related to the fracture toughness, of the unirradiated materials have been obtained, (2) the irradiation of the 1st instrumented capsule, a preliminary test capsule containing miniature specimens, has been completed and is being stored for testing in IMEF, and (3) the 2nd instrumented capsule is being manufactured and will be irradiated in the beginning or 1999. This report includes mainly the experimental methods and results. The status of the design and manufacturing of the instrumented capsules and specimens was also briefly described. (author). 13 refs., 15 figs., 10 tabs.

  8. Residual effects of TMOF-Bti formulations against 1 st instar Aedes aegypti Linnaeus larvae outside laboratory

    Institute of Scientific and Technical Information of China (English)

    Saiful AN; Lau MS; Sulaiman S; Hidayatulfathi O

    2012-01-01

    Objective: To evaluate the effectiveness and residual effects of trypsin modulating oostatic factor-Bacillus thuringiensis israeliensis (TMOF-Bti) formulations against Aedes aegypti (Ae. aegypti) (L.) larvae at UKM Campus Kuala Lumpur. Methods: Twenty first instar Ae. aegypti larvae were added in each bucket containing 4 L of water supplied with crushed dried leaf powder as their source of food. Combination of TMOF-Bti in rice husk formulation with the following weights viz 10, 25, 50 and 100 mg, respectively in duplicate was distributed in the buckets; while TMOF-Bti in wettable powder formulation each weighing viz 2, 5, 10 and 20 mg, respectively in duplicate was also placed in the buckets. The control buckets run in duplicate with 4 L of water and 20 first instar Ae. aegypti larvae. All buckets were covered with mosquito netting. Larval mortality was recorded after 24 hours and weekly for five weeks. A new batch of 20 1st instar larvaeAe. aegypti was introduced into each bucket weekly without additional TMOF-Bti rice husk formulation or wettable powder. The experiment was repeated for four times. Results: The result of the study showed that all formulations were very effective on the first two weeks by giving 100%larval mortality for all concentrations applied. The TMOF (2%) + Bti (2%) had a good residual effect until the end of 3rd week, TMOF (4%) + Bti (4%) until 4th week, wettable powder TMOF (20%) + Bti (20%) until the third week. Conclusions: From the results it can be concluded that the TMOF-Bti formulations can be utilized in dengue vector control.

  9. High resolution survey for topographic surveying

    Science.gov (United States)

    Luh, L. C.; Setan, H.; Majid, Z.; Chong, A. K.; Tan, Z.

    2014-02-01

    In this decade, terrestrial laser scanner (TLS) is getting popular in many fields such as reconstruction, monitoring, surveying, as-built of facilities, archaeology, and topographic surveying. This is due the high speed in data collection which is about 50,000 to 1,000,000 three-dimensional (3D) points per second at high accuracy. The main advantage of 3D representation for the data is that it is more approximate to the real world. Therefore, the aim of this paper is to show the use of High-Definition Surveying (HDS), also known as 3D laser scanning for topographic survey. This research investigates the effectiveness of using terrestrial laser scanning system for topographic survey by carrying out field test in Universiti Teknologi Malaysia (UTM), Skudai, Johor. The 3D laser scanner used in this study is a Leica ScanStation C10. Data acquisition was carried out by applying the traversing method. In this study, the result for the topographic survey is under 1st class survey. At the completion of this study, a standard of procedure was proposed for topographic data acquisition using laser scanning systems. This proposed procedure serves as a guideline for users who wish to utilize laser scanning system in topographic survey fully.

  10. Grid平台上的NGS编译技术%The Compiler Technology of NGS on the Grid

    Institute of Scientific and Technical Information of China (English)

    丛杨; 王雷; 朱凯佳; 刘又诚

    2003-01-01

    随着网络技术的发展,在异构平台上使用共同的计算和信息资源将很快成为可能.Grid(网格)就是这样一种提供资源共享的新兴平台,而在其之上的下一代软件程序(NGS)则对编译器提出了新的挑战[1].未来Grid平台上的编译系统将是能够进行动态编译和优化,根据实时系统以及网络的性能不断进行自我调整的软件模型,同时它还能为具有自适应性的应用程序提供编译支持.

  11. NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds.

    Science.gov (United States)

    Diaz-Real, J; Serrano, D; Piriz, A; Jovani, R

    2015-10-01

    Understanding the ecological function of species and the structure of communities is crucial in the study of ecological interactions among species. For this purpose, not only the occurrence of particular species but also their abundance in ecological communities is required. However, abundance quantification of species through morphological characters is often difficult or time/money consuming when dealing with elusive or small taxa. Here we tested the use of next-generation sequencing (NGS) for abundance estimation of two species of feather mites (Proctophyllodes stylifer and Pteronyssoides parinus) under five proportions (16:1, 16:4, 16:16, 16:64, and 16:256 mites) against a mock community composed by Proctophyllodes clavatus and Proctophyllodes sylviae. In all mixtures, we retrieved sequence reads from all species. We found a strong linear relationship between 454 reads and the real proportion of individuals in the mixture for both focal species. The slope for Pr. stylifer was close to one (0.904), and the intercept close to zero (-0.007), thus showing an almost perfect correspondence between real and estimated proportions. The slope for Pt. parinus was 0.351 and the intercept 0.307, showing that while the estimated proportion increased linearly relative to real proportions of individuals in the samples, proportions were overestimated at low real proportions and underestimated at larger ones. Additionally, pyrosequencing replicates from each DNA extraction were highly repeatable (R = 0.920 and 0.972, respectively), showing that the quantification method is highly consistent given a DNA extract. Our study suggests that NGS is a promising tool for abundance estimation of feather mites' communities in birds.

  12. Detailed finite element analysis of Darlington NGS feeder pipes with locally thinned regions below pressure minimum thickness

    Energy Technology Data Exchange (ETDEWEB)

    Haq, I.; Stojakovic, M.; Li, M. [Ontario Power Generation Inc., Pickering, Ontario (Canada)

    2011-07-01

    Feeder Pipes in CANDU nuclear stations are experiencing wall thinning due to flow accelerated corrosion (FAC) resulting in locally thinned regions in addition to general thinning. In Darlington NGS these locally thinned regions can be below pressure based minimum thickness (t{sub min}), required as per ASME Code Section III NB-3600 Equation (1). A methodology is presented to qualify the locally thinned regions under NB-3200 (NB-3213 and NB-3221) for internal pressure loading only. Detailed finite element models are used for internal pressure analysis using ANSYS v11.0. All other loadings such as deadweight, thermal and seismic loadings are qualified under NB-3600 using a general purpose piping stress analysis software. The piping stress analysis is based on average thickness equal to t{sub min} along with maximum values of ASME Code stress indices (Table NB-3681(a)-1). The requirement for the use of this methodology is that the average thickness of each cross-section with the locally thinned region shall be at least t{sub min}. The finite element analysis models are thinned to 0.75 t{sub min} (in increments of 0.05 t{sub min}) all-around the circumference in the straight section region allowing for flexible inspection requirements. Two different thicknesses of 1.10 t{sub min} and 1.30 t{sub min} are assigned to the bends. Thickness vs the allowable axial extent curves were developed for different types of feeder pipes in service. Feeders differ in pipe size, straight section length, bend angle and orientation. The stress analysis results show that all Darlington NGS outlet feeder pipes are fit for service with locally thinned regions up to 75% of the pressure based minimum thickness. This paper demonstrates the effectiveness of finite element analysis in extending the useful life of degraded piping components. (author)

  13. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

    Science.gov (United States)

    Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

    2014-03-01

    Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

  14. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  15. PREFACE: 1st International School and Conference "Saint Petersburg OPEN 2014" on Optoelectronics, Photonics, Engineering and Nanostructures

    Science.gov (United States)

    2014-09-01

    Dear Colleagues, 1st International School and Conference "Saint Petersburg OPEN 2014" on Optoelectronics, Photonics, Engineering and Nanostructures was held on March 25 - 27, 2014 at St. Petersburg Academic University - Nanotechnology Research and Education Centre of the Russian Academy of Sciences. The School and Conference included a series of invited talks given by leading professors with the aim to introduce young scientists with actual problems and major advances in physics and technology. The keynote speakers were: Mikhail Glazov (Ioffe Physico-Technical Institute RAS, Russia) Vladimir Dubrovskii (Saint Petersburg Academic University RAS, Russia) Alexey Kavokin (University of Southampton, United Kingdom and St. Petersburg State University, Russia) Vladimir Korenev (Ioffe Physico-Technical Institute RAS, Russia) Sergey Kukushkin (Institute of Problems of Mechanical Engineering RAS, Russia) Nikita Pikhtin (Ioffe Physico-Technical Institute RAS, Russia and "Elfolum" Ltd., Russia) Dmitry Firsov (Saint Petersburg State Polytechnical University, Russia) During the poster session all undergraduate and graduate students attending the conference presented their works. Sufficiently large number of participants with more than 160 student attendees from all over the world allowed the Conference to provide a fertile ground for the fruitful discussions between the young scientists as well as to become a perfect platform for the valuable discussions between student authors and highly experienced scientists. The best student papers, which were selected by the Program Committee and by the invited speakers basing on the theses and their poster presentation, were awarded with diplomas of the conference - see the photos. This year's School and Conference is supported by SPIE (The International Society for Optics and Photonics), OSA (The Optical Society), St. Petersburg State Polytechnical University and by Skolkovo Foundation. It is a continuation of the annual schools and

  16. Points to consider in the clinical use of NGS panels for mitochondrial disease: an analysis of gene inclusion and consent forms.

    Science.gov (United States)

    Platt, Julia; Cox, Rachel; Enns, Gregory M

    2014-08-01

    Mitochondrial next generation sequencing (NGS) panels offer single-step analysis of the numerous nuclear genes involved in the structure, function, and maintenance of mitochondria. However, the complexities of mitochondrial biology and genetics raise points for consideration in clinical use of these tests. To understand the current status of mitochondrial genetic testing, we assessed the gene offerings and consent forms of mitochondrial NGS panels available from seven US-based clinical laboratories. The NGS panels varied markedly in number of genes (101-1204 genes), and the proportion of genes causing "classic" mitochondrial diseases and their phenocopies ranged widely between labs (18 %-94 % of panel contents). All panels included genes not associated with classic mitochondrial diseases (6 %-28 % of panel contents), including genes causing adult-onset neurodegenerative disorders, cancer predisposition, and other genetic syndromes or inborn errors of metabolism. Five of the panels included genes that are not listed in OMIM to be associated with a disease phenotype (5 %-49 % of panel contents). None of the consent documents reviewed had options for patient preference regarding receipt of incidental findings. These findings raise points of discussion applicable to mitochondrial diagnostics, but also to the larger arenas of exome and genome sequencing, including the need to consider the boundaries between clinical and research testing, the necessity of appropriate informed consent, and the responsibilities of clinical laboratories and clinicians. Based on these findings, we recommend careful evaluation by laboratories of the genes offered on NGS panels, clear communication of the predicted phenotypes, and revised consent forms to allow patients to make choices about receiving incidental findings. We hope that our analysis and recommendations will help to maximize the considerable clinical utility of NGS panels for the diagnosis of mitochondrial disease.

  17. THE AFFECTION OF TIME AND DISTANCE TO NGS-2000GPS SURVEYING PRECISION%时间距离因子对南方NGS-200GPS测量精度的影响

    Institute of Scientific and Technical Information of China (English)

    费鲜芸; 亓学翔; 刘文杰; 高祥伟

    2003-01-01

    GPS是一项在逐渐兴起的技术.与传统的测量技术相比,它具有无可比拟的优越性.本文通过对观测分析,得出测量时间的长短及测量时段的分布对测量结果都具有明显的影响.

  18. 1st Guidelines of the Brazilian Society of Cardiology on processes and skills for education in cardiology in Brazil--executive summary.

    Science.gov (United States)

    Sousa, Marcos Roberto de; Mourilhe-Rocha, Ricardo; Paola, Angelo Amato Vincenzo de; Köhler, Ilmar; Feitosa, Gilson Soares; Schneider, Jamil Cherem; Feitosa-Filho, Gilson Soares; Nicolau, José Carlos; Ferreira, João Fernando Monteiro; Morais, Nelson Siqueira de

    2012-02-01

    This article summarizes the "1st Guidelines of the Brazilian Society of Cardiology on Processes and Skills for Education in Cardiology in Brazil," which can be found in full at: . The guideline establishes the education time required in Internal Medicine and Cardiology with Specialization through theoretical and practical training. These requirements must be available at the center forming Specialists in Cardiology and the Cardiology contents.

  19. The 1st European Summer School on 'proteomic basics'--the students view. 12-18 August, 2007 Kloster Neustift, Brixen/Bressanone, South Tyrol, Italy.

    Science.gov (United States)

    Collins, Emily S; Little, Samantha J

    2008-01-01

    Fifty postgraduate and postdoctoral delegates from all over Europe attended the week-long '1st European Summer School on Proteomic Basics' in Kloster Neustift in the Italian South Tyrol in August 2007. Invited proteomics experts gave tutorial lectures on Proteomics techniques with an emphasis on sample preparation, protein separation and purification in the first of an annual series of Proteomics Summer Schools funded by the EU and the Volkswagen Stiftung.

  20. Improving Students’ Vocabulary Through A Smartphone Application, Learn English With Music Songs: A Case Study Of The 1st Grade Students Of Sma Indonesia Membangun Medan

    OpenAIRE

    Nababan, Elysabeth

    2016-01-01

    This thesis entitled Improving Students’ Vocabulary through a Smartphone Application, Learn English with Music Songs: A Case Study 1st Grade Students of SMA Indonesia Membangun Medan. The aim of the study is to improve the students’ vocabulary through a smartphone application (Learn English with Music Songs). The students have difficulties in remembering new vocabulary and confused to understand the vocabulary. The students think that English is difficult and boring. To improve students’ voca...

  1. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015); Budapest (Hungary); September 16-20, 2015; Session “Brain & Development”

    OpenAIRE

    Various Authors

    2015-01-01

    Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015); Budapest (Hungary); September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN), European Society for Paediatric Research (ESPR), Union of European Neonatal & Perinatal Societies (UENPS), European Foundation for the Care of Newborn Infants (EFCNI), with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT), supp...

  2. The analysis of the physical statement of cadets of the 1st course of the military Institute on the starting stage of studying

    Directory of Open Access Journals (Sweden)

    Ovcharuk I.S.

    2010-11-01

    Full Text Available The physical state of the youth which fulfills the rows of military forces of Ukraine has no tendency to improve according to the health and physical preparation. The physical state of cadets of the 1st course is analyzed. 69 cadets took part in research. It improves from the first month of being in educational establishment. Studying curriculum of this educational establishment must provide the fulfillment of all the tasks of physical preparation of military forces of Ukraine.

  3. The rate of symptomatic improvement of congenital nasolacrimal duct obstruction in Japanese infants treated with conservative management during the 1st year of age

    Directory of Open Access Journals (Sweden)

    Hirohiko Kakizaki

    2008-06-01

    Full Text Available Hirohiko Kakizaki1, Yasuhiro Takahashi2, Shinsuke Kinoshita1, Kunihiko Shiraki2, Masayoshi Iwaki11Department of Ophthalmology, Aichi Medical University, Aichi, Japan; 2Department of Ophthalmology and Visual Sciences, Osaka City University Graduate School of Medicine, Osaka, JapanAbstract: This study aimed to examine the rate of symptomatic improvement of congenital nasolacrimal duct obstruction (CNLDO in Japanese infants treated with conservative management within the 1st year of age. Thirty-five lacrimal ducts in 27 patients diagnosed with CNLDO were included in the study. During the observational period, lacrimal ducts were massaged. As well, antibiotic eye drops, to be administered 4 times a day, were sometimes prescribed for obvious conjunctivitis. Two lacrimal ducts in 2 patients were probed before the 1st year of age because of dacryocystitis or severe blepharitis; these patients were included in the unimproved group. Twenty-nine lacrimal ducts in 21 patients resolved during the period (82.9%; with 16 lacrimal ducts resolving before six months of age. Therefore, a comparatively high percentage of resolution for CNLDO (82.9% following conservative management was shown before the 1st year of age in Japanese infants.Keywords: congenital nasolacrimal duct obstruction, symptomatic improvement, conservative management, massage, probing

  4. EVALUATION OF ANXIETY & DEPRESSIVE SYMPTOMS IN PATIENTS WITH 1 ST EPISODE OF CHEST PAIN ATTENDING MEDICINE OUT PATIENT DEPARTMENT OF TERTIARY CARE TEACHING HOSPITAL

    Directory of Open Access Journals (Sweden)

    Bhavik S.

    2015-06-01

    Full Text Available INTRODUCTION: As chest pain is an important symptom of coronary artery disease (CAD and other non - cardiac diseases , the presentation of the symptom often prompts referral to physicians for further investigation. Previous studies h ad shown significant as sociation between chest pain and D e pr e ssive and anxiety symptoms. AIMS AND OBJECTIVES: Evaluate and screen depressive symptoms , anxiety symptoms and somatic symptoms in patients with 1 st episode of chest pain attending medicine out - patient department of tertiary care teaching hospital. METHODOLGY : Cross - sectional observational study. Prior permission from institutional ethics committee of ‘SUMANDEEP VIDYAPEETH’ had been taken. 100 patients having first episosde of chest pain coming to M edicine opd of DHIRAJ HOSPITAL are recruited randomly after 1st December 2014. Each patient is given case r eport form containing sociodemographic data , patients medical history , depression and somatic symptoms scale and Hamilton’s anxiety scale (HAM - A. All data are entered in spss 16 and analysed with different ( S tatistical tests. Differences on categorical m easures will be reported as P value. The result is significant if P <0.05. RESULT: 38% & 49% patients have clinically significant depression and anxiety respectively. DSSS score is positively correlated with duration of chest pain. CONCLUSION : significant level of depression and anxiety found in 1 st episode of chest pain patients.

  5. PREFACE: 1st Nano-IBCT Conference 2011 - Radiation Damage of Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy

    Science.gov (United States)

    Huber, Bernd A.; Malot, Christiane; Domaracka, Alicja; Solov'yov, Andrey V.

    2012-07-01

    The 1st Nano-IBCT Conference entitled 'Radiation Damage in Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy' was held in Caen, France, in October 2011. The Meeting was organised in the framework of the COST Action MP1002 (Nano-IBCT) which was launched in December 2010 (http://fias.uni-frankfurt.de/nano-ibct). This action aims to promote the understanding of mechanisms and processes underlying the radiation damage of biomolecular systems at the molecular and nanoscopic level and to use the findings to improve the strategy of Ion Beam Cancer Therapy. In the hope of achieving this, participants from different disciplines were invited to represent the fields of physics, biology, medicine and chemistry, and also included those from industry and the operators of hadron therapy centres. Ion beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal healthy tissue, while maximizing cell killing within the tumour. Several ion beam cancer therapy clinical centres are now operating in Europe and elsewhere. However, the full potential of such therapy can only be exploited by better understanding the physical, chemical and biological mechanisms that lead to cell death under ion irradiation. Considering a range of spatio-temporal scales, the proposed action therefore aims to combine the unique experimental and theoretical expertise available within Europe to acquire greater insight at the nanoscopic and molecular level into radiation damage induced by ion impact. Success in this endeavour will be both an important scientific breakthrough and give great impetus to the practical improvement of this innovative therapeutic technique. Ion therapy potentially provides an important advance in cancer therapy and the COST action MP1002 will be very significant in ensuring Europe's leadership in this field, providing the scientific background, required data and mechanistic insight which

  6. The Integrated Status and Effectiveness Monitoring Program : Expansion of Existing Smolt Trapping Program and Steelhead Spawner Surveys : March 1st, 2008 - February 28th, 2009.

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Todd; Tonseth, Michael

    2009-01-01

    The Integrated Status and Effectiveness Monitoring Program (ISEMP - BPA project No.2003-0017) has been created as a cost effective means of developing protocols and new technologies, novel indicators, sample designs, analytical, data management and communication tools and skills, and restoration experiments that support the development of a region-wide Research, Monitoring and Evaluation (RME) program to assess the status of anadromous salmonid populations, their tributary habitat and restoration and management actions. The most straightforward approach to developing a regional-scale monitoring and evaluation program would be to increase standardization among status and trend monitoring programs. However, the diversity of species and their habitat, as well as the overwhelming uncertainty surrounding indicators, metrics, and data interpretation methods, requires the testing of multiple approaches. Thus, the approach ISEMP has adopted is to develop a broad template that may differ in the details among subbasins, but one that will ultimately lead to the formation of a unified RME process for the management of anadromous salmonid populations and habitat across the Columbia River Basin. ISEMP has been initiated in three pilot subbasins, the Wenatchee/Entiat, John Day, and Salmon. To balance replicating experimental approaches with the goal of developing monitoring and evaluation tools that apply as broadly as possible across the Pacific Northwest, these subbasins were chosen as representative of a wide range of potential challenges and conditions, e.g., differing fish species composition and life histories, ecoregions, institutional settings, and existing data. ISEMP has constructed a framework that builds on current status and trend monitoring infrastructures in these pilot subbasins, but challenges current programs by testing alternative monitoring approaches. In addition, the ISEMP is: (1) Collecting information over a hierarchy of spatial scales, allowing for a greater flexibility of data aggregation for multi-scale recovery planning assessments, and; (2) Designing methods that: (a) Identify factors limiting fish production in watersheds; (b) Determine restoration actions to address these problems; (c) Implement actions as a large-scale experiment (e.g., Before After Control Impact, or BACI design), and (d) Implement intensive monitoring and research to evaluate the action's success. The intent of the ISEMP project is to design monitoring programs that can efficiently collect information to address multiple management objectives over a broad range of scales. This includes: Evaluating the status of anadromous salmonids and their habitat; Identifying opportunities to restore habitat function and fish performance, and Evaluating the benefits of the actions to the fish populations across the Columbia River Basin. The multi-scale nature of this goal requires the standardization of protocols and sampling designs that are statistically valid and powerful, properties that are currently inconsistent across the multiple monitoring programs in the region. Other aspects of the program will aid in the ability to extrapolate information beyond the study area, such as research to elucidate causal mechanisms, and a classification of watersheds throughout the Columbia River Basin. Obviously, the scale of the problem is immense and the ISEMP does not claim to be the only program working towards this goal. As such, ISEMP relies heavily on the basin's current monitoring infrastructure to test and develop monitoring strategies, while acting as a coordinating body and providing support for key elements such as data management and technical analyses. The ISEMP also ensures that monitoring programs can address large-scale management objectives (resulting largely from the ESA) through these local efforts. While the ISEMP maintains a regional focus it also returns the necessary information to aid in management at the smaller spatial scales (individual projects) where manipulations (e.g., habitat restoration actions) actually occur. The work captured in this report is a component of the overall Integrated Status and Effectiveness Monitoring Program, and while it stands alone as an important contribution to the management of anadromous salmonids and their habitat, it also plays a key role within ISEMP. Each component of work within ISEMP is reported on individually, as is done so here, and in annual and triennial summary reports that present all of the overall project components in their programmatic context and shows how the data and tools developed can be applied to the development of regionally consistent, efficient and effective Research, Monitoring, and Evaluation.

  7. 2005年美国卷筒纸胶印市场调查(上)%American Web Offset 2005 Survey (1st)

    Institute of Scientific and Technical Information of China (English)

    鑫淼

    2005-01-01

    印刷行业由于经济发展而获利不少,不过,仍然还会遇到业务量基本不变的问题。由于目录册和直邮邮件需求的上升,一些卷筒纸印刷商已经尝到销售增长的甜头。但是,并不是所有印刷项目都能够分享这块蛋糕。那些内部效率并非最佳的印刷商正在为在高度竞争的市场分得一杯羹而努力挣扎。

  8. Bioinformatics for NGS-based metagenomics and the application to biogas research.

    Science.gov (United States)

    Jünemann, Sebastian; Kleinbölting, Nils; Jaenicke, Sebastian; Henke, Christian; Hassa, Julia; Nelkner, Johanna; Stolze, Yvonne; Albaum, Stefan P; Schlüter, Andreas; Goesmann, Alexander; Sczyrba, Alexander; Stoye, Jens

    2017-08-18

    Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  9. An Infrared Census of DUST in Nearby Galaxies with Spitzer (DUSTiNGS), I. Overview

    CERN Document Server

    Boyer, Martha L; Barmby, Pauline; Bonanos, Alceste Z; Gehrz, Robert D; Gordon, Karl D; Groenewegen, M A T; Lagadec, Eric; Lennon, Daniel; Marengo, Massimo; Meixner, Margaret; Skillman, Evan; Sloan, G C; Sonneborn, George; van Loon, Jacco Th; Zijlstra, Albert

    2014-01-01

    Nearby resolved dwarf galaxies provide excellent opportunities for studying the dust-producing late stages of stellar evolution over a wide range of metallicity (-2.7 75% complete at the tip of the Red Giant Branch for all targeted galaxies, with the exception of the crowded inner regions of IC 10, NGC 185, and NGC 147. This photometric depth ensures that the majority of the dust-producing stars, including the thermally-pulsing AGB stars, are detected in each galaxy. The images map each galaxy to at least twice the half-light radius to ensure that the entire evolved star population is included and to facilitate the statistical subtraction of background and foreground contamination, which is severe at these wavelengths. In this overview, we describe the survey, the data products, and preliminary results. We show evidence for the presence of dust-producing AGB stars in 8 of the targeted galaxies, with metallicities as low as [Fe/H] = -1.9, suggesting that dust production occurs even at low metallicity.

  10. Lectures given at the 1st Session of the Centro Internazionale Matematico Estivo (C.I.M.E.)

    CERN Document Server

    Jameson, Antony; Strang, Gilbert; Deuflhard, Peter; Lions, Jacques-Louis; Capasso, Vincenzo; Periaux, Jacques; Engl, Heinz

    2000-01-01

    These lecture notes by very authoritative scientists survey recent advances of mathematics driven by industrial application showing not only how mathematics is applied to industry but also how mathematics has drawn benefit from interaction with real-word problems. The famous David Report underlines that innovative high technology depends crucially for its development on innovation in mathematics. The speakers include three recent presidents of ECMI, one of ECCOMAS (in Europe) and the president of SIAM.

  11. Future perspectives in melanoma research : Meeting report from the "Melanoma Bridge". Napoli, December 1st-4th 2015.

    Science.gov (United States)

    Ascierto, Paolo A; Agarwala, Sanjiv; Botti, Gerardo; Cesano, Alessandra; Ciliberto, Gennaro; Davies, Michael A; Demaria, Sandra; Dummer, Reinhard; Eggermont, Alexander M; Ferrone, Soldano; Fu, Yang Xin; Gajewski, Thomas F; Garbe, Claus; Huber, Veronica; Khleif, Samir; Krauthammer, Michael; Lo, Roger S; Masucci, Giuseppe; Palmieri, Giuseppe; Postow, Michael; Puzanov, Igor; Silk, Ann; Spranger, Stefani; Stroncek, David F; Tarhini, Ahmad; Taube, Janis M; Testori, Alessandro; Wang, Ena; Wargo, Jennifer A; Yee, Cassian; Zarour, Hassane; Zitvogel, Laurence; Fox, Bernard A; Mozzillo, Nicola; Marincola, Francesco M; Thurin, Magdalena

    2016-11-15

    The sixth "Melanoma Bridge Meeting" took place in Naples, Italy, December 1st-4th, 2015. The four sessions at this meeting were focused on: (1) molecular and immune advances; (2) combination therapies; (3) news in immunotherapy; and 4) tumor microenvironment and biomarkers. Recent advances in tumor biology and immunology has led to the development of new targeted and immunotherapeutic agents that prolong progression-free survival (PFS) and overall survival (OS) of cancer patients. Immunotherapies in particular have emerged as highly successful approaches to treat patients with cancer including melanoma, non-small cell lung cancer (NSCLC), renal cell carcinoma (RCC), bladder cancer, and Hodgkin's disease. Specifically, many clinical successes have been using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and the programmed cell death-1 (PD-1) and its ligand PD-L1. Despite demonstrated successes, responses to immunotherapy interventions occur only in a minority of patients. Attempts are being made to improve responses to immunotherapy by developing biomarkers. Optimizing biomarkers for immunotherapy could help properly select patients for treatment and help to monitor response, progression and resistance that are critical challenges for the immuno-oncology (IO) field. Importantly, biomarkers could help to design rational combination therapies. In addition, biomarkers may help to define mechanism of action of different agents, dose selection and to sequence drug combinations. However, biomarkers and assays development to guide cancer immunotherapy is highly challenging for several reasons: (i) multiplicity of immunotherapy agents with different mechanisms of action including immunotherapies that target activating and inhibitory T cell receptors (e.g., CTLA-4, PD-1, etc.); adoptive T cell therapies that include tissue infiltrating lymphocytes (TILs), chimeric antigen receptors (CARs), and

  12. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST.

    Science.gov (United States)

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the "IMGT clonotype (AA)" (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for "IMGT clonotype (AA)" diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT(®) tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package "IMGTStatClonotype," with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT(®) for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V-D-J associations, in immunoprofiles from normal or pathological immune responses.

  13. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

    Science.gov (United States)

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses. PMID:27667992

  14. 南水北调西线一期工程中的长深引水隧洞%LONG AND DEEP DIVERSION TUNNELS OF 1ST STAGE PROJECT IN WEST ROUTE OF SOUTH-NORTH WATER TRANSFER PROJECT

    Institute of Scientific and Technical Information of China (English)

    沈凤生; 刘新

    2003-01-01

    West Route of South-North Water Transfer Project,situated in southeastern Qinghai-Tibet Plateau,is a giant project,which will deliver 17 billion m3 of water from the main stream and tributaries upstream of the Yangtze River to the upper reaches of the Yellow River. It is to be constructed in 3 stages, of which the 1st stage project includes delivering 4 billion m3 of water by gravity from two tributaries of Yalong River and three tributaries of Dadu River. The project consists of 5 dams,7 tunnels and a channel in series,with the dam height of 63~123 m and water transfer length of 260.3 km,of which the tunnels measure 244.1 km. The special climatic,environmental and geologic conditions make the project much more complicated in construction,especially 3 tunnels with the length longer than 50 km each create challenges to the technical requirements of engineering survey,design and construction.

  15. FGFR2 mutation in a patient without typical features of Pfeiffer syndrome--The emerging role of combined NGS and phenotype based strategies.

    Science.gov (United States)

    Flöttmann, Ricarda; Knaus, Alexej; Zemojtel, Tomasz; Robinson, Peter N; Mundlos, Stefan; Horn, Denise; Spielmann, Malte

    2015-08-01

    Pfeiffer syndrome (MIM: #101600) is a rare autosomal dominant disorder classically characterized by limb and craniofacial anomalies. It is caused by heterozygous mutations in the fibroblast growth factor receptors types 1 and 2 (FGFR1 and FGFR2). We applied a next generation sequencing (NGS) panel approach comprising all 2877 genes currently known to be causative for one or more Mendelian diseases combined with the phenotype based computational tool PhenIX (Phenotypic Interpretation of eXomes). We report on a patient presenting with multiple anomalies of hands and feet including brachydactyly and symphalangism. No clinical diagnosis could be established based on the clinical findings and testing of several genes associated with brachydactyly and symphalangism failed to identify mutations. Via next generation sequencing (NGS) panel approach we then identified a novel de novo missense FGFR2 mutation affecting an amino acid reported to be mutated in Pfeiffer syndrome. Since our patient shows typical radiological findings of Pfeiffer syndrome in hands and feet but at the same time lacks several characteristic features such as clinical signs of craniosynostosis and prominent eyes we suggest introducing the term "FGFR2 associated phenotypes" for similar cases. Our results highlight the emerging role of combined NGS and phenotype based bioinformatics strategies to establish clinical diagnoses.

  16. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    Science.gov (United States)

    Pasmant, Eric; Parfait, Béatrice; Luscan, Armelle; Goussard, Philippe; Briand-Suleau, Audrey; Laurendeau, Ingrid; Fouveaut, Corinne; Leroy, Chrystel; Montadert, Annelore; Wolkenstein, Pierre; Vidaud, Michel; Vidaud, Dominique

    2015-05-01

    Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of ∼150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with ∼90[euro ] for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours.

  17. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    Science.gov (United States)

    Pasmant, Eric; Parfait, Béatrice; Luscan, Armelle; Goussard, Philippe; Briand-Suleau, Audrey; Laurendeau, Ingrid; Fouveaut, Corinne; Leroy, Chrystel; Montadert, Annelore; Wolkenstein, Pierre; Vidaud, Michel; Vidaud, Dominique

    2015-01-01

    Molecular diagnosis of neurofibromatosis type 1 (NF1) is challenging owing to the large size of the tumour suppressor gene NF1, and the lack of mutation hotspots. A somatic alteration of the wild-type NF1 allele is observed in NF1-associated tumours. Genetic heterogeneity in NF1 was confirmed in patients with SPRED1 mutations. Here, we present a targeted next-generation sequencing (NGS) of NF1 and SPRED1 using a multiplex PCR approach (230 amplicons of ∼150 bp) on a PGM sequencer. The chip capacity allowed mixing 48 bar-coded samples in a 4-day workflow. We validated the NGS approach by retrospectively testing 30 NF1-mutated samples, and then prospectively analysed 279 patients in routine diagnosis. On average, 98.5% of all targeted bases were covered by at least 20X and 96% by at least 100X. An NF1 or SPRED1 alteration was found in 246/279 (88%) and 10/279 (4%) patients, respectively. Genotyping throughput was increased over 10 times, as compared with Sanger, with ∼90€ for consumables per sample. Interestingly, our targeted NGS approach also provided quantitative information based on sequencing depth allowing identification of multiexons deletion or duplication. We then addressed the NF1 somatic mutation detection sensitivity in mosaic NF1 patients and tumours. PMID:25074460

  18. On the Discovery of Eastern Hellenistic Initiatory Altar of the 3rd – 1st Centuries BC Depicting the Plot of Bull Sacrifice in the City of Stavropol

    Directory of Open Access Journals (Sweden)

    Prokopenko Yuriy A.

    2016-10-01

    Full Text Available The article is devoted to the semantic and chronological analysis of the images on the plate of white tuff discovered in the city of Stavropol. The central part of the relief is occupied with the image of table – an altar with hoisted bull head (in the background and the hanging part of bull skin (in the foreground. Between the protruding edges of the hanging skin and lower to the ground (between the legs of the altar an ancient Greek phrase carved in three lines. The composition is completed by flanking images of two figures in long robes depicted in profile, symmetrically turned to the head of the bull. The figure at the right is an image of a man with a long beard, the lower edge of which is bent forward (priest or king. The figure at the left is a female (queen. Both the man and the woman are holding ritual vessels in hands. The plot of bull sacrifice is typical for the cultural traditions of ancient Greece as well as for ancient eastern states. The fact of combining images and inscriptions peculiar of the Hellenistic culture and ancient Iranian mythology on the Stavropol altar should be associated with the religious policy pursued by the Pontic kings since the second half of the 3rd century BC till the Common Era. This policy was focused on the gradual replacement of local cults by Greek ones in the official pantheon. The reasons for the Asia Minor altar existence in the Stavropol Upland include: 1 the military expeditions of the Sarmatians to Asia Minor in 2nd – 1st centuries BC; 2 the establishment of political and economic ties by the North Caucasus population with the state of Seleucids in the 2nd century BC, with Parthia in the 2nd – 1st centuries BC, and especially with the kingdom of Pontus in the 1st century BC.

  19. High-level cross-resistance to didanosine observed in South African children failing an abacavir- or stavudine-based 1st-line regimen.

    Directory of Open Access Journals (Sweden)

    Kim Steegen

    Full Text Available BACKGROUND: The knowledge-base of emerging drug resistance profiles in children exposed to abacavir-based antiretroviral regimens in South Africa is very limited. This study investigated the suitability of didanosine-based 2nd-line regimens for children in the context of antiretroviral drug resistance patterns emerging after 1st-line virologic failure. METHODS: A retrospective dataset of 354 antiretroviral drug resistant genotypes from children failing either abacavir (n = 81 or stavudine (n = 273 based 1st-line regimens, was analysed. Samples were sent to the HIV genotyping laboratory at Charlotte Maxeke Johannesburg Academic Hospital, for routine testing. Pol sequences were submitted to the Stanford HIV drug resistance database for genotypic predictions. RESULTS: Children were exposed to abacavir or stavudine-based 1st-line regimens for an average of 21 and 36 months, respectively. The frequency of reduced susceptibility to didanosine was substantial in the abacavir-exposed group (69.1%.This reduced susceptibility was commonly attributed to L74V/I (n = 44 and to a lesser extent K65R (n = 10 mutations. Didanosine resistance was observed in 43.2% of patients exposed to stavudine-based regimens. In contrast, most children remained susceptible to stavudine regardless of exposure to abacavir (77.8% or stavudine (74.7%. At least 80% of children remained susceptible to zidovudine irrespective of stavudine or abacavir-exposure. The presence of the K65R mutation was more common after abacavir pressure (12.3% vs 1.8%. CONCLUSION: Analysis revealed that didanosine-based 2nd-line regimens have limitations for South African children, given the high frequency of mutations that confer cross-resistance to didanosine; especially after abacavir-exposure. This data has influenced South African paediatric treatment guidelines, which now recommend zidovudine-based 2nd-line regimens.

  20. Characterization of the 1st and 2nd EF-hands of NADPH oxidase 5 by fluorescence, isothermal titration calorimetry, and circular dichroism

    Directory of Open Access Journals (Sweden)

    Wei Chin-Chuan

    2012-04-01

    Full Text Available Abstract Background Superoxide generated by non-phagocytic NADPH oxidases (NOXs is of growing importance for physiology and pathobiology. The calcium binding domain (CaBD of NOX5 contains four EF-hands, each binding one calcium ion. To better understand the metal binding properties of the 1st and 2nd EF-hands, we characterized the N-terminal half of CaBD (NCaBD and its calcium-binding knockout mutants. Results The isothermal titration calorimetry measurement for NCaBD reveals that the calcium binding of two EF-hands are loosely associated with each other and can be treated as independent binding events. However, the Ca2+ binding studies on NCaBD(E31Q and NCaBD(E63Q showed their binding constants to be 6.5 × 105 and 5.0 × 102 M-1 with ΔHs of -14 and -4 kJ/mol, respectively, suggesting that intrinsic calcium binding for the 1st non-canonical EF-hand is largely enhanced by the binding of Ca2+ to the 2nd canonical EF-hand. The fluorescence quenching and CD spectra support a conformational change upon Ca2+ binding, which changes Trp residues toward a more non-polar and exposed environment and also increases its α-helix secondary structure content. All measurements exclude Mg2+-binding in NCaBD. Conclusions We demonstrated that the 1st non-canonical EF-hand of NOX5 has very weak Ca2+ binding affinity compared with the 2nd canonical EF-hand. Both EF-hands interact with each other in a cooperative manner to enhance their Ca2+ binding affinity. Our characterization reveals that the two EF-hands in the N-terminal NOX5 are Ca2+ specific. Graphical abstract

  1. Lectures given at the 1st Session of the Centro Internazionale Matematico Estivo (C.I.M.E.)

    CERN Document Server

    Picardello, Massimo; Zampieri, Giuseppe

    1998-01-01

    This book contains the notes of five short courses delivered at the "Centro Internazionale Matematico Estivo" session "Integral Geometry, Radon Transforms and Complex Analysis" held in Venice (Italy) in June 1996: three of them deal with various aspects of integral geometry, with a common emphasis on several kinds of Radon transforms, their properties and applications, the other two share a stress on CR manifolds and related problems. All lectures are accessible to a wide audience, and provide self-contained introductions and short surveys on the subjects, as well as detailed expositions of selected results.

  2. 1st Quarter Transportation Report FY2017: Waste Shipments To and From the Nevada National Security Site (NNSS), Radioactive Waste Management Complex

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, Louis [National Security Technologies, LLC. (NSTec), Las Vegas, NV (United States)

    2017-01-31

    This report satisfies the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) commitment to prepare a quarterly summary report of waste shipments to the Nevada National Security Site (NNSS) Radioactive Waste Management Complex (RWMC) at Area 5. This report summarizes the 1st quarter of fiscal year (FY) 2017 low-level radioactive waste (LLW), mixed low-level radioactive waste (MLLW) and classified non-radioactive (CNR) shipments. There were no shipments sent for offsite treatment from a NNSS facility and returned to the NNSS this quarter of FY2017.

  3. U.S. Army Chemical Corps Historical Studies, Gas Warfare in World War I: The 1st Division at Ansauville, January-April 1918

    Science.gov (United States)

    1958-01-01

    princip•al target of both enemy HE and gas fire at Ansauville was the 1st Division artillery, not the infantry. On both quiet and active fronts in the...of the gas fire was postponed on account of storm and rain. 434 JA. % *.. .. t .. t-. ,t. ,t.,,.4.:’... ,, ’. . w’. * ." .7 . , , , q I Io thought...against the enemy with gas fire . Butler’s journal indicates much more frequent use of gas, and this is confirmed by the artillery brigade summary which

  4. 1st October 2010 - Chinese Vice President of the Academy of Sciences signing the guest book and exchanging gifts with CERN Director for Research and Scientific Computing S. Bertolucci, witnessed by Adviser R. Voss

    CERN Multimedia

    Maximilien Brice

    2010-01-01

    1st October 2010 - Chinese Vice President of the Academy of Sciences signing the guest book and exchanging gifts with CERN Director for Research and Scientific Computing S. Bertolucci, witnessed by Adviser R. Voss

  5. Chinese Commission of Science Technology and Industry for National Defense Senior Vice Minister CHEN Qiufa exchanging gifts at luncheon and signing the Guest Book on 1st November 2007 with CERN Director-General R. Aymar.

    CERN Multimedia

    Maximilien Brice

    2007-01-01

    Chinese Commission of Science Technology and Industry for National Defense Senior Vice Minister CHEN Qiufa exchanging gifts at luncheon and signing the Guest Book on 1st November 2007 with CERN Director-General R. Aymar.

  6. CHANNEL EVOLUTION AFTER THE CONSTRUCTION OF THE 1ST PHASE OF THE DEEPWATER CHANNEL PROJECT OF THE YANGTZE ESTUARY

    Institute of Scientific and Technical Information of China (English)

    Hualin WU; Huanting SHEN; Yonghong WANG

    2006-01-01

    In order to deepen the navigation channel, the Chinese government authorized the construction of the Yangtze Estuary Deepwater Channel Project in 1997. The project is divided into three phases,increasing the navigation channel depth to 8.5, 10.0, and 12.5 m stage by stage. The evolution of the North Passage after the construction of the first phase of the deepwater channel project is analyzed,based on surveyed topographic data. Then, the paper summarizes the comprehensive effect of the first phase of the project. Regarding hydrologic data monitored during the constructing process, the effects of the training dikes and groins on the riverbed erosion of the North Passage is studied.Finally, the evolution mechanism is analyzed and summarized. The evolution mechanism found can be helpful for regulation of other braided rivers or estuaries.

  7. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

    Science.gov (United States)

    Bastías, Adriana; Correa, Francisco; Rojas, Pamela; Almada, Rubén; Muñoz, Carlos; Sagredo, Boris

    2016-01-01

    Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species. PMID:27459734

  8. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz Using Next-Generation Sequencing (NGS.

    Directory of Open Access Journals (Sweden)

    Adriana Bastías

    Full Text Available Maqui (Aristotelia chilensis [Molina] Stunz is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%, followed by tetranucleotide (26% and trinucleotide motifs (24%. The motif AG/CT (28.4% was the most abundant, while the motif AC (89 bp was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.

  9. Final Report for the 1st Surveillance Test of the Reactor Pressure Vessel Material (CAPSULE 2) of Ulchin Nuclear Power Plant Unit 3

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Kee Ok; Kim, Byoung Chul; Lee, Sam Lai (and others)

    2006-12-15

    Surveillance testing for reactor vessel materials is performed in order to evaluate the irradiation embrittlement due to neutrons during operation and set the condition of safe operation of nuclear reactor. The 1st surveillance testing was performed completely by Korea Atomic Energy Research Institute at Taejon after the capsule was transported from Ulchin site including its removal from reactor. Fast neutron fluences for capsules were calculated and various testing including mechanical and chemistry analysis were performed in order to evaluate the integrity of Ulchin unit 3 reactor vessel during the operation until life time. The evaluation results are as follows; Fast neutron fluences for capsule 2 is 4.674E 18n/cm{sup 2}. The bias factor, the ratio of calculation/measurement, was 0.920 for the 1st testing and the calculational uncertainty,7.0% satisfied the requirement of USNRC Reg.Guide 1.190, 20%. The best estimated neutron fluence for reactor vessel inside surface was 3.913E 18n/cm{sup 2} based on the end of 6th fuel cycle and it was predicted that the fluences of vessel inside surface at 16 and 32EFPY would reach 9.249E 18 and 1.834E 19n/cm{sup 2} based on the current calculation. The result through this analysis for Ulchin unit 3 showed that there would be no problem for the pressurized thermal shock(PTS) during the operation until design life.

  10. Final Report for the 1st Surveillance Test of the Reactor Pressure Vessel Material (Capsule 2) of Ulchin Nuclear Power Plant Unit 4

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Kee Ok; Kim, Byoung Chul; Lee, Sam Lai (and others)

    2007-04-15

    Surveillance testing for reactor vessel materials is performed in order to evaluate the irradiation embrittlement due to neutrons during operation and set the condition of safe operation of nuclear reactor. The 1st surveillance testing was performed completely by Korea Atomic Energy Research Institute at Daejon after the capsule was transported from Ulchin site including its removal from reactor. Fast neutron fluences for capsules were calculated and various testing including mechanical and chemistry analysis were performed in order to evaluate the integrity of Ulchin Unit 4 reactor vessel during the operation until life time. The evaluation results are as follows; Fast neutron fluences for capsule 2 is 4.306E+18n/cm{sup 2}. The bias factor, the ratio of calculation/measurement, was 0.918 for the 1st testing and the calculational uncertainty,7.0% satisfied the requirement of USNRC Reg.Guide 1.190, 20%. The best estimated neutron fluence for reactor vessel inside surface was 3.615E+18n/cm{sup 2} based on the end of 6th fuel cycle and it was predicted that the fluences of vessel inside surface at 16 and 32EFPY would reach 8.478E+18 and 1.673E+19n/cm{sup 2} based on the current calculation. The result through this analysis for Ulchin Unit 4 showed that there would be no problem for the pressurized thermal shock(PTS) during the operation until design life.

  11. Despina Hatzifotiadou: ALICE Master Class 2 - Demonstration of the software for the 1st part of the exercise - visual identification of V0s

    CERN Document Server

    CERN. Geneva

    2016-01-01

    This is the 2nd of 4 short online videos. It contains a demonstration of the software used for the 1st part of the exercise, related to the theory explained in Master Class 1 - visual identification of V0s. More details and related links on this indico event page. In more detail: What is Physics Master Classes Students after morning lectures, run programmes in the afternoon to do measurements. These tutorials are about how to use the software required to do these measurements. Background info and examples  Looking for strange particles with ALICE http://aliceinfo.cern.ch/Public/MasterCL/MasterClassWebpage.html Introduction to first part of the exercise : what are strange particles, V0 decays, invariant mass. Demonstration of the software for the 1st part of the exercise - visual identification of V0s Introduction to second part of the exercise : strangeness enhancement; centrality of lead-lead collisions; explanation of efficiency, yield, background etc Demonstration of the software for the ...

  12. Army Malaria Institute – its Evolution and Achievements – Third Decade (1st half: 1985-1990

    Directory of Open Access Journals (Sweden)

    Karl H Rieckmann

    2012-11-01

    Full Text Available The first half of the third decade (1985-1990 after the establishment of the Malaria Research Unit was characterised by a substantial increase in laboratory and field activities. Various new procedures were developed to discover and counter the increasing problem of parasite resistance to established antimalarial drug regimens. After early findings that the currently-used pyrimethamine/dapsone (Maloprim® prophylaxis was no longer effective against Plasmodium falciparum malaria, in vitro, ex vivo and pharmacological investigations were undertaken with proguanil and a low dose of dapsone. This led to a field study in Papua New Guinea (PNG which indicated that such a drug combination might be more effective than Maloprim®. Before the effectiveness of this combination could be determined further, it became obvious that Maloprim®/chloroquine had become inadequate for the protection of ADF soldiers on exercises in PNG. During one of these exercises, the landmark discovery that P. vivax had developed resistance to chloroquine was the first documented evidence that this previously successful standard medication had lost its efficacy against vivax malaria. These findings in 1988/1989 led to the evaluation of mefloquine and doxycycline as alternative prophylactic regimens for ADF personnel serving in malarious areas. In efforts to identify and assess other potential antimalarial drugs, in vitro studies were continued with various strains of P. falciparum. These studies were supplemented by investigations with P. falciparum and P. vivax in non-human primates and by malaria transmission studies with Anopheles farauti mosquitoes. The survey of anopheline mosquitoes in northern Australia indicated the widespread presence of three isomorphic species of An. farauti and the ever-present possibility of re-introducing malaria into northern Australia. Investigations relating to the biological control of mosquitoes were gradually phased out and emphasis was given

  13. VizieR Online Data Catalog: Planet candidates discovered using K2's 1st yr (Crossfield+, 2016)

    Science.gov (United States)

    Crossfield, I. J. M.; Ciardi, D. R.; Petigura, E. A.; Sinukoff, E.; Schlieder, J. E.; Howard, A. W.; Beichman, C. A.; Isaacson, H.; Dressing, C. D.; Christiansen, J. L.; Fulton, B. J.; Lepine, S.; Weiss, L.; Hirsch, L.; Livingston, J.; Baranec, C.; Law, N. M.; Riddle, R.; Ziegler, C.; Howell, S. B.; Horch, E.; Everett, M.; Teske, J.; Martinez, A. O.; Obermeier, C.; Benneke, B.; Scott, N.; Deacon, N.; Aller, K. M.; Hansen, B. M. S.; Mancini, L.; Ciceri, S.; Brahm, R.; Jordan, A.; Knutson, H. A.; Henning, T.; Bonnefoy, M.; Liu, M. C.; Crepp, J. R.; Lothringer, J.; Hinz, P.; Bailey, V.; Skemer, A.; Defrere, D.

    2016-10-01

    We select our FGK stellar sample from the all-sky Transiting Exoplanet Survey Satellite (TESS) Dwarf Catalog (TDC; Stassun et al. 2014, arXiv:1410.6379). We extract time-series photometry from the target pixel files provided by the K2 project using circular, stationary, soft-edged apertures. See section 2 for further explanations. We obtained high-resolution optical spectra of 83 planet candidate hosts using the HIRES echelle spectrometer on the 10m Keck I telescope (R=55000). We obtained spectra of 27 candidate host stars using the Levy high-resolution optical spectrograph mounted at the Automated Planet Finder (APF; R~80000 or 100000). We obtained spectra of a small number of candidate stellar hosts using the FEROS fiber-fed echelle spectrograph at the 2.2m MPG telescope (R~48000). See section 3.1 for further details. We obtained high-resolution imaging (HRI) for 164 of our candidate systems. Our primary instrument for this work was NIRC2 at the 10m Keck II telescope, with which we observed 110 systems. As part of multi-semester program GN-2015B-LP-5 (PI Crossfield) at Gemini Observatory, we observed 40 systems with the NIRI camera in the K-band. We also observed 33 stars with PHARO/PALM-3000 at the 5m Hale Telescope and 14 systems with LMIRCam at LBT, all at the K-band. We observed 39 stars at visible wavelengths using the automated Robo-AO laser adaptive optics system at the Palomar 1.5m telescope. Through our Long-Term Gemini program we also acquired high-resolution speckle imaging of 32 systems in narrowband filters centered at 692 and 880nm using the DSSI camera at the Gemini North telescope. See section 3.3 for further explanations. (7 data files).

  14. Effect of milk feed source, frequency of feeding and age at turnout on calf performance, live-weight at mating and 1st lactation milk production.

    Science.gov (United States)

    Gleeson, David; O'Brien, Bernadette

    2012-10-18

    Female calves (n = 108) were assigned to 6 cold milk feeding treatments in two experiments for a 70-day period. Live-weight (LW) was measured weekly, with an additional LW taken at day 410 and post-calving for animals in experiment 1. In Experiment 1, the effect of feeding frequency and age of turnout to pasture on calf performance and 1st lactation milk yields were evaluated. The whole milk (WM) feeding treatments applied were (i) once daily feeding (OD), (ii) twice daily feeding (TD), (iii) OD feeding, outdoors at 38 days (ODO). In Experiment 2, the effects of feeding milk replacer (MR) as opposed to WM and age of turnout to pasture on calf performance were evaluated. The treatments applied were (i) OD feeding with WM (OD), (ii) OD feeding with milk replacer (MR) (ODMR), (iii) OD feeding with MR, outdoors at 38 days (ODMRO). Experiment 1: There were no differences (P > 0.05) in LW or average daily gain between TD and OD calves at day 80 or 410. ODO calves had lower LW at day 80 as compared to OD or TD (P Calf LW at day 80 was 86, 89 and 85 kg and at day 410 was 304, 309 and 316 kg for OD, TD and ODO, respectively. Milk feeding frequency or time of calf turnout had no effect on LW post calving, milk composition or 1st lactation milk yields. Experiment 2: Total LW at day 80 was higher (P Calf LW was 87, 95, and 88 kg for OD, ODMR and ODMRO, respectively. However, LW at day 410 did not differ between treatments.This study showed that while some differences were observed in calf LW at day 80, these differences had no effect on LW at day 410 or 1st lactation milk yield. It can be concluded that calves can be successfully reared when fed OD with WM or MR, indoors and when turned out to pasture at 38 days of age.

  15. Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil. by NGS and de novo transcriptome assembly.

    Directory of Open Access Journals (Sweden)

    Humberto J Debat

    Full Text Available Yerba mate (Ilex paraguariensis A. St.-Hil. is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge

  16. NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial.

    Science.gov (United States)

    Endris, Volker; Stenzinger, Albrecht; Pfarr, Nicole; Penzel, Roland; Möbs, Markus; Lenze, Dido; Darb-Esfahani, Silvia; Hummel, Michael; Sabine-Merkelbach-Bruse; Jung, Andreas; Lehmann, Ulrich; Kreipe, Hans; Kirchner, Thomas; Büttner, Reinhard; Jochum, Wolfram; Höfler, Gerald; Dietel, Manfred; Weichert, Wilko; Schirmacher, Peter

    2016-06-01

    With the approval of olaparib as monotherapy treatment in platinum-sensitive, relapsed high-grade serous ovarian cancer by the European Medical Agency (EMA), comprehensive genotyping of BRCA1 and BRCA2 in tumor tissue has become a mandatory pre-therapeutic test. This requires significant advances in routine tumor test methodologies due to the large size of both genes and the lack of mutational hot spots. Classical focused screening approaches, like Sanger sequencing, do not allow for a sensitive, rapid, and economic analysis of tumor tissue. Next-generation sequencing (NGS) approaches employing targeted panels for BRCA1/2 to interrogate formalin-fixed and paraffin-embedded tumor samples from either surgical resection or biopsy specimens can overcome these limitations. Although focused NGS methods have been implemented by few centers in routine molecular diagnostics for the analysis of some druggable oncogenic mutations, the reliable diagnostic testing of the entire coding regions of BRCA1 and BRCA2 was a new challenge requiring extensive technological improvement and quality management. Here, we describe the implementation and results of the first round robin trial for BRCA1/2 mutation testing in tumor tissue that was conducted in central Europe on May 2015, shortly after the approval and prior to the official release of olaparib. The high success rate of 81 % (21/26 test centers) demonstrates that BRCA1/2 multicenter mutation testing is well feasible in FFPE tumor tissue, extending to other tumor entities beyond ovarian cancer. The high number of test centers passing the trial demonstrates the success of the concerted efforts by German, Swiss, and Austrian pathology centers to ensure quality-controlled NGS-based testing and proves the potential of this technology in routine molecular pathology. On the basis of our results, we provide recommendations for predictive testing of tumor tissue for BRCA1/2 to clinical decision making in ovarian cancer patients.

  17. 1(st) EMBL/DFG Women in Science Network Conference Heidelberg 2016: From Genes, Cells and the Immune System towards Therapies - Meeting Report.

    Science.gov (United States)

    Stripecke, Renata; Gouttefangeas, Cécile; Förster, Irmgard

    2016-11-01

    The 1(st) EMBL/DFG Women in Science (WiS) Conference "From Genes, Cells and the Immune System towards Therapies" was held on 19(th) - 20(th) September 2016 in Heidelberg, Germany. The WiS conference was funded by nine Collaborative Research Centers (CRCs) of the German Research Council (Deutsche Forschungsgemeinschaft, DFG; Table 1) and benefited from an outstanding hosting environment at the Advanced Training Center of the European Molecular Biology Laboratory (EMBL). Scientific talks focused at genetic, cellular and immunologic mechanisms, and immune therapy, and progress from all stages of development covering basic research to clinical developments was described. The presentations were embedded between structured networking sessions and a round table discussion with representatives of the DFG, EMBL, European Molecular Biology Organisation (EMBO), and the German Society of Immunology (DGfI). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Understanding Stress-Related Behavioral Phenotypes: Report from the 1st International Neuroscience Summer School and the 11th International “Stress and Behavior” Conference

    Directory of Open Access Journals (Sweden)

    J. L. LaPorte

    2008-01-01

    Full Text Available The 1st International Neuroscience Summer School and the 11th International Multidisciplinary Neuroscience and Biopsychiatry Conference on Stress and Behavior were held in St. Petersburg, Russia, during May 9–20, 2008. The summer school gathered 30 talented young scientists from 15 countries worldwide, and was dedicated to different topics of behavioral neuroscience. Many interactive courses were provided on neuropharmacology, animal phenotyping, and biopsychology. The conference's excellent scientific and social program attracted almost 500 delegates from 40 countries from many areas of stress research. The eclectic interaction between medical doctors, basic scientists, psychologists, and students made for a productive and collaborative environment, which contributed greatly to the success of the school and conference.

  19. Comparative analysis of effectiveness of treatment with anti-TB drugs of the 1st and 2nd lines for children and adolescents with multidrug resistant tuberculosis

    Directory of Open Access Journals (Sweden)

    Tleukhan Abildaev

    2012-05-01

    Full Text Available The paper shows results of study on comparative treatment effectiveness in children and adolescents with from multi drug resistant tuberculosis MDR TB (2000-2008 treated with anti-TB drugs of the 2nd line (80 patients and 1st line (80 patients in the Kazakhstan. It was stated in patients with MDR TB that outcomes of treatment were successful in 91.2%, but relapse development of TB disease occurred in 12.7% of cases, and 5 (6.2% patients died (P ≤0.05. Thus, patients with MDR TB need to be treated with anti-TB drugs of the 2nd line accordingly to their DST.

  20. 1st European Congress of Medical Physics September 1-4, 2016; Medical Physics innovation and vision within Europe and beyond.

    Science.gov (United States)

    Tsapaki, Virginia; Kagadis, George C; Brambilla, Marco; Ciocca, Mario; Clark, Catharine H; Delis, Harry; Mettivier, Giovanni

    2017-09-01

    Medical Physics is the scientific healthcare profession concerned with the application of the concepts and methods of physics in medicine. The European Federation of Organisations for Medical Physics (EFOMP) acts as the umbrella organization for European Medical Physics societies. Due to the rapid advancements in related scientific fields, medical physicists must have continuous education through workshops, training courses, conferences, and congresses during their professional life. The latest developments related to this increasingly significant medical speciality were presented during the 1st European Congress of Medical Physics 2016, held in Athens, September 1-4, 2016, organized by EFOMP, hosted by the Hellenic Association of Medical Physicists (HAMP), and summarized in the current volume. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  1. [State of the reproductive systemin in male rats of 1st generation obtained from irradiated parents and exposed to electromagnetic radiation (897 MHz) during embryogenesis and postnatal development].

    Science.gov (United States)

    Vereshchako, G G; Chueshova, N V; Gorokh, G A; Naumov, A D

    2014-01-01

    The consequences of prolonged exposure to electromagnetic radiation from cellular phone (897 MHz, daily 8 h/day) in male rats of the 1st generation obtained from irradiated parents and subjected to prolonged exposure to electromagnetic radiation of the range of mobile communications during ontogeny and postnatal development were studied. It has been found that irradiation causes a decrease in the number of births of animals, changing the sex ratio towards the increase in the number of males. It had a significant impact on the reproductive system of males, accelerating their sexual development, revealed at the age of two months. Radiation from cell phones led to significant disproportions in the cell number at different stages of spermatogenesis. It increased the number of mature spermatozoa which decreased viability.

  2. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Epidemiology”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Epidemiology”ABS 1. A PERFORMANCE INDICATOR FOR THE PROLONGATION OF GESTATIONAL AGE • N. LackABS 2. LATE PRETERM NEONATES AND CAUSES OF ADMISSION TO THE NICU • S. Arayici, G. Kadioglu Simsek, B. Say, E. Alyamac Dizdar, N. Uras, F.E. Canpolat, S.S. OguzABS 3. INCIDENCE AND OUTCOMES OF METABOLIC DISORDERS IN VERY PRETERM INFANTS • O. Dobush, D. Dobryanskyy, Z. Salabay, O. Detsyk, O. Novikova, Y. KuzminovABS 4. MATERNAL FACTORS INFLUENCE INFANT’S VITAMIN D STATUS • H. Hauta-alus, E. Holmlund-Suila, M. Enlund-Cerullo, J. Rosendahl, S. Valkama, O. Helve, H-M. Surcel, O. Mäkitie, S. Andersson, H. ViljakainenABS 5. THE HIGH PREVALENCE OF VITAMIN D DEFICIENCY IN A LARGE NUMBER OF PREGNANT WOMEN AND RELATED FACTORS IN ANKARA, TURKEY • G. Kadioglu Simsek, F. E. Canpolat, S. Arayici, G. Kanmaz Kutman, H.I. Yakut, Ö. Moraloğlu, B. ÖzkanABS 6. SNAPPE-II: A VALUABLE PREDICTOR OF ADVERSE OUTCOMES IN PREMATURITY • P. Costa-Reis, R. Monteiro, M. Abrantes, P. Costa, A. Graça, C. MonizABS 7. THE ASSOCIATION BETWEEN MATERNAL AND FETAL 25OHD AND INFANT SIZE AND ADIPOSITY AT BIRTH, 6 MONTHS AND 2 YEARS OF AGE • M

  3. Effect of milk feed source, frequency of feeding and age at turnout on calf performance, live-weight at mating and 1st lactation milk production

    Directory of Open Access Journals (Sweden)

    Gleeson David

    2012-10-01

    Full Text Available Abstract Female calves (n = 108 were assigned to 6 cold milk feeding treatments in two experiments for a 70-day period. Live-weight (LW was measured weekly, with an additional LW taken at day 410 and post-calving for animals in experiment 1. In Experiment 1, the effect of feeding frequency and age of turnout to pasture on calf performance and 1st lactation milk yields were evaluated. The whole milk (WM feeding treatments applied were (i once daily feeding (OD, (ii twice daily feeding (TD, (iii OD feeding, outdoors at 38 days (ODO. In Experiment 2, the effects of feeding milk replacer (MR as opposed to WM and age of turnout to pasture on calf performance were evaluated. The treatments applied were (i OD feeding with WM (OD, (ii OD feeding with milk replacer (MR (ODMR, (iii OD feeding with MR, outdoors at 38 days (ODMRO. Experiment 1: There were no differences (P > 0.05 in LW or average daily gain between TD and OD calves at day 80 or 410. ODO calves had lower LW at day 80 as compared to OD or TD (P  This study showed that while some differences were observed in calf LW at day 80, these differences had no effect on LW at day 410 or 1st lactation milk yield. It can be concluded that calves can be successfully reared when fed OD with WM or MR, indoors and when turned out to pasture at 38 days of age.

  4. Effect of maternal dietary counselling during the 1st year of life on glucose profile and insulin resistance at the age of 8 years: a randomised field trial.

    Science.gov (United States)

    Costa, Cintia S; Campagnolo, Paula D B; Lumey, L H; Vitolo, Marcia R

    2017-01-01

    Education interventions that stimulate complementary feeding practices can improve the nutritional status of children and may protect against future chronic diseases. We assessed the long-term effectiveness of dietary intervention during the 1st year of life on insulin resistance levels, and investigated the relationship between insulin resistance and weight changes over time. A randomised field trial was conducted among 500 mothers who gave birth to full-term infants between October 2001 and June 2002 in a low-income area in São Leopoldo, Brazil. Mother-child pairs were randomly assigned to intervention (n 200) and control groups (n 300), and the mothers in the intervention group received dietary counselling on breast-feeding and complementary feeding of their children during the 1st year of life. Fieldworkers blinded to assignment assessed socio-demographic, dietary and anthropometric data during follow-up at ages 1, 4 and 8 years. Blood tests were performed in 305 children aged 8 years to measure fasting serum glucose and insulin concentrations and the homoeostasis model assessment index of insulin resistance (HOMA-IR). At the age of 8 years, the intervention group showed no changes in glucose and insulin concentrations or HOMA-IR values (change 0·07; 95 % CI -0·06, 0·21 for girls; and change -0·07; 95 % CI -0·19, 0·04 for boys) compared with study controls. Insulin resistance was highly correlated, however, with increases in BMI between birth and 8 years of age. Although this dietary intervention had no impact on glucose profile at age 8 years, our findings suggest that BMI changes in early childhood can serve as an effective marker of insulin resistance.

  5. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies.

    Science.gov (United States)

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-03-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes.

  6. Impact of NGS in the medical sciences: genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    Directory of Open Access Journals (Sweden)

    Pablo Lapunzina

    2014-01-01

    Full Text Available The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH, SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes.

  7. Next-generation sequencing (NGS) as a fast molecular diagnosis tool for left ventricular noncompaction in an infant with compound mutations in the MYBPC3 gene.

    Science.gov (United States)

    Schaefer, Elise; Helms, Pauline; Marcellin, Luc; Desprez, Philippe; Billaud, Philippe; Chanavat, Valérie; Rousson, Robert; Millat, Gilles

    2014-03-01

    Left ventricular noncompaction (LVNC) is a clinically heterogeneous disorder characterized by a trabecular meshwork and deep intertrabecular myocardial recesses that communicate with the left ventricular cavity. LVNC is classified as a rare genetic cardiomyopathy. Molecular diagnosis is a challenge for the medical community as the condition shares morphologic features of hypertrophic and dilated cardiomyopathies. Several genetic causes of LVNC have been reported, with variable modes of inheritance, including autosomal dominant and X-linked inheritance, but relatively few responsible genes have been identified. In this report, we describe a case of a severe form of LVNC leading to death at 6 months of life. NGS sequencing using a custom design for hypertrophic cardiomyopathy panel allowed us to identify compound heterozygosity in the MYBPC3 gene (p.Lys505del, p.Pro955fs) in 3 days, confirming NGS sequencing as a fast molecular diagnosis tool. Other studies have reported neonatal presentation of cardiomyopathies associated with compound heterozygous or homozygous MYBPC3 mutations. In this family and in families in which parental truncating MYBPC3 mutations are identified, preimplantation or prenatal genetic screening should be considered as these genotypes leads to neonatal mortality and morbidity.

  8. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    Science.gov (United States)

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-01-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes. PMID:24764758

  9. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    Directory of Open Access Journals (Sweden)

    Alexandre G. de Brevern

    2015-01-01

    Full Text Available Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  10. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.

    Science.gov (United States)

    de Brevern, Alexandre G; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  11. [Identification of key markers of normal and pathogenic microbiota determining health of periodontium by NGS-sequencing 16S-rDNA libraries of periodontal swabs].

    Science.gov (United States)

    Zorina, O A; Petrukhina, N B; Basova, A A; Shibaeva, A V; Trubnikova, E V; Shevelev, A B

    2014-01-01

    By using NGS-sequencing libraries of DNA from periodontal swabs with primers specific to V6 region of 16S rDNA prevalence of bacterial genera and species in periodontal microbiota of patients with aggressive periodontitis and healthy donors was analyzed. Six genera of putative periodontal protectors and eight periodontal pathogens were identified with respect to aggressive (but not chronic) periodontitis. Statistically relevant over-colonization by general Porphyromonas, Treponema, Synergistes, Tannerella, Filifactor, Ruminococcus, Parvimonas and Mycoplasma was found to be associated with the condition. From these, only three genera Porphyromonas, Treponema and Tannerella are traditionally considered as periodontal pathogens. Statistically confidential over-colonization by genus Veillonella was found in healthy patients. This genus should be considered as a relevant marker of a healthy periodontium. Genera Streptococcus, Bergeyella, Granulicatella, Kingella and Corynebacterium may be considered as putative periodontal protectors. Comparison of data of NGS-sequencing and real-time PCR demonstrated a good agreement if different PCR efficiency using independent primer pairs is taken into account.

  12. 2014 Post-Hurricane Sandy SC to NY NOAA NGS Lidar-Derived Dune Crest, Toe and Shoreline

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Storm-Induced Coastal Change Hazards component of the National Assessment of Coastal Change Hazards project focuses on understanding the magnitude and...

  13. 1st Iberian Robotics Conference

    CERN Document Server

    Sanfeliu, Alberto; Ferre, Manuel; ROBOT2013; Advances in robotics

    2014-01-01

    This book contains the proceedings of the ROBOT 2013: FIRST IBERIAN ROBOTICS CONFERENCE and it can be said that included both state of the art and more practical presentations dealing with implementation problems, support technologies and future applications. A growing interest in Assistive Robotics, Agricultural Robotics, Field Robotics, Grasping and Dexterous Manipulation, Humanoid Robots, Intelligent Systems and Robotics, Marine Robotics, has been demonstrated by the very relevant number of contributions. Moreover, ROBOT2013 incorporates a special session on Legal and Ethical Aspects in Robotics that is becoming a topic of key relevance. This Conference was held in Madrid (28-29 November 2013), organised by the Sociedad Española para la Investigación y Desarrollo en Robótica (SEIDROB) and by the Centre for Automation and Robotics - CAR (Universidad Politécnica de Madrid (UPM) and Consejo Superior de Investigaciones Científicas (CSIC)), along with the co-operation of Grupo Temático de Robótica CEA-GT...

  14. 1st National Mechanics Congress

    CERN Document Server

    Nieuwstadt, F

    1990-01-01

    The Department of Applied Mechanics of the Royal Institution of Engineers in the Netherlands (Koninklijk Instituut van Ingenieurs) organised on April 2-4, 1990 the first National Applied Mechanics Congress about the theme: "Integration of Theory and Applications in Applied Mechanics" The idea behind this initiative was to bring together the Applied Mechanics communities in The Netherlands and Belgium and to create an environment in which new developments in the field could be discussed and in which connections to other disciplines could be established. Among an extensive list of possible subjects the following were selected as congress topics: - non-linear material behaviour, - chaos, - mechatronics, - liquid-solid interactions, - mathematics and applied mechanics, - integration of Applied Mechanics and other disciplines. Applied Mechanics comprises both solid mechanics and fluid mechanics. These can be subdivided further into: rheology, plasticity, theory of plates and shells, theory of elasticity, multibody...

  15. Molecular cloning, functional characterization and expression of potato (Solanum tuberosum) 1-deoxy-d-xylulose 5-phosphate synthase 1 (StDXS1) in response to Phytophthora infestans.

    Science.gov (United States)

    Henriquez, Maria Antonia; Soliman, Atta; Li, Genyi; Hannoufa, Abdelali; Ayele, Belay T; Daayf, Fouad

    2016-02-01

    1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the initial step of the plastidial 2C-methyl-D-erythritol-4-phosphate (DOXP-MEP) pathway involved in isoprenoid biosynthesis. In this study, we cloned the complete cDNA of potato DXS gene that was designated StDXS1. StDXS1 cDNA encodes for 719 amino acid residues, with MW of 77.8 kDa, and is present in one copy in the potato genome. Phylogenetic analysis and protein sequence alignments assigned StDXS1 to a group with DXS homologues from closely related species and exhibited homodomain identity with known DXS proteins from other plant species. Late blight symptoms occurred in parallel with a reduction in StDXS1 transcript levels, which may be associated with the levels of isoprenoids that contribute to plant protection against pathogens. Subcellular localization indicated that StDXS1 targets the chloroplasts where isoprenoids are synthesized. Arabidopsis expressing StDXS1 showed a higher accumulation of carotenoids and chlorophyll as compared to wild type controls. Lower levels of ABA and GA were detected in the transgenic DXS lines as compared to control plants, which reflected on higher germination rates of the transgenic DXS lines. No changes were detected in JA or SA contents. Selected downstream genes in the DOXP-MEP pathway, especially GGPPS genes, were up-regulated in the transgenic lines.

  16. “ASSESSMENT OF DIFFERENT TEACHING AIDS AND TEACHING METHODS FOR THE BETTER PERCEPTION OF BIOCHEMISTRY B Y 1 ST MBBS STUDENTS”

    Directory of Open Access Journals (Sweden)

    Priyadarshini

    2012-12-01

    Full Text Available ABSTRACT: BACKGROUND: Medical students during their first year of MBBS c ourse, find Biochemistry difficult and volatile. In this regard , we studied the feedback from students about the effectiveness of prevailing teaching aids and me thods, so that best teaching aid and method can be adopted to improve their academic performance. METHODS: This study comprises of total 117 students of 1st MBBS course, who have com pleted the 2nd semester of academic year 2011-12. Irrespective of the teacher and topic, the s tudents were asked to grade the teaching aids and methods that were used to teach Biochemist ry for the period of 10 months (from August 2011 to May 2012. RESULTS: In our study high Satisfaction Index (SI was noti ced for combination method of teaching aid (blackboard+ Pow erPoint*(PPT and teaching preceded and followed by asking questions + assessment + tut orials, teaching method. CONCLUSION: This observation may probably be due to the fact tha t, inherent deficiency of each teaching aid is compensated by the other. With regard to teaching me thod, the combination of teaching methods is more effective when compared to didactic lectures.

  17. Extrapolating the Trends of Test Drop Data with Opening Shock Factor Calculations: the Case of the Orion Main and Drogue Parachutes Inflating to 1st Reefed Stage

    Science.gov (United States)

    Potvin, Jean; Ray, Eric

    2017-01-01

    We describe a new calculation of the opening shock factor C (sub k) characterizing the inflation performance of NASA's Orion spacecraft main and drogue parachutes opening under a reefing constraint (1st stage reefing), as currently tested in the Capsule Parachute Assembly System (CPAS) program. This calculation is based on an application of the Momentum-Impulse Theorem at low mass ratio (R (sub m) is less than 10 (sup -1)) and on an earlier analysis of the opening performance of drogues decelerating point masses and inflating along horizontal trajectories. Herein we extend the reach of the Theorem to include the effects of payload drag and gravitational impulse during near-vertical motion - both important pre-requisites for CPAS parachute analysis. The result is a family of C (sub k) versus R (sub m) curves which can be used for extrapolating beyond the drop-tested envelope. The paper proves this claim in the case of the CPAS Mains and Drogues opening while trailing either a Parachute Compartment Drop Test Vehicle or a Parachute Test Vehicle (an Orion capsule boiler plate). It is seen that in all cases the values of the opening shock factor can be extrapolated over a range in mass ratio that is at least twice that of the test drop data.

  18. Excerpts from the 1st international NTNU symposium on current and future clinical biomarkers of cancer: innovation and implementation, June 16th and 17th 2016, Trondheim, Norway.

    Science.gov (United States)

    Robles, Ana I; Olsen, Karina Standahl; Tsui, Dana W T; Georgoulias, Vassilis; Creaney, Jenette; Dobra, Katalin; Vyberg, Mogens; Minato, Nagahiro; Anders, Robert A; Børresen-Dale, Anne-Lise; Zhou, Jianwei; Sætrom, Pål; Nielsen, Boye Schnack; Kirschner, Michaela B; Krokan, Hans E; Papadimitrakopoulou, Vassiliki; Tsamardinos, Ioannis; Røe, Oluf D

    2016-10-19

    The goal of biomarker research is to identify clinically valid markers. Despite decades of research there has been disappointingly few molecules or techniques that are in use today. The "1st International NTNU Symposium on Current and Future Clinical Biomarkers of Cancer: Innovation and Implementation", was held June 16th and 17th 2016, at the Knowledge Center of the St. Olavs Hospital in Trondheim, Norway, under the auspices of the Norwegian University of Science and Technology (NTNU) and the HUNT biobank and research center. The Symposium attracted approximately 100 attendees and invited speakers from 12 countries and 4 continents. In this Symposium original research and overviews on diagnostic, predictive and prognostic cancer biomarkers in serum, plasma, urine, pleural fluid and tumor, circulating tumor cells and bioinformatics as well as how to implement biomarkers in clinical trials were presented. Senior researchers and young investigators presented, reviewed and vividly discussed important new developments in the field of clinical biomarkers of cancer, with the goal of accelerating biomarker research and implementation. The excerpts of this symposium aim to give a cutting-edge overview and insight on some highly important aspects of clinical cancer biomarkers to-date to connect molecular innovation with clinical implementation to eventually improve patient care.

  19. Wages in the food chain in South Sudan: WageIndicator survey 2013

    NARCIS (Netherlands)

    Besamusca, J.; Tijdens, K.

    2013-01-01

    This WageIndicator Data Report presents the results of the face-to-face WageIndicator survey in South Sudan, conducted between the 1st of June and the 19th of July 2013 in the southern and eastern regions of South Sudan. In total 1,329 persons were interviewed; 71% were men, 29% women and 37% were u

  20. Wages in the food chain in Mozambique: WageIndicator survey 2013

    NARCIS (Netherlands)

    Tijdens, K.; Besamusca, J.

    2013-01-01

    This WageIndicator Data Report presents the results of the face-to-face WageIndicator survey of the labour force, conducted between the 27th of May and the 1st of June 2013 in all provinces of Mozambique. In total 1,679 persons were interviewed; 53% were men, 47% women and 43% were under 30 years

  1. Wages in the food chain in Mozambique: WageIndicator survey 2013

    NARCIS (Netherlands)

    Tijdens, K.; Besamusca, J.

    2013-01-01

    This WageIndicator Data Report presents the results of the face-to-face WageIndicator survey of the labour force, conducted between the 27th of May and the 1st of June 2013 in all provinces of Mozambique. In total 1,679 persons were interviewed; 53% were men, 47% women and 43% were under 30 years ol

  2. Wages in the food chain in Mozambique: WageIndicator survey 2013

    NARCIS (Netherlands)

    Tijdens, K.; Besamusca, J.

    2013-01-01

    This WageIndicator Data Report presents the results of the face-to-face WageIndicator survey of the labour force, conducted between the 27th of May and the 1st of June 2013 in all provinces of Mozambique. In total 1,679 persons were interviewed; 53% were men, 47% women and 43% were under 30 years ol

  3. Wages in the food chain in South Sudan: WageIndicator survey 2013

    NARCIS (Netherlands)

    Besamusca, J.; Tijdens, K.

    2013-01-01

    This WageIndicator Data Report presents the results of the face-to-face WageIndicator survey in South Sudan, conducted between the 1st of June and the 19th of July 2013 in the southern and eastern regions of South Sudan. In total 1,329 persons were interviewed; 71% were men, 29% women and 37% were u

  4. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS).

    Science.gov (United States)

    Barbosa, Amanda D; Gofton, Alexander W; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%), T. gilletti (25%, 95% CI: 18.7-32.3%), T. copemani (27.4%, 95% CI: 20.8-34.8%) and T. vegrandis (10.1%, 95% CI: 6.0-15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21-35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the

  5. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Other”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Other”ABS 1. TELEMEDICINE IN NEONATAL HOMECARE • K.G. Holm, A. Brodsgaard, G. Zachariassen, J. ClemensenABS 2. ACCEPTABILITY OF PARENT REPORT QUESTIONNAIRES FOR ROUTINE FOLLOW-UP IN LATE/MODERATELY PRETERM INFANTS • N. Armstrong, S. Johnson, E.M. BoyleABS 3. INTERNATIONAL CARE PRACTICES AROUND AN INFANT’S DEATH IN THE NICU; A SURVEY STUDY • C.M.C. van den Berg, K. Alferink, J.M. Latour, N. Valkenburg, M. van DijkABS 4. ANXIETY AND DEPRESSION OVER TIME, IN MOTHERS OF VERY PRETERM BORN CHILDREN • M. Jeukens-Visser, M. Husson, D. Meijssen, M. Flierman, P. van Schie, K. Koldewijn, A. Wassenaer-van LeemhuisABS 5. LONGITUDINAL CHANGE OF HEALTH-RELATED QUALITY OF LIFE EXPERIENCED OVER TIME BY MOTHER WITH LATE PRETERM INFANT • L.Y. Tsai, S.C. Mu, Y.L. Chen, Y.L. Guo, P.C. ChenABS 6. RELATIONSHIP BETWEEN ANXIETY LEVELS AND CLINICAL PRACTICE SKILLS AMONG STUDENTS OF PEDIATRIC NURSING LECTURE • A.S. Kurt, F.T. Arslan, S. Özkan, R. Çelen, D.A. ÇakırABS 7. ACCURACY OF SMARTPHONES FOR REVIEWING TRANSMITTED IMAGES OF NEONATAL X-RAYS • T. Vasko, M. Westberg, J.A. Dawson, L.S. Owen, M. Thio, R. Bhatia, S. Donath

  6. Competition to design a new logo for the CERN Staff Association : an award ceremony was held on Friday 1st March in the Main building in the presence of the six laureates.

    CERN Document Server

    Jacques Hervé Fichet

    2013-01-01

    The six laureates received a price offered as follows: 1st prize: an Ezee Suisse electric bike. - 2nd prize (equal second) : a voucher for Go Sport with a value of 200 €. - 4th to 6th prize: a voucher for Go Sport with a value of 50 €

  7. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

    Science.gov (United States)

    Massart, Sebastien; Candresse, Thierry; Gil, José; Lacomme, Christophe; Predajna, Lukas; Ravnikar, Maja; Reynard, Jean-Sébastien; Rumbou, Artemis; Saldarelli, Pasquale; Škorić, Dijana; Vainio, Eeva J.; Valkonen, Jari P. T.; Vanderschuren, Hervé; Varveri, Christina; Wetzel, Thierry

    2017-01-01

    Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios. PMID:28174561

  8. Diagnosis for choroideremia in a large Chinese pedigree by next-generation sequencing (NGS) and non-invasive prenatal testing (NIPT)

    Science.gov (United States)

    Zhu, Li; Cheng, Jingliang; Zhou, Boxu; Wei, Chunli; Yang, Weichan; Jiang, Dong; Ijaz, Iqra; Tan, Xiaojun; Chen, Rui; Fu, Junjiang

    2017-01-01

    To develop an effective strategy to isolate and use cell-free fetal DNA (cffDNA) for the combined use of next-generation sequencing (NGS) for diagnosing choroideremia and non-invasive prenatal testing (NIPT) for Y chromosome determination, a large Chinese family with an X-linked recessive disease, choroideremia, was recruited. Cell-free DNA was extracted from maternal plasma, and SRY polymerase chain reaction amplification was performed using NIPT. Sanger sequencing was subsequently used for fetal amniotic fluid DNA verification. A nonsense mutation (c.C799T:p.R267X) of the CHM gene on the X chromosome of the proband (IV:7) and another 5 males with choroideremia were detected, while 3 female carriers with no symptoms were also identified. The fetus (VI:7) was identified as female from the cffDNA, and the same heterozygous nonsense mutation present in her mother was also confirmed. At one and a half years of age, the female baby did not present with any associated symptoms of choroideremia. Therefore, cffDNA was successfully used for the combined use of NGS for diagnosing choroideremia in a large Chinese pedigree, and NIPT for Y chromosome determination. This approach should result in a markedly increased use of prenatal diagnosis and improvement, and more sophisticated clinical management of diseases in China and other developing countries. The establishment of a highly accurate method for prenatal gene diagnosis will allow for more reliable gene diagnosis, improved genetic counseling, and personalized clinical management of our patients. PMID:28098911

  9. Termo do 1º Consenso em Disfunção Temporomandibular e Dor Orofacial Statement of the 1st Consensus on Temporomandibular Disorders and Orofacial Pain

    Directory of Open Access Journals (Sweden)

    Simone Vieira Carrara

    2010-06-01

    Full Text Available O Termo do 1º Consenso em Disfunção Temporomandibular e Dor Orofacial* foi criado com o propósito de substituir divergências por evidência científica dentro dessa especialidade da Odontologia. O documento oferece informações claras e fundamentadas para orientar o cirurgião-dentista e demais profissionais de saúde sobre os cuidados demandados pelo paciente, tanto no processo de diagnóstico diferencial quanto na fase de aplicação das terapias de controle da dor e disfunção. O Termo foi aprovado no mês de janeiro de 2010 em reunião realizada durante o Congresso Internacional de Odontologia do Estado de São Paulo e converge o pensamento dos profissionais mais conceituados do Brasil na especialidade Disfunção Temporomandibular e Dor Orofacial.This Statement of the 1st Consensus on Temporomandibular Disorders and Orofacial Pain was created with the purpose of substituting controversies for scientific evidence within this specialty field of dentistry. The document provides clear and well-grounded guidance to dentists and other health professionals about the care required by patients both in the process of differential diagnosis and during the stage when they undergo treatment to control pain and dysfunction. The Statement was approved in January 2010 at a meeting held during the International Dental Congress of São Paulo and draws together the views of Brazil's most respected professionals in the specialty of Temporomandibular Disorders and Orofacial Pain.

  10. [Indications, diagnoses and quality markers in upper and lower endoscopies in 2010 and 2011 at the 1st Department of Medicine, Semmelweis University, Budapest].

    Science.gov (United States)

    Gönczi, Lóránt; Kürti, Zsuzsanna; Golovics, Petra; Végh, Zsuzsanna; Lovász, Barbara; Dorkó, Andrea; Seres, Anna; Sümegi, Liza; Menyhárt, Orsolya; Kiss, Lajos; Papp, János; Gecse, Krisztina; Lakatos, Péter László

    2016-12-01

    The aim was to assess the incidence of endoscopic findings based on the indication of the procedures in upper/lower endoscopies, and measuring quality indicators of colonoscopies at the 1st Department of Medicine, Semmelweis University, Budapest. Data of 2987 patients (male/female:1361/1626, mean age: 60.7 years(y), SD: 16.7y) between 01.01.2010 and 31.12.2011 were analyzed. Both inpatient and outpatient records were collected. Incidence of peptic ulcer disease, esophageal varices, gastric polyps and gastric cancer were 10.8%, 4.5%, 6.1%, 2.9% in upper endoscopies, respectively. In colonoscopies colorectal polyps, diverticulosis, colorectal cancer and IBD were found in 29.9%, 22.4%, 6.9%, 9.7%, respectively. In patients having upper endoscopy with GI bleeding indication, older age (p<0.001), male gender (p<0.001, OR: 1.64), acenocoumarol/heparin use (p<0,001, peptic ulcers and esophageal varices were more frequent (p<0.001, OR: 2.83 and p<0.001, OR: 2.79), while in colonoscopies colorectal cancer had higher incidence (p<0.001, OR:3.27). 81% of colonoscopies were complete. Causes of incomplete procedures were ineffective bowel preparation (38.2%), technical difficulties (25.1%) and strictures (20.5%). The endoscopic findings and quality indicators (adenoma detection rate, coecal intubation rate) were in line with that reported in published series. Orv. Hetil., 2016, 157(52), 2074-2081.

  11. The 1999 activities and the 1st seminar on human resources development in the nuclear field as part of Asian regional cooperation (contract research)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-12-01

    In August, 1999, the Project for Human Resources Development (HRD) was initiated as defined in the framework of the Forum for Nuclear Cooperation in Asia, organized by the Atomic Energy Commission based on a resolution of the 10th International Conference for Nuclear Cooperation in Asia, held in March, 1999. The resolution was adopted as a recognition that 'human resources development' was an important area that should be added to the existing fields of cooperation. The Project was organized by the Atomic Energy Bureau of the Science and Technology Agency (STA) and is administrated by the Nuclear Technology and Education Center (NuTEC) of the Japan Atomic Energy Research Institute. The objective of the HRD Project is to solidify the foundation of technologies for nuclear development and utilization in Asia by promoting human resources development in Asian countries. In the Project there are two kind of activities: in-workshop activities and outside-of-workshop activities, as the time of the workshops themselves is too short to achieve the objectives. As In-workshop activities, 1st Seminar on Human Resources Development in the Nuclear Field was held on November 25 and 26, 1999, at the Tokyo International Forum. Participating countries were China, Indonesia, South Korea, Japan, Malaysia, the Philippines, Thailand, and Vietnam, with Australia submitting a study report only. This report consists of presentation papers at the Seminar as in-workshop activities, and a letter of proposal from the project leader of Japan to the project leaders of participating countries after the Seminar and a presentation paper on Human Resources Development at the First Coordinators Meeting on March 7 and 8, 2000 as outside-of-workshop activities. The 10 of the presented papers are indexed individually. (J.P.N.)

  12. Experimental and numerical validation of the effective medium theory for the B-term band broadening in 1st and 2nd generation monolithic silica columns.

    Science.gov (United States)

    Deridder, Sander; Vanmessen, Alison; Nakanishi, Kazuki; Desmet, Gert; Cabooter, Deirdre

    2014-07-18

    Effective medium theory (EMT) expressions for the B-term band broadening in monolithic silica columns are presented at the whole-column as well as at the mesoporous skeleton level. Given the bi-continuous nature of the monolithic medium, regular as well as inverse formulations of the EMT-expressions have been established. The established expressions were validated by applying them to a set of experimental effective diffusion (Deff)-data obtained via peak parking on a number of 1st and 2nd generation monolithic silica columns, as well as to a set of numerical diffusion simulations in a simplified monolithic column representation (tetrahedral skeleton model) with different external porosities and internal diffusion coefficients. The numerically simulated diffusion data can be very closely represented over a very broad range of zone retention factors (up to k″=80) using the established EMT-expressions, especially when using the inverse variant. The expressions also allow representing the experimentally measured effective diffusion data very closely. The measured Deff/Dmol-values were found to decrease significantly with increasing retention factor, in general going from about Deff/Dmol=0.55 to 0.65 at low k″ (k″≅1.5-3.8) to Deff/Dmol=0.25 at very high k″ (k″≅40-80). These values are significantly larger than observed in fully-porous and core-shell particles. The intra-skeleton diffusion coefficient (Dpz) was typically found to be of the order of Dpz/Dmol=0.4, compared to Dpz/Dmol=0.2-0.35 observed in most particle-based columns. These higher Dpz/Dmol values are the cause of the higher Deff/Dmol values observed. In addition, it also appears that the higher internal diffusion is linked to the higher porosity of the mesoporous skeleton that has a relatively open structure with relatively wide pores. The observed (weak) relation between Dpz/Dmol and the zone retention factor appears to be in good agreement with that predicted when applying the regular

  13. Mathematics at matriculation level as an indicator of success or failure in the 1st year of the Veterinary Nursing Diploma at the Faculty of Veterinary Science, University of Pretoria.

    Science.gov (United States)

    Botha, A E; McCrindle, C M E; Owen, J H

    2003-12-01

    Mathematics at matriculation level (Grade 12) is one of the subjects required for admission to the Veterinary Nursing Diploma in the Faculty at Veterinary Science of the University of Pretoria. The present study shows that there is no statistically significant relationship between the grade of mathematics at matriculation level and the success or failure in the 1st year of study. There is, however, a statistical difference in the adjusted mark obtained for mathematics at matriculation level between the groups that passed and failed the 1st year of the veterinary nursing course. The results of this research are not consistent with other research which showed that secondary school mathematics results are not a significant factor in tertiary education. It is recommended that selection criteria for veterinary nurses should in future still include mathematics, but that cognisance should be taken of the mark obtained and students with higher marks (above 57%) given preference.

  14. Mathematics at matriculation level as an indicator of success or failure in the 1st year of the Veterinary Nursing Diploma at the Faculty of Veterinary Science, University of Pretoria

    Directory of Open Access Journals (Sweden)

    A.E. Botha

    2003-07-01

    Full Text Available Mathematics at matriculation level (Grade 12 is one of the subjects required for admission to the Veterinary Nursing Diploma in the Faculty at Veterinary Science of the University of Pretoria. The present study shows that there is no statistically significant relationship between the grade of mathematics at matriculation level and the success or failure in the 1st year of study. There is, however, a statistical difference in the adjusted mark obtained for mathematics at matriculation level between the groups that passed and failed the 1st year of the veterinary nursing course. The results of this research are not consistent with other research which showed that secondary school mathematics results are not a significant factor in tertiary education. It is recommended that selection criteria for veterinary nurses should in future still include mathematics, but that cognisance should be taken of the mark obtained and students with higher marks (above 57 % given preference.

  15. Mathematics at matriculation level as an indicator of success or failure in the 1st year of the Veterinary Nursing Diploma at the Faculty of Veterinary Science, University of Pretoria

    OpenAIRE

    Botha, A. E.; C.M.E. McCrindle; J. H. Owen

    2003-01-01

    Mathematics at matriculation level (Grade 12) is one of the subjects required for admission to the Veterinary Nursing Diploma in the Faculty at Veterinary Science of the University of Pretoria. The present study shows that there is no statistically significant relationship between the grade of mathematics at matriculation level and the success or failure in the 1st year of study. There is, however, a statistical difference in the adjusted mark obtained for mathematics at matriculation level b...

  16. Fourier analysis of multi-tracer cosmological surveys

    CERN Document Server

    Abramo, L Raul; Loureiro, Arthur

    2015-01-01

    We present optimal quadratic estimators for the Fourier analysis of cosmological surveys that detect several different types of tracers of large-scale structure. Our estimators can be used to simultaneously fit the matter power spectrum and the biases of the tracers - as well as redshift-space distortions (RSDs), non-Gaussianities (NGs), or any other effects that are manifested through differences between the clusterings of distinct species of tracers. Our estimators reduce to the one by Feldman, Kaiser & Peacock (ApJ 1994, FKP) in the case of a survey consisting of a single species of tracer. We show that the multi-tracer estimators are unbiased, and that their covariance is given by the inverse of the multi-tracer Fisher matrix (Abramo, MNRAS 2013; Abramo & Leonard, MNRAS 2013). When the biases, RSDs and NGs are fixed to their fiducial values, and one is only interested in measuring the underlying power spectrum, our estimators are projected into the estimator found by Percival, Verde & Peacock ...

  17. Preliminary findings of China's detailed fertility survey (the first phase).

    Science.gov (United States)

    1986-10-01

    This article summarizes findings of a fertility sampling survey conducted in April 1985 in the Hebei and Shaanxi provinces and Shanghai, China. Altogether, 13,307 married women of reproductive age were interviewed. The results of the nuptiality section, which surveyed 19,956 women aged 15-49 show that 1) a high marriage rate, a low divorce rate, and a stable marriage relationship exist; 2) during the past 30 years, the number of early marriages has declined remarkably and the median age at marriage has risen; 3) in the past 30 years, the peak age at 1st marriage has risen rapidly for women in Shanghai and Hebei while it has risen relatively slowly for women in Shaanxi; 4) in the past 10 years, the mean age at 1st marriage has increased more than 1 year for Shanghai women, has fluctuated for Shaanxi women, and has decreased for Hebei women; and 5) the total 1st marriage rates were high in the early 1980s, but declined slightly in 1984. Factors which influence nuptiality include 1) education on late marriage, and 2) elimination of arranged marriage. The results of the fertility and infant mortality section show that 1) the number of children ever born has been decreasing year by year, 2) a low proportion of primarily infertile women exists, 3) the parity progressive ratio declined rapidly in Shanghai, but more slowly in Hebei and Shaanxi; 4) infant mortality has declined considerably in the last 25 years, because of improvements in medical and health services; 5) age at 1st birth is increasing; and 6) the magnitude of the rise in median age at 1st birth is smaller than the median age at 1st marriage. During the last 10 years, 1) fertility has declined in both Shaanxi and Hebei; 2) the mean age at childbirth has decreased somewhat; 3) the 1-child policy has won wide response; and 4) among infants born 1980-1983, the mortality rate is 19.3 per 1000 in Shanghai and over 34 per 1000 in both Hebei and Shaanxi. The results of the contraception section show that 1

  18. Preliminary results of the Geoid Slope Validation Survey 2014 in Iowa

    Science.gov (United States)

    Wang, Y. M.; Becker, C.; Breidenbach, S.; Geoghegan, C.; Martin, D.; Winester, D.; Hanson, T.; Mader, G. L.; Eckl, M. C.

    2014-12-01

    The National Geodetic Survey conducted a second Geoid Slope Validation Survey in the summer of 2014 (GSVS14). The survey took place in Iowa along U.S Route 30. The survey line is approximately 200 miles long (325 km), extending from Denison, IA to Cedar Rapids, IA. There are over 200 official survey bench marks. A leveling survey was performed, conforming to 1st order, class II specifications. A GPS survey was performed using 24 to 48 hour occupations. Absolute gravity, relative gravity, and gravity gradient measurements were also collected during the survey. In addition, deflections of the vertical were acquired at 200 eccentric survey benchmarks using the Compact Digital Astrometric Camera (CODIAC) camera. This paper presents the preliminary results of the survey, including the accuracy analysis of the leveling data, GPS ellipsoidal heights, and the deflections of the vertical which serves as an independent data set in addition to the GPS/leveling implied geoid heights.

  19. Implication of anthropometric profile and alimentary consumption on risk for diseases among school children in the 1st to 4th grades

    Directory of Open Access Journals (Sweden)

    Vanessa Monteiro

    2010-09-01

    Full Text Available This study aimed to determine the anthropometric profile and diet of 652 school children from the 1st to 4th grades of elementary education in six private schools in the city of Maringá, Paraná, Brazil. Children's weight and height were classified according to the Body Mass Index proposed by Must et al. (1991. Food consumption was evaluated by means of a questionnaire about daily food frequency. Statistical analysis was carried out using linear and logistic regression tests, with a significance level of 5%. High rates of overweight and obesity, 21.9% and 13.3% respectively, were observed, which did not show a significant relationship with total food consumption. The data obtained were: high consumption of foods rich in energy, such as sugar- and fat-rich foods, and insufficient consumption of low-energy foods that are sources of micronutrients, such as vegetables. It is necessary to enhance the promotion of good alimentary and health habits within schools to lower risk factors for developing diseases, as well as to develop and validate a questionnaire to reliably assess the diet of the infant population.Este trabalho objetivou determinar o perfil antropométrico e o consumo alimentar entre escolares de 1ª a 4ª séries do ensino fundamental de escolas privadas de Maringá - PR. A amostra de estudo foi de 652 alunos. Verificou-se o peso e a estatura e classificados de acordo com o Índice de Massa Corporal proposto por Must et al. (1991. O consumo alimentar foi avaliado por meio de um questionário de freqüência alimentar diária. A análise estatística foi realizada pelos testes de associação e regressão logística linear, com nível de significância de 5%. Verificaram-se índices altos de sobrepeso e obesidade, 21,9% e 13,3%, respectivamente, os quais não mostraram relação significativa com o consumo alimentar. Os dados obtidos foram: alto consumo de alimentos ricos em energia, como aqueles ricos em açúcares e gorduras, e um

  20. The truncated Newton using 1st and 2nd order adjoint-state method: a new approach for traveltime tomography without rays

    Science.gov (United States)

    Bretaudeau, F.; Metivier, L.; Brossier, R.; Virieux, J.

    2013-12-01

    named as the truncated Newton (TCN) (Métivier et al. 2012) with a more accurate estimation of the impact of the Hessian. We propose an efficient implementation for first-arrival traveltime tomography. In TCN, the model update Δm is obtained through the iterative resolution of the Newton linear system H Δm = - g. Based on a matrix-free conjugate gradient resolution, the iterative solver requires only the computation of the gradient and of Hessian-vector products. We propose a generalization of the computation of the gradient using the adjoint-state method that allows to consider receivers located anywhere. Then the Hessian-vector products are computed using an original formulation based on a 2nd-order adjoint-state method, at the cost of an additional forward modeling. The TCN algorithm is composed of two nested loops: an internal loop to compute Δm, and an external loop where a line search is performed to update the subsurface parameters. TCN thus considers locally the inversion of the traveltime data using an estimation of the full Hessian (both 1st and 2nd order terms) at an acceptable cost. Tomography with TCN is an improvement over the simple gradient-based adjoint-state tomography due to its good convergence property, to the better consideration of illumination, and is a promising tool for multi-parameter inversion as rescaling is given by the Hessian.

  1. Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS).

    Science.gov (United States)

    Tang, Yi; Lin, Lin; Sebastian, Aswathy; Lu, Huaguang

    2016-04-19

    Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1-100% and 51.4-100% aa identity between the two variant strains, and 54.3-89.4% and 49.5-98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens.

  2. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    Science.gov (United States)

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-06-07

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

  3. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  4. Direct assessment of anchovy by the PELGAS05 acoustic survey

    OpenAIRE

    Masse, Jacques; Beillois, Pierre; Duhamel, Erwan

    2005-01-01

    An acoustic survey was carried out in the bay of Biscay from May 3rd to June 1st on board the French research vessel Thalassa. The objective of PELGAS05 survey was to study the abundance and distribution of pelagic fish in the Bay of Biscay. The target species were mainly anchovy and sardine and were considered in a multi-specific context. The results have to be used during ICES working groups in charge of the assessment of sardine, anchovy, mackerel and horse mackerel and in the frame of t...

  5. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Pharmacology”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Pharmacology”ABS 1. BABY SKIN CARE PRODUCTS • P. Doro, R. Abraham, D. Agoston, J. Balog, R.Z. CsomaABS 2. MATHEMATICAL MODELING TO PREDICT IN-HOSPITAL NATURAL WEIGHT CHANGES IN TERM NEONATES • S. Kasser, M. Wilbaux, C. De Angelis, H. Rickenbacher, N. Klarer, J.N. Van Den Anker, M. Pfister, S. WellmannABS 3. IMPROVING PARENTERAL NUTRITION IN THE NEONATE – A PRACTICAL GUIDELINE • H. Reigstad, D. Moster, I. Grønlie, A. BlystadABS 4. INVOLUTION OF RETINOPATHY OF PREMATURITY AND NEURODEVELOPMENTAL OUTCOME AFTER BEVACIZUMAB TREATMENT • Y.-S. Chang, P.-N. Tsao, C.-Y. Chen, H.-C. Chou, W.-S. Hsieh, P.-T. YehABS 5. RELATIONSHIP BETWEEN ADVERSE DRUG REACTIONS AND OFF-LABEL/UNLICENSED DRUG USE IN HOSPITALISED CHILDREN. EREMI STUDY • K.A. Nguyen, Y. Mimouni, A. Lajoinie, N. Paret, S. Malik, L. El-Amrani, L. Milliat-Guittard, C. Carcel, A. Portefaix, A.M. Schott, T. Vial, B. KassaiABS 6. A SYSTEMATIC REVIEW OF OFF-LABEL AND UNLICENSED DRUGS USE AND ADVERSE DRUG REACTIONS IN HOSPITALIZED CHILDREN • N. David, K.A. Nguyen, Y. Mimouni, A. Lajoinie, S. Malik, B. KassaiABS 7. EFFICACY AND SAFETY OF PROPOFOL SEDATION

  6. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Brain & Development”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Brain & Development”ABS 1. SEPARATE EFFECTS OF LOW PATERNAL AND MATERNAL EDUCATIONAL LEVEL ON RISK OF DEVELOPMENTAL DELAY IN 4-YEAR-OLD BOYS AND GIRLS • S. de Jong, M.R. Potijk, A.E. den Heijer, S.A. Reijneveld, A.F. Bos, J.M. KerstjensABS 2. THE ASSOCIATION BETWEEN PATERNAL EDUCATIONAL LEVEL AND DEVELOPMENTAL DELAY IN PRETERM AND TERM-BORN CHILDREN AT AGE 4 • S. de Jong, J.M. Kerstjens, A.E. den Heijer, A.F. Bos, S.A. Reijneveld, M.R. PotijkABS 3. NEUROPROTECTION BY NEURONAL OVEREXPRESSION OF THE SMALL GTPase-Ras IN HYPEROXIA-INDUCED NEONATAL BRAIN INJURY • M. Serdar, K. Kempe, J. Herz, R. Herrmann, B.S. Reinboth, R. Heumann, A. Ehrkamp, U. Felderhoff-Mueser, I. BendixABS 4. REFERENCE RANGES FOR CEREBRAL TISSUE OXYGEN INDEX (cTOI IN NEONATES DURING IMMEDIATE NEONATAL TRANSITION AFTER BIRTH • N. Baik, B. Urlesberger, B. Schwaberger, G. Schmölzer, A. Avian, L. Mileder, G. PichlerABS 4. REFERENCE RANGES FOR CEREBRAL TISSUE OXYGEN INDEX (cTOI IN NEONATES DURING IMMEDIATE NEONATAL TRANSITION AFTER BIRTH • N. Baik, B. Urlesberger, B. Schwaberger, G. Schmölzer, A. Avian, L. Mileder, G. PichlerABS 6. N

  7. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs.

    Science.gov (United States)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter; Børsting, Claus; Morling, Niels

    2016-03-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase (http://www.cstl.nist.gov/strbase/). The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a

  8. A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.

    Science.gov (United States)

    Pérez-Porro, A R; Navarro-Gómez, D; Uriz, M J; Giribet, G

    2013-05-01

    Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

  9. Integration of historical, archaeoseismic and paleoseismological data for the reconstruction of the early seismic history in Messina Strait (south Italy: the 1st and 4th centuries AD earthquakes

    Directory of Open Access Journals (Sweden)

    Maria Serafina Barbano

    2014-03-01

    Full Text Available Historical accounts, archaeoseismic and paleoseismological evidence allowed us to reappraise two earthquakes affecting northeastern Sicily and southern Calabria in the 1st (probably between 14 and 37 and 4th (likely between 361 and 363 centuries AD, to obtain a better reconstruction of their effects and to reconsider their sources.The 1st century event damaged the area from Oppido (Calabria to Tindari (Sicily, roughly that of the February 6, 1783 Calabria earthquake. The similitude of these earthquakes is further stressed by the fact that they generated tsunamis, as recorded by historical data and by the tsunami deposits found at Capo Peloro, the oldest dated 0-125 AD, the youngest linked to the 1783 event. These earthquakes could be related to the same Calabria seismic source: the Scilla fault. Northeastern Sicily and southern Calabria were also damaged by one or more earthquakes in the 4th century AD and several towns were rebuilt/restored at that time. The hit area roughly coincides with that of the Messina 1908 earthquake suggesting similar seismic sources for the events. However, because close in time, historical descriptions of the 4th century Sicilian earthquake were mixed with those of the 365 Crete earthquake that generated a basin-wide tsunami most likely reaching also the Sicilian coasts. Reevaluating location, size, damage area and tsunamigenic potential of these two earthquakes of the 1st and 4th centuries AD is relevant for reassessing the seismogenic and tsunamigenic potential of the faults around the Messina Strait and the seismic hazard of the affected areas.

  10. Metastatic non-small-cell lung cancer: consensus on pathology and molecular tests, first-line, second-line, and third-line therapy: 1st ESMO Consensus Conference in Lung Cancer; Lugano 2010

    DEFF Research Database (Denmark)

    Felip, E; Gridelli, C; Baas, P;

    2011-01-01

    the conference, the expert panel prepared clinically relevant questions concerning five areas: early and locally advanced non-small-cell lung cancer (NSCLC), first-line metastatic NSCLC, second-/third-line NSCLC, NSCLC pathology and molecular testing, and small-cell lung cancer to be addressed through discussion......The 1st ESMO Consensus Conference on lung cancer was held in Lugano, Switzerland on 21 and 22 May 2010 with the participation of a multidisciplinary panel of leading professionals in pathology and molecular diagnostics, medical oncology, surgical oncology and radiation oncology. Before...

  11. Proceedings of the 1st Ibero-Latin American and Caribbean Congress on Medical Physics. Mexico 98; Memorias. 1er Congreso Iberolatinoamericano y del Caribe de Fisica Medica. Mexico 98

    Energy Technology Data Exchange (ETDEWEB)

    Gaona, E. [ed.] [Universidad Autonoma Metropolitana, Mexico D.F. (Mexico); Huitron, B.G. [ed.] [Universidad Autonoma del Estado de Mexico, Toluca (Mexico)

    1998-12-31

    This book composes the works received for the 1st Ibero-Latin American and the Caribbean Congress on Medical Physics. There are 68 works which represent a sample of the recent advances of the medical physics which are indicators about the level of development of the speciality in these regions of the world. Thus, the Congress represents the greatest event of medical physics of Ibero-Latin America and the Caribbean besides its consolidation and regional organization. The book also contains useful counsels for the education, yours researches and the daily hospitable practice. (Author)

  12. Investigation of environmental radioactivity in waste dumping areas of the far eastern seas. JAERI`s activities in the 1st Japanese-Korean-Russian joint expedition 1994

    Energy Technology Data Exchange (ETDEWEB)

    Amano, Hikaru; Matsunaga, Takeshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Yabuuchi, Noriaki

    1996-10-01

    Large quantities of radioactive waste have been dumped in the Far Eastern Sea by the former USSR and Russia. In order to survey marine radioactive contamination in the Far Eastern Sea, the first Japanese-Korean-Russian joint expedition was conducted according to the governmental agreement. The joint expedition was conducted at the areas of the Russian radioactive waste dumping site from March 18 1994 to April 6, 1994. JAERI participated in this expedition according to the request from STA Japan, and conducted mainly on-board measurement of marine radioactivities. The results showed that the radionuclides concentrations in seawater and seabed sediment samples from the study site were not different from those in the western North Pacific. This report summarises JAERI`s activities in the expedition. Final report by Japanese-Korean-Russian government and IAEA is annexed. (author)

  13. Astronomical data analysis software and systems I; Proceedings of the 1st Annual Conference, Tucson, AZ, Nov. 6-8, 1991

    Science.gov (United States)

    Worrall, Diana M. (Editor); Biemesderfer, Chris (Editor); Barnes, Jeannette (Editor)

    1992-01-01

    Consideration is given to a definition of a distribution format for X-ray data, the Einstein on-line system, the NASA/IPAC extragalactic database, COBE astronomical databases, Cosmic Background Explorer astronomical databases, the ADAM software environment, the Groningen Image Processing System, search for a common data model for astronomical data analysis systems, deconvolution for real and synthetic apertures, pitfalls in image reconstruction, a direct method for spectral and image restoration, and a discription of a Poisson imagery super resolution algorithm. Also discussed are multivariate statistics on HI and IRAS images, a faint object classification using neural networks, a matched filter for improving SNR of radio maps, automated aperture photometry of CCD images, interactive graphics interpreter, the ROSAT extreme ultra-violet sky survey, a quantitative study of optimal extraction, an automated analysis of spectra, applications of synthetic photometry, an algorithm for extra-solar planet system detection and data reduction facilities for the William Herschel telescope.

  14. A comparative analysis of in vitro toxicity of diesel exhaust particles from combustion of 1st- and 2nd-generation biodiesel fuels in relation to their physicochemical properties-the FuelHealth project.

    Science.gov (United States)

    Lankoff, Anna; Brzoska, Kamil; Czarnocka, Joanna; Kowalska, Magdalena; Lisowska, Halina; Mruk, Remigiusz; Øvrevik, Johan; Wegierek-Ciuk, Aneta; Zuberek, Mariusz; Kruszewski, Marcin

    2017-07-03

    Biodiesels represent more carbon-neutral fuels and are introduced at an increasing extent to reduce emission of greenhouse gases. However, the potential impact of different types and blend concentrations of biodiesel on the toxicity of diesel engine emissions are still relatively scarce and to some extent contradictory. The objective of the present work was to compare the toxicity of diesel exhaust particles (DEP) from combustion of two 1st-generation fuels: 7% fatty acid methyl esters (FAME; B7) and 20% FAME (B20) and a 2nd-generation 20% FAME/HVO (synthetic hydrocarbon biofuel (SHB)) fuel. Our findings indicate that particulate emissions of each type of biodiesel fuel induce cytotoxic effects in BEAS-2B and A549 cells, manifested as cell death (apoptosis or necrosis), decreased protein concentrations, intracellular ROS production, as well as increased expression of antioxidant genes and genes coding for DNA damage-response proteins. The different biodiesel blend percentages and biodiesel feedstocks led to marked differences in chemical composition of the emitted DEP. The different DEPs also displayed statistically significant differences in cytotoxicity in A549 and BEAS-2B cells, but the magnitude of these variations was limited. Overall, it seems that increasing biodiesel blend concentrations from the current 7 to 20% FAME, or substituting 1st-generation FAME biodiesel with 2nd-generation HVO biodiesel (at least below 20% blends), affects the in vitro toxicity of the emitted DEP to some extent, but the biological significance of this may be moderate.

  15. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Pulmonology”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Pulmonology”ABS 1. URINE NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN AS A MARKER OF BRONCHOPULMONARY DYSPLASIA AND RETINOPATHY OF PREMATURITY IN PRETERM NEONATES • H. Ergin, T. Atilgan, M. Dogan, O.M.A. Ozdemir, C. YeniseyABS 2. LUNG COMPLIANCE AND LUNG ULTRASOUND DURING POSTNATAL ADAPTATION IN HEALTHY NEWBORN INFANTS • L. Süvari, L. Martelius, C. Janér, A. Kaskinen, O. Pitkänen, T. Kirjavainen, O. Helve, S. AnderssonABS 3. PRE-DISCHARGE RESPIRATORY OUTCOMES IN SMALL-FOR-GESTATIONAL-AGE AND APPROPRIATE-FOR-GESTATIONAL-AGE VERY PRETERM INFANTS • A. Matic, A. RistivojevicABS 4. THE EFFECT OF CHANGING OXYGEN SATURATION TARGET RANGE ON COMPLIANCE IN OXYGEN SATURATION TARGETING IN THE NEONATAL INTENSIVE CARE UNIT • H.A. van Zanten, S. Pauws, E.C.H. Beks, B.J. Stenson, E. Lopriore, A.B. te PasABS 5. BINASAL PRONG VERSUS NASAL MASK FOR APPLYING CPAP TO PRETERM INFANTS: RANDOMIZED CONTROLLED TRIAL • B. Say, G. Kanmaz, S.S. OguzABS 6. TRAINING AND RAISING AWARENESS IMPROVES COMPLIANCE IN OXYGEN SATURATION TARGETING IN THE NEONATAL INTENSIVE CARE UNIT • H.A. van Zanten, S. Pauws, E.C.H. Beks, B.J. Stenson, E

  16. Findings of the fertility survey in Beijing municipality and other five provinces.

    Science.gov (United States)

    1988-12-01

    The findings of the 2nd Chinese Fertility Survey, conducted in Beijing Municipality and the provinces of Liaoning, Shandong, Guangdong, Guizhou, and Gansu, indicate progress in the postponement of age at 1st marriage as well as increasing marital stability. The divorce rate ranged from 0.2-0.6% in the areas studied. Median age at 1st marriage is 3 years higher among women 25-29 years of age than among women 45-49 years of age. Among these younger women, median age at 1st marriage now stands at 23 years in Beijing Municipality and Liaoning, Shandong, and Guangdong Provinces and at 21-22 years in Guizhou and Gansu Provinces. The average. At present, the average number of children born is 1.63 in Beijing Municipality, 1.97 in Liaoning Province, 2.19 in Shandong, 2.67 in Guangdong, 2.79 in Gansu, and 3.47 in Guizhou Province. All the women surveyed were able to cite 4-7 birth control methods and have themselves used 1-2 methods (a low of 1 method in Guizhou and Gansu Provinces to a high of 1.7 in Beijing). Overall, 70% of the women of childbearing age surveyed were using contraceptive method at present. The highest contraceptive prevalence rate (84%) exists in Beijing Municipality.

  17. An exploratory cluster randomised trial of a university halls of residence based social norms marketing campaign to reduce alcohol consumption among 1st year students.

    Science.gov (United States)

    Moore, Graham F; Williams, Annie; Moore, Laurence; Murphy, Simon

    2013-04-18

    This exploratory trial examines the feasibility of implementing a social norms marketing campaign to reduce student drinking in universities in Wales, and evaluating it using cluster randomised trial methodology. Fifty residence halls in 4 universities in Wales were randomly assigned to intervention or control arms. Web and paper surveys were distributed to students within these halls (n = 3800), assessing exposure/contamination, recall of and evaluative responses to intervention messages, perceived drinking norms and personal drinking behaviour. Measures included the Drinking Norms Rating Form, the Daily Drinking Questionnaire and AUDIT-C. A response rate of 15% (n = 554) was achieved, varying substantially between sites. Intervention posters were seen by 80% and 43% of students in intervention and control halls respectively, with most remaining materials seen by a minority in both groups. Intervention messages were rated as credible and relevant by little more than half of students, though fewer felt they would influence their behaviour, with lighter drinkers more likely to perceive messages as credible. No differences in perceived norms were observed between intervention and control groups. Students reporting having seen intervention materials reported lower descriptive and injunctive norms than those who did not. Attention is needed to enhancing exposure, credibility and perceived relevance of intervention messages, particularly among heavier drinkers, before definitive evaluation can be recommended. A definitive evaluation would need to consider how it would achieve sufficient response rates, whilst hall-level cluster randomisation appears subject to a significant degree of contamination. ISRCTN: ISRCTN48556384.

  18. An exploratory cluster randomised trial of a university halls of residence based social norms marketing campaign to reduce alcohol consumption among 1st year students

    Science.gov (United States)

    2013-01-01

    Aims This exploratory trial examines the feasibility of implementing a social norms marketing campaign to reduce student drinking in universities in Wales, and evaluating it using cluster randomised trial methodology. Methods Fifty residence halls in 4 universities in Wales were randomly assigned to intervention or control arms. Web and paper surveys were distributed to students within these halls (n = 3800), assessing exposure/contamination, recall of and evaluative responses to intervention messages, perceived drinking norms and personal drinking behaviour. Measures included the Drinking Norms Rating Form, the Daily Drinking Questionnaire and AUDIT-C. Results A response rate of 15% (n = 554) was achieved, varying substantially between sites. Intervention posters were seen by 80% and 43% of students in intervention and control halls respectively, with most remaining materials seen by a minority in both groups. Intervention messages were rated as credible and relevant by little more than half of students, though fewer felt they would influence their behaviour, with lighter drinkers more likely to perceive messages as credible. No differences in perceived norms were observed between intervention and control groups. Students reporting having seen intervention materials reported lower descriptive and injunctive norms than those who did not. Conclusions Attention is needed to enhancing exposure, credibility and perceived relevance of intervention messages, particularly among heavier drinkers, before definitive evaluation can be recommended. A definitive evaluation would need to consider how it would achieve sufficient response rates, whilst hall-level cluster randomisation appears subject to a significant degree of contamination. Trial registration ISRCTN: ISRCTN48556384 PMID:23594918

  19. Iodine status and thyroid volume changes during pregnancy: results of a survey in Aran Valley (Catalan Pyrenees).

    Science.gov (United States)

    Vila, L; Legaz, G; Barrionuevo, C; Espinel, M L; Casamitjana, R; Muñoz, J; Serra-Prat, M; Puig-Domingo, M

    2008-10-01

    The Aran Valley (Catalan Pyrenees, Spain) has a long-standing history of iodine deficiency. A survey was performed to determine the prevalence of iodine deficiency (urinary iodine<150 microg/l) in pregnant women from this region during the 1st and 3rd trimesters of gestation and to evaluate the changes in thyroid volume (TV). Of all the registered pregnancies in the area, in the first semester of the year 2000, 35 women (90%) were studied. Urinary iodine (UI) was measured and a thyroid ultrasonography performed during the 1st and 3rd trimester and their iodized salt consumption was recorded. Of the whole group, 77.1% of pregnant women reported regular intake of iodized salt.Median UI in the first trimester was 134.5 microg/l. Iodine deficiency was observed in 57.1%of women in the 1st trimester and in 46.7% in the 3rd trimester (p=0.1). In 10 women supplemented with iodine (150 microg/day) from the 1st trimester, median UI increased from 138.5 microg/l in the 1st trimester to 168 mug/l in the 3rd trimester (p=0.037), and no changes were observed in the rest. TV increased in the whole group during pregnancy (median 7.5 ml in the 1st trimester vs 9.5 ml in the 3rd trimester; p<0.001). The change in TV was significant in those cases with iodine deficiency in the 1st trimester, 3rd trimester or both (median 7.5ml in the 1st trimester vs 10.01 ml in the 3rd trimester; p=0.001) and between multiparous women (8.2 vs 10.9 ml; p=0.005). In 2000, iodine deficiency among pregnant women in the Aran Valley was still very high. Iodine deficiency as well as multiparity contributes to goitrogenesis during pregnancy. Taking this data in account, pre-conceptional supplements with iodine are required for its prevention.

  20. Current practice of epidemiology in Africa: highlights of the 3rd conference of the African epidemiological association and 1st conference of the Cameroon society of epidemiology, Yaoundé, Cameroon, 2014.

    Science.gov (United States)

    Nkwescheu, Armand Seraphin; Fokam, Joseph; Tchendjou, Patrice; Nji, Akindeh; Ngouakam, Hermann; Andre, Bita Fouda; Joelle, Sobngwi; Uzochukwu, Benjamin; Akinroye, Kingsley; Mbacham, Wilfred; Colizzi, Vittorio; Leke, Rose; Victora, Cesar

    2015-01-01

    As the study of disease occurrence and health indicators in human populations, Epidemiology is a dynamic field that evolves with time and geographical context. In order to update African health workers on current epidemiological practices and to draw awareness of early career epidemiologists on concepts and opportunities in the field, the 3(rd) African Epidemiology Association and the 1st Cameroon Society of Epidemiology Conference was organized in June 2-6, 2014 at the Yaoundé Mont Febe Hotel, in Cameroon. Under the theme«Practice of Epidemiology in Africa: Stakes, Challenges and Perspectives», the conference attracted close to five hundred guest and participants from all continents. The two main programs were the pre-conference course for capacity building of African Early Career epidemiologists, and the conference itself, providing a forum for scientific exchanges on recent epidemiological concepts, encouraging the use of epidemiological methods in studying large disease burden and neglected tropical diseases; and highlighting existing opportunities.

  1. Despre mormântul de incineraţie în situlă de bronz de la Sipoteni (sec. II-I a. Chr. / Cremated remains in bronze situla from Sipoteni (2nd-1st centuries BC

    Directory of Open Access Journals (Sweden)

    Ion Tentiuc

    2016-10-01

    Full Text Available In the work on the materials of a cremation burial in bronze situla of the 2nd-1st centuries BC, which was found in Mana village (Orhei district, we have taken for comparative and anthropological analysis remains of calcined bones from the burial in situla from Sipoteni (Călăraşi district published in 1950s. Osteological research of the contents of the bronze vessel from Sipoteni showed that the remains belonged to a man 20-30 years old. In the burial urn a fragment of a black-burnished vessel, a silver fi bula of the Middle La Tene type, an iron ring, and an amorphous iron object were found. The grave goods also contain a bronze situla, identical in shape and size, which was found near the funeral urn. Researches attributed the Sipoteni burial to the 2nd-1st centuries BC, a period of domination of Bastarnae tribes in the central and northern part of the Carpathian-Dniester region. Our own comparative analysis of this type of bronze vessels showed that they are similar with identical containers from the Middle Danube sites, as well as from northern Italy, southern France and Spain, which were used by Celtic tribes as funeral urns. To the east of the Carpathians identical bronze vessels were found in the village of Mana, at the site of Bădeni (Iaşi, and as part of the so-called odd hoards from Bădragii Noi, Vesela Dolina, and Maryevka (in the region from the Eastern Carpathians to the Dnieper and the Don at least 50 so-called hoards were found, including ones in the bronze vessels, which we have mentioned. Some researchers’ attempts to attribute the situlae from Sipoteni, Bădragii Noi, Vesela Dolina, Maryevka, etc. to the type of Eggers 18-23 or the type of Bargfeld seem to us to fail, because these bronze vessels have slender shape, riveted bronze or iron attaches and the maximum diameter of the vessels is at the height of the fourth part. The East Carpathian situlae are of less slender proportions, and the largest diameter is located

  2. The Role of Educational Practice in the Learning of Basic Psychological Concepts (Based on Practical Training of 1st year Master Students Studying “Cultural-Historical Psychology and Activity Approach in Education”

    Directory of Open Access Journals (Sweden)

    Ulanovskaya I. M.

    2015-11-01

    Full Text Available The article describes experience of the practical training for 1st year master students studying «cultural-historical psychology and activity approach in education» entitled “Study of the educational environment of the school”. The basis for training was provided by Moscow school #91 which systematically implemented in the elementary school the program of developing training, developed in the framework of Elkonin-Davydov theory of learning activity. There are examples of tools proposed and developed by teams of master students to evaluate certain characteristics of the educational environment and the results of their use to solve diagnostic problems. It is shown how techniques of deep studying, setting difficult practically significant substantive issues, independent work, group discussions, group projects development and defence, the master students applied, contribute to the formation of the bases of professional critical thinking, reflection and cognitive attitudes.

  3. 第1届中德焊接模拟国际研讨会在柏林举行%1st Sino-German Workshop on Simulation of Welding held at BAM in Berlin

    Institute of Scientific and Technical Information of China (English)

    中国焊接学会计算机辅助焊接工程专业委员会

    2010-01-01

    @@ 第1届中德焊接模拟国际研讨会(1st Sino-German Workshop on simulation of Welding)于2010年10月25~29日在德国柏林成功举行.此次研讨会由中国焊接学会计算机辅助焊接工程专业委员会与德国联邦材料试验研究院(BAM)连接构件安全性分部(Division V.5)联合举办:由德国BAM的Rethmeier教授和山东大学的武传松教授担任共同主席.

  4. Prevalence of ST1193 clone and IncI1/ST16 plasmid in E-coli isolates carrying blaCTX-M-55 gene from urinary tract infections patients in China.

    Science.gov (United States)

    Xia, Liang; Liu, Yang; Xia, Shu; Kudinha, Timothy; Xiao, Shu-Nian; Zhong, Nan-Shan; Ren, Guo-Sheng; Zhuo, Chao

    2017-03-24

    To study molecular epidemiology of CTX-M-55-carrying Escherichia coli isolates from urinary tract infections (UTIs) in China. 111 blaCTX-M-55-positive E.coli isolates from UTIs patients in China were studied. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analyze the homologies among the strains. Conjugation experiments, S1nuclease PFGE and PCR analysis were performed to characterize plasmids harboring blaCTX-M-55 and their genetic environment. 111 isolates were clustered into 86 individual pulsotypes and three clusters by PFGE. Fifty-five (49.5%) of the isolates belonged to 8 STs. Most of the ST1193 isolates belonged to one PFGE cluster. Transconjugants (n = 45) derived from randomly selected blaCTX-M-55 donors (n = 58), were found to contain a single 90-kb conjugative plasmid, which mainly belonged to the IncI1 groups (34, 76%). Among the IncI1 plasmids, the blaCTX-M-55/IncI1/ST16 predominated (23/34, 68%). The blaTEM-1 and aac (3')-II genes were frequently detected on the IncI1 plasmids, and the insertion of ISEcp1 or IS26 was observed at the 48 bp or 45 bp upstream of the start codon of blaCTX-M-55 gene. The dissemination of blaCTX-M-55 gene among E. coli UTI isolates, appeared to be due to both the major clonal lineage of ST1193 and the horizontal transfer of epidemic plasmid IncI1/ST16.

  5. Proinflammatory effects of diesel exhaust particles from moderate blend concentrations of 1st and 2nd generation biodiesel in BEAS-2B bronchial epithelial cells-The FuelHealth project.

    Science.gov (United States)

    Skuland, Tonje S; Refsnes, Magne; Magnusson, Pål; Oczkowski, Michał; Gromadzka-Ostrowska, Joanna; Kruszewski, Marcin; Mruk, Remigiusz; Myhre, Oddvar; Lankoff, Anna; Øvrevik, Johan

    2017-06-01

    Biodiesel fuel fuels are introduced at an increasing extent as a more carbon-neutral alternative to reduce CO2-emissions, compared to conventional diesel fuel. In the present study we have investigated the impact of increasing the use of 1st generation fatty acid methyl ester (FAME) biodiesel from current 7% blend (B7) to 20% blend (B20), or by increasing the biodiesel content by adding 2nd generation hydrotreated vegetable oil (HVO) based biodiesel (SHB; Synthetic Hydrocarbon Biofuel) on toxicity of diesel exhaust particles (DEP) in an in vitro system. Human bronchial epithelial BEAS-2B cells were exposed for 4 and 20h to DEP from B7, B20 and SHB at different concentrations, and examined for effects on gene expression of interleukin 6 (IL-6), CXCL8 (IL-8), CYP1A1 and heme oxygenase-1 (HO-1). The results show that both B20 and SHB were more potent inducers of IL-6 expression compared to B7. Only B20 induced statistically significant increases in CXCL8 expression. By comparison the rank order of potency to induce CYP1A1 was SHB>B7>B20. No statistically significant difference were observed form HO-1 expression, suggesting that the differences in cytokine responses were not due to oxidative stress. The results show that even moderate increases in biodiesel blends, from 7% to 20%, may increase the proinflammatory potential of emitted DEP in BEAS-2B cells. This effect was observed for both addition of 1st generation FAME and 2nd generation HVO biodiesel. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Prevalence of ST1193 clone and IncI1/ST16 plasmid in E-coli isolates carrying blaCTX-M-55 gene from urinary tract infections patients in China

    Science.gov (United States)

    Xia, Liang; Liu, Yang; Xia, Shu; Kudinha, Timothy; Xiao, Shu-nian; Zhong, Nan-shan; Ren, Guo-sheng; Zhuo, Chao

    2017-01-01

    To study molecular epidemiology of CTX-M-55-carrying Escherichia coli isolates from urinary tract infections (UTIs) in China. 111 blaCTX-M-55-positive E.coli isolates from UTIs patients in China were studied. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analyze the homologies among the strains. Conjugation experiments, S1nuclease PFGE and PCR analysis were performed to characterize plasmids harboring blaCTX-M-55 and their genetic environment. 111 isolates were clustered into 86 individual pulsotypes and three clusters by PFGE. Fifty-five (49.5%) of the isolates belonged to 8 STs. Most of the ST1193 isolates belonged to one PFGE cluster. Transconjugants (n = 45) derived from randomly selected blaCTX-M-55 donors (n = 58), were found to contain a single 90-kb conjugative plasmid, which mainly belonged to the IncI1 groups (34, 76%). Among the IncI1 plasmids, the blaCTX-M-55/IncI1/ST16 predominated (23/34, 68%). The blaTEM-1 and aac (3′)-II genes were frequently detected on the IncI1 plasmids, and the insertion of ISEcp1 or IS26 was observed at the 48 bp or 45 bp upstream of the start codon of blaCTX-M-55 gene. The dissemination of blaCTX-M-55 gene among E. coli UTI isolates, appeared to be due to both the major clonal lineage of ST1193 and the horizontal transfer of epidemic plasmid IncI1/ST16. PMID:28338012

  7. 神灯联合消炎1号治疗老年患者输液外渗的效果观察%TDP joint anti-inflammatory on the 1st infusion extravasation treatment effect observed

    Institute of Scientific and Technical Information of China (English)

    韩艳秋

    2014-01-01

    Objective TDP observed on the 1st joint anti-inflammatory treatment of elderly patients intravenous infusion extravasation effect. Methods The 60 cases of elderly patients intravenous infusion extravasation randomly divided into control group and observation group of 30 patients in the control group to 50%magnesium sulfate wet after TDP irradiation treatment,the observation group to the anti-inflammatory cream with 1 lamp after irradiation topical treatment effect was observed in both groups of patients. Results The efficiency of observation group was higher than the control group, and the difference has statistical significance. Conclusion TDP irradiation combined with anti-inflammatory on the 1st Plaster extravasation of intravenous infusion therapy is better than TDP irradiation combined with magnesium sulfate wet,worthy of clinical application.%目的:观察神灯联合消炎1号治疗老年静脉输液外渗的效果。方法将60例静脉输液外渗的老年患者随机分为对照组和观察组各30例,对照组采用神灯照射后给予50%硫酸镁湿敷治疗,观察组采用神灯照射后给予消炎1号膏外敷。观察2组患者的治疗效果。结果观察组总有效率高于对照组,差异有统计学意义(P<0.05)。结论神灯照射联合消炎1号膏外敷治疗静脉输液外渗效果优于神灯照射联合硫酸镁湿敷,值得临床推广应用。

  8. Geodetic Control Points, Geodetic control points constructed and occupied per NGS GPS standards, Published in 2001, 1:600 (1in=50ft) scale, Cochise County.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Geodetic Control Points dataset, published at 1:600 (1in=50ft) scale, was produced all or in part from Field Survey/GPS information as of 2001. It is described...

  9. Airborne Gravity: NGS' Gravity Data for the US and Territories (2008-2022) - National Geospatial Data Asset (NGDA) Airborne Gravity (GRAV-D)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gravity for the Re-definition of the American Vertical Datum (GRAV-D) is a project initiated by NOAA's National Geodetic Survey to collect and monitor gravity data...

  10. "Suntelligence" Survey

    Science.gov (United States)

    ... to the American Academy of Dermatology's "Suntelligence" sun-smart survey. Please answer the following questions to measure ... be able to view a ranking of major cities suntelligence based on residents' responses to this survey. ...

  11. NGS detection for Chinese primary lung cancer patients gene mutation on EGFR, KRAS, BRAF and PIK3CA%NGS技术检测中国原发性肺癌患者的EGFR、KRAS、BRAF和PIK3CA基因突变

    Institute of Scientific and Technical Information of China (English)

    支修益; 胡牧; 王鑫

    2015-01-01

    Objective To evaluate the feasibility of application of next generation sequencing (NGS) technology in clinical molecular diagnosis of lung cancer. Method The NGS platform-Ion Torrent was utilized in this study to examine the mutational status of EGFR, KRAS, BRAF and PIK3CA in 30 cases of lung cancer. The NGS results were compared with qPCR results. Result The technical parameters of NGS method were stable and the NGS results were entirely consistent with qPCR results (100%). Conclusion After further technical validation of more clinical samples, NGS technology is expected to be applied broadly in clinical setting. It is believed to elevate the molecular diagnosis and individualized treatment of lung cancer to a new level.%目的:评估下一代测序(NGS)技术在原发性肺癌临床分子诊断中应用的可行性。方法本研究应用Ion Torrent NGS平台,一次性检测30例肺癌病理样本EGFR、KRAS、BRAF和PIK3CA基因的突变情况,并与实时荧光定量核酸扩增检测(qPCR)技术检测结果进行对比。结果 NGS检测方法技术参数稳定,且与qPCR技术检测结果完全一致(100%)。结论经过更多临床样本的方法验证后, NGS技术有望得到临床推广,并将原发性肺癌分子诊断和个体化诊疗提高到一个新的水平。

  12. Survey Says

    Science.gov (United States)

    McCarthy, Susan K.

    2005-01-01

    Survey Says is a lesson plan designed to teach college students how to access Internet resources for valid data related to the sexual health of young people. Discussion questions based on the most recent available data from two national surveys, the Youth Risk Behavior Surveillance-United States, 2003 (CDC, 2004) and the National Survey of…

  13. FOREWORD: 13th International Workshop on Plasma-Facing Materials and Components for Fusion Applications/1st International Conference on Fusion Energy Materials Science 13th International Workshop on Plasma-Facing Materials and Components for Fusion Applications/1st International Conference on Fusion Energy Materials Science

    Science.gov (United States)

    Jacob, Wolfgang; Linsmeier, Christian; Rubel, Marek

    2011-12-01

    The 13th International Workshop on Plasma-Facing Materials and Components (PFMC-13) jointly organized with the 1st International Conference on Fusion Energy Materials Science (FEMaS-1) was held in Rosenheim (Germany) on 9-13 May 2011. PFMC-13 is a successor of the International Workshop on Carbon Materials for Fusion Applications series. Between 1985 and 2003 ten 'Carbon Workshops' were organized in Jülich, Stockholm and Hohenkammer. Then it was time for a change and redefinition of the scope of the symposium to reflect the new requirements of ITER and the ongoing evolution in the field. Under the new name (PFMC-11), the workshop was first organized in 2006 in Greifswald, Germany and PFMC-12 took place in Jülich in 2009. Initially starting in 1985 with about 40 participants as a 1.5 day workshop, the event has continuously grown to about 220 participants at PFMC-12. Due to the joint organization with FEMaS-1, PFMC-13 set a new record with more than 280 participants. The European project Fusion Energy Materials Science, FEMaS, coordinated by the Max-Planck-Institut für Plasmaphysik (IPP), organizes and stimulates cooperative research activities which involve large-scale research facilities as well as other top-level materials characterization laboratories. Five different fields are addressed: benchmarking experiments for radiation damage modelling, the application of micro-mechanical characterization methods, synchrotron and neutron radiation-based techniques and advanced nanoscopic analysis based on transmission electron microscopy. All these fields need to be exploited further by the fusion materials community for timely materials solutions for a DEMO reactor. In order to integrate these materials research fields, FEMaS acted as a co-organizer for the 2011 workshop and successfully introduced a number of participants from research labs and universities into the PFMC community. Plasma-facing materials experience particularly hostile conditions as they are

  14. 我院肿瘤Ⅰ科癌痛治疗药物使用情况分析%Analysis of the utilization of pain-relief drugs of cancer in the 1st tumor department in our hospital

    Institute of Scientific and Technical Information of China (English)

    毛伟; 袁孔现

    2016-01-01

    Objective To analyze and evaluate the pain-relief drugs of cancer used in the 1st tumor department in our hospital .Meth-ods Varieties of the pain-relief drugs of cancer ,the amount of drug scheduling and medication frequency(DDDs) sort ratio and daily expense (DDC) in 2014 were used as the evaluation index .Results 15 pain-relief drugs of cancer were used in the 1st tumor department .The top four in DDDs were Oxycodone Hydrochloride Prolonged-Release Tablets(10 mg) ,Oxycodone Hydrochloride Prolonged-release Tablets(40 mg) ,Acetaminophen Tablets(5 mg/325 mg) and Morphine Hydrochloride Tablets(10 mg) .Con-clusion With the establishment of the Good Pain Management Ward(GPD-Ward) ,the application of pain-relief drugs of cancer was tending to be reasonable .%目的:调查分析我院肿瘤Ⅰ科癌痛治疗药物使用情况。方法对我院肿瘤Ⅰ科2014年癌痛治疗用药的品种、数量、用药金额、用药频度(DDDs)和日均费用(DDC)进行统计分析。结果我院肿瘤Ⅰ科治疗癌痛的药物有15个品规,DDDs居前4位的依次是:盐酸羟考酮缓释片(10 mg)、盐酸羟考酮缓释片(40 mg)、氨酚羟考酮片(5 mg/325 mg)和盐酸吗啡片(10 mg)。结论随着癌痛规范化治疗病房的建立和运行,我院肿瘤Ⅰ科癌痛治疗用药情况趋于合理,遵循口服给药、按阶梯用药、按时服药、个体化给药及注意具体细节的方案给药。

  15. Tigecycline Nonsusceptibility Occurs Exclusively in Fluoroquinolone-Resistant Escherichia coli Clinical Isolates, Including the Major Multidrug-Resistant Lineages O25b:H4-ST131-H30R and O1-ST648.

    Science.gov (United States)

    Sato, Toyotaka; Suzuki, Yuuki; Shiraishi, Tsukasa; Honda, Hiroyuki; Shinagawa, Masaaki; Yamamoto, Soh; Ogasawara, Noriko; Takahashi, Hiroki; Takahashi, Satoshi; Tamura, Yutaka; Yokota, Shin-Ichi

    2017-02-01

    Tigecycline (TGC) is a last-line drug for multidrug-resistant Enterobacteriaceae We investigated the mechanism(s) underlying TGC nonsusceptibility (TGC resistant/intermediate) in Escherichia coli clinical isolates. The MIC of TGC was determined for 277 fluoroquinolone-susceptible isolates (ciprofloxacin [CIP] MIC, resistant isolates (CIP MIC, >2 mg/liter). The MIC50 and MIC90 for TGC in fluoroquinolone-resistant isolates were 2-fold higher than those in fluoroquinolone-susceptible isolates (MIC50, 0.5 mg/liter versus 0.25 mg/liter; MIC90, 1 mg/liter versus 0.5 mg/liter, respectively). Two fluoroquinolone-resistant isolates (O25b:H4-ST131-H30R and O125:H37-ST48) were TGC resistant (MICs of 4 and 16 mg/liter, respectively), and four other isolates of O25b:H4-ST131-H30R and an isolate of O1-ST648 showed an intermediate interpretation (MIC, 2 mg/liter). No TGC-resistant/intermediate strains were found among the fluoroquinolone-susceptible isolates. The TGC-resistant/intermediate isolates expressed higher levels of acrA and acrB and had lower intracellular TGC concentrations than susceptible isolates, and they possessed mutations in acrR and/or marR The MICs of acrAB-deficient mutants were markedly lower (0.25 mg/liter) than those of the parental strain. After continuous stepwise exposure to CIP in vitro, six of eight TGC-susceptible isolates had reduced TGC susceptibility. Two of them acquired TGC resistance (TGC MIC, 4 mg/liter) and exhibited expression of acrA and acrB and mutations in acrR and/or marR In conclusion, a population of fluoroquinolone-resistant E. coli isolates, including major extraintestinal pathogenic lineages O25b:H4-ST131-H30R and O1-ST648, showed reduced susceptibility to TGC due to overexpression of the efflux pump AcrAB-TolC, leading to decreased intracellular concentrations of the antibiotics that may be associated with the development of fluoroquinolone resistance.

  16. 1st International Conference of Serviceology

    CERN Document Server

    Ueda, Kanji; Takenaka, Takeshi

    2014-01-01

    Services are key activities in the globalization of the economy and also underlie the quality of life of local residents. The advanced work presented in this book was selected from the proceedings of the First International Conference on Serviceology (ICServ2013), held October 16–18, 2013 in Tokyo. This book provides a useful overall guide to the state of the art in theory and practice of services for researchers in various fields, including engineering, marketing, economics, and others. This work also facilitates the scientific systematization of services and promotes technological developments for solutions of industrial issues.

  17. 1st SaporeGravis Workshop

    CERN Document Server

    2013-01-01

    English: Retequarkonii is a networking of the I3 Hadron Physics 2 program of the EU 7th FP. Retequarkonii aims at studying the production of quarkonia in hadronic collisions at ultra relativistic energies. In the next 10 years, the future Large Hadron Collider (LHC) will open new possibilities for studying the properties of the strongly interacting matter at high temperature and for studying non-perturbative features of QCD. Quarkonia will be abundantly produced and correlations with other global observables of the heavy ion collision like centrality and/or reaction plane will allow for studying the properties of the QGP phases. At such high-energy hadronic collisions, Quarkonia will also be abundantly produced in diffractive and electromagnetic processes including both diffractive pomeron- and photon- induced quarkonium production. About 27 research groups of 12 different countries participate to the Retequarkonii project. Retequarkonii will organize one training school for phD and two conferences between ex...

  18. 1st International Conference on Network Analysis

    CERN Document Server

    Kalyagin, Valery; Pardalos, Panos

    2013-01-01

    This volume contains a selection of contributions from the "First International Conference in Network Analysis," held at the University of Florida, Gainesville, on December 14-16, 2011. The remarkable diversity of fields that take advantage of Network Analysis makes the endeavor of gathering up-to-date material in a single compilation a useful, yet very difficult, task. The purpose of this volume is to overcome this difficulty by collecting the major results found by the participants and combining them in one easily accessible compilation. Network analysis has become a major research topic over the last several years. The broad range of applications that can be described and analyzed by means of a network is bringing together researchers, practitioners and other scientific communities from numerous fields such as Operations Research, Computer Science, Transportation, Energy, Social Sciences, and more. The contributions not only come from different fields, but also cover a broad range of topics relevant to the...

  19. 1st National Conference on Sensors

    CERN Document Server

    D’Amico, Arnaldo; Natale, Corrado; Siciliano, Pietro; Seeber, Renato; Stefano, Luca; Bizzarri, Ranieri; Andò, Bruno

    2014-01-01

    This book contains a selection of papers presented at the First National Conference on Sensors held in Rome 15-17 February 2011. The conference highlighted state-of-the-art results from both theoretical and applied research in the field of sensors and related technologies. This book presents material in an interdisciplinary approach, covering many aspects of the disciplines related to sensors, including physics, chemistry, materials science, biology and applications.   ·         Provides a selection of the best papers from the First Italian National Conference on Sensors; ·         Covers a broad range of topics relating to sensors and microsystems, including physics, chemistry, materials science, biology and applications;       ·        Offers interdisciplinary coverage, aimed at defining a common ground for sensors beyond the specific differences among the different particular implementation of sensors.

  20. Anthological Project: Newspaper, 1st April, 1984.

    Science.gov (United States)

    Langan, Charles

    1969-01-01

    The conventional textbook approach to English, at Saint Augustine's Secondary School in Glasgow, was replaced with an anthological project--a class newspaper. To prevent plagiarism and to stimulate creative thought, students were asked to use April 1, 1984, as the publication date. Initially, the class was divided into six groups to represent the…

  1. 1st International AsiaHaptics conference

    CERN Document Server

    Ando, Hideyuki; Kyung, Ki-Uk

    2015-01-01

    This book is aimed not only at haptics and human interface researchers, but also at developers and designers from manufacturing corporations and the entertainment industry who are working to change our lives. This publication comprises the proceedings of the first International AsiaHaptics conference, held in Tsukuba, Japan, in 2014. The book describes the state of the art of the diverse haptics- (touch-) related research, including scientific research into haptics perception and illusion, development of haptics devices, and applications for a wide variety of fields such as education, medicine, telecommunication, navigation, and entertainment.

  2. 1st AtMol European Workshop

    CERN Document Server

    Atomic Scale Interconnection Machines

    2012-01-01

    This volume documents the first International Workshop on Atomic Scale Interconnection Machines organised by the European Integrated Project AtMol in June 2011 in Singapore. The four sessions, discussed here in revised contributions by high level speakers, span topics such as: multi-probe UHV instrumentation, atomic scale nano-material nanowires characterization, atomic scale surface conductance measurements and surface atomic scale mechanical machineries. This state-of-the-art account allows academic researchers and industry engineers access to the tools they need to be at the forefront of the atomic scale technology revolution.

  3. WP2 Annual Report 1st year

    DEFF Research Database (Denmark)

    Jensen, Jørgen Juncher

    2006-01-01

    This report constitutes a contribution to the consolidated annual report covering the activities in SAFEDOR for the first year (1/2-2005 to 1/2-2006). The report deals in five separate chapters one for each of the five subprojects. The objectives of WP2 are • To develop and / or refine...

  4. The 1st Asian Lightning Protection Forum

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ The First Asian Lightning Protection Forum was held on October 28-29, 2003 in Beijing, China.The forum was sponsored by the China Association for Standardization and was organized by Chinese National Committee for Lightning Protection Technology Standardization, Department of Electrical Engineering Tsinghua University, China Electricity Council, Zhongguang High-tech Industrial Development Co.,Ltd, and Lightning Protection Center of Guangdong Province.

  5. Systems Engineering & Supportability Workshop (1st)

    Science.gov (United States)

    1998-09-01

    Solution for Legacy System Upgrades" by Michael J. Cook ....................... 131 "Data in Supportof a Programs Long Term Needs" by Carol Gutierrez ...n-~(~ (1 0 (D- -0 D r-1. - Ciw < :2 Q( 70V (n .- 0( C 0 0 - P, CID 2 . w D M ;; =0CD CL 07- h~ -- C mcn U)- CL~ ~ -(nCDef -1 CD 0 C~0 3) o oD ’-’o...0UP 282 o X. 910 0’ CID CD C Cl) @, 5-,.0 0 -0 CDM 0x (N0 (0 ~= m M C: 0 CD = (n~ CD ~W CD --12. a 0 -0 M 0 w CD _1 ( 0-* ; o 0na = 0D 0 -@ C M o o :CD

  6. International Symposium on Polymer Electrolytes (1st)

    Science.gov (United States)

    1987-06-01

    been attributed to the greater stability of the trifluoromethane sulphonate anion and a lower degree of ion-pairing, trifluoromethane sulphonic acid ...Electrolytes’. 31. R. TANAKA, T. IWASE, T. HORI and S. SAITO, ’Proton Conduction In Linear Poly(ethyleneimine)-Sulphuric Acid and Phosphoric Acid Systems’. 32...relaxation time requires some thought since the macroscopic viscosity in high molecular weight systems may not reflect at all the relaxation time for

  7. 1st International ATZ Conference 2016

    CERN Document Server

    2017-01-01

    The UN Climate Change Conference in Paris, with its key topics of global warming and deteriorating air quality, will speed up the advance of electric mobility. CO2-neutral and zero-emission mobility require electricity to be generated from regenerative sources of energy. Power generation from wind and solar energy, however is dependent on the weather and is therefore not stable. The irregularities that occur in nature can result in unacceptable voltage fluctuations in the power grid. For that reason, the availability of highly flexible loads and storage systems is becoming particularly important. Electric vehicles, with their grid-relevant properties as controllable power consumers and electricity storage systems, could help to stabilize future power grids. Contents Markets.- Traffic and energy systems.- Local energy systems.- Information and communication technology.- System behavior.- Overall energy systems II. Target audiences Automotive engineers and chassis specialists as well as students looking for sta...

  8. 1st Large Hadron Collider Physics Conference

    CERN Document Server

    Juste, A; Martínez, M; Riu, I; Sorin, V

    2013-01-01

    The conference is the result of merging two series of international conferences, "Physics at Large Hadron Collider" (PLHC2012) and "Hadron Collider Physics Symposium" (HCP2012). With a program devoted to topics such as the Standard Model and Beyond, the Higgs Boson, Supersymmetry, Beauty and Heavy Ion Physics, the conference aims at providing a lively forum for discussion between experimenters and theorists of the latest results and of new ideas. LHCP 2013 will be hosted by IFAE (Institut de Fisica d'Altes Energies) in Barcelona (Spain), and will take place from May 13 to 18, 2013. The venue will be the Hotel Catalonia Plaza, Plaza España (Barcelona). More information will be posted soon. For questions, please contact lhcp2013@ifae.es.

  9. 78 FR 73880 - Proposal To Withdraw Spatial Data Transfer Standard, Parts 1-7

    Science.gov (United States)

    2013-12-09

    ... precision National Geodetic Survey (NGS) geodetic network control point data and Bureau of Land Management (BLM) survey point data can use this profile. The NGS is the maintenance authority for Part 6. The NGS no longer supports download of NGS datasheets in SDTS format. The NGS now offers users the ability...

  10. Preseismic oscillating electric field "strange attractor like" precursor, of T = 6 months, triggered by Ssa tidal wave. Application on large (Ms > 6.0R) EQs in Greece (October 1st, 2006 - December 2nd, 2008)

    CERN Document Server

    Thanassoulas, C; Verveniotis, G; Zymaris, N

    2009-01-01

    In this work the preseismic "strange attractor like" precursor is studied, in the domain of the Earth's oscillating electric field for T = 6 months. It is assumed that the specific oscillating electric field is generated by the corresponding lithospheric oscillation, triggered by the Ssa tidal wave of the same wave length (6 months) under excess strain load conditions met in the focal area of a future large earthquake. The analysis of the recorded Earth's oscillating electric field by the two distant monitoring sites of PYR and HIO and for a period of time of 26 months (October 1st, 2006 - December 2nd, 2008) suggests that the specific precursor can successfully resolve the predictive time window in terms of months and for a "swarm" of large EQs (Ms > 6.0R), in contrast to the resolution obtained by the use of electric fields of shorter (T = 1, 14 days, single EQ identification) wave length. More over, the fractal character of the "strange attractor like" precursor in the frequency domain is pointed out. Fina...

  11. Different Forms Aluminum Contents in the Soil of the 1st and 2nd Generation Pinus massoniana Plantations%1,2代马尾松林土壤不同形态铝含量

    Institute of Scientific and Technical Information of China (English)

    仝雅娜; 丁贵杰

    2012-01-01

    pH and aluminum content in different forms in the soil of the 1st and 2nd generation Pinus massoniana plantations were investigated. The results showed that pH decreased with the stand age and successive rotation increase. Both the exchangeable aluminum and the soluble aluminum content increased with the stand age and successive rotation increase. Humic acid aluminum and organic complexation state aluminum decreased with the increase of successive rotation. Hydroxy monomer aluminum and acid soluble inorganic aluminum had no significant change, and had little effect on soil acidification.%分析1,2代马尾松林地土壤pH值和不同形态铝含量.结果表明:土壤pH值随林龄增加和连栽而下降;交换性铝和可溶性铝含量均随林龄增加和连栽而增加;腐殖酸铝和有机络合态铝含量随连栽而降低;单聚体羟基铝和酸溶无机铝含量无明显变化规律,且对土壤酸化影响不大.

  12. 2014 Female Athlete Triad Coalition Consensus Statement on Treatment and Return to Play of the Female Athlete Triad: 1st International Conference held in San Francisco, California, May 2012 and 2nd International Conference held in Indianapolis, Indiana, May 2013.

    Science.gov (United States)

    De Souza, Mary Jane; Nattiv, Aurelia; Joy, Elizabeth; Misra, Madhusmita; Williams, Nancy I; Mallinson, Rebecca J; Gibbs, Jenna C; Olmsted, Marion; Goolsby, Marci; Matheson, Gordon

    2014-02-01

    The Female Athlete Triad is a medical condition often observed in physically active girls and women, and involves three components: (1) low energy availability with or without disordered eating, (2) menstrual dysfunction and (3) low bone mineral density. Female athletes often present with one or more of the three Triad components, and an early intervention is essential to prevent its progression to serious endpoints that include clinical eating disorders, amenorrhoea and osteoporosis. This consensus statement represents a set of recommendations developed following the 1st (San Francisco, California, USA) and 2nd (Indianapolis, Indiana, USA) International Symposia on the Female Athlete Triad. It is intended to provide clinical guidelines for physicians, athletic trainers and other healthcare providers for the screening, diagnosis and treatment of the Female Athlete Triad and to provide clear recommendations for return to play. The 2014 Female Athlete Triad Coalition Consensus Statement on Treatment and Return to Play of the Female Athlete Triad expert panel has proposed a risk stratification point system that takes into account magnitude of risk to assist the physician in decision-making regarding sport participation, clearance and return to play. Guidelines are offered for clearance categories, management by a multidisciplinary team and implementation of treatment contracts. This consensus paper has been endorsed by the Female Athlete Triad Coalition, an International Consortium of leading Triad researchers, physicians and other healthcare professionals, the American College of Sports Medicine and the American Medical Society for Sports Medicine.

  13. 中心与周边-从地缘学看新疆双年展%Center and Periphery:An Geopolitical Interpretation of the 1st International Art Exhibition of Xinjiang Biennale

    Institute of Scientific and Technical Information of China (English)

    彭锋

    2014-01-01

    新疆在地缘政治学上具有重要意义。随着未来欧亚高铁的开通,新疆将再现往日扮演的欧亚交通的桥梁的作用,乌鲁木齐将成为新的丝绸之路上的明珠。首届中国新疆国际艺术双年展采取了“相遇丝绸之路”的主题,旨在用地缘政治学来诠释当代艺术和组织展览。中亚各国和新疆本地艺术家的积极参与,让本届新疆双年展独具特色。%Xinjiang is very important in geopolitics. With the launch of high-speed rail lines which wil connect China and Europe in the near future, Xinjiang wil be the bridge connecting Asia and Europe as it did in the history, and the capital Urumqi wil be a bright pearl shinning on the new silk road in this global age. The 1st international art exhibition was organized under the theme “Encounterings on the Silk Road,” that was aimed at interpret contemporary art with geopolitics. The participation of artists from Central Asia and Xinjiang province made the biennale very different.

  14. Preseismic electric field "strange attractor" like precursor analysis applied on large (Ms > 5.5R) EQs, which occurred in Greece during December 1st, 2007 - April 30th, 2008

    CERN Document Server

    Thanassoulas, C; Verveniotis, G; Zymaris, N

    2008-01-01

    In order to investigate the capability of the preseismic electric field "strange attractor like" precursor as a time predictor of a large EQ within a short time window (short-term prediction), the specific methodology was applied on the Earth's electric field recorded during a rather long seismically active period (December 1st, 2007 - April 30th, 2008) of Greece. During this period of time a number (8) of large (Ms > 5.5R) earthquakes took place. The particular analysis is presented in detail for the following EQs: the Monemvasia EQ (January 6th 2008, Ms = 6.6R), the Methoni EQs (February 14th 2008 Ms = 6.7R, February 19th 2008 Ms = 5.6R, February 20th 2008 Ms = 6.5R, February 26th 2008 Ms = 5.7R), the Skyros EQ (March 19th 2008 Ms = 5.5R) and the Mid Southern Creta EQ (March 28th 2008 Ms = 5.6R). The obtained results from the analysis of the afore mentioned EQs, in conjunction to the ones obtained from an earlier presentation of the particular methodology (Thanassoulas et al. 2008a), suggest: an average tim...

  15. Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015; Session “Circulation, O2 Transport and Haematology”

    Directory of Open Access Journals (Sweden)

    Various Authors

    2015-09-01

    Full Text Available Selected Abstracts of the 1st Congress of joint European Neonatal Societies (jENS 2015; Budapest (Hungary; September 16-20, 2015ORGANIZING INSTITUTIONSEuropean Society for Neonatology (ESN, European Society for Paediatric Research (ESPR, Union of European Neonatal & Perinatal Societies (UENPS, European Foundation for the Care of Newborn Infants (EFCNI, with the local host of Hungarian Society of Perinatology and Obstetric Anesthesiology, Hungarian Society of Perinatology (MPT, supported by Council of International Neonatal Nurses (COINN, organizing secretariat MCA Scientific EventsPROGRAMME COMMITTEEArtúr Beke (Hungarian Society, Morten Breindahl (ESN, Giuseppe Buonocore (UENPS, Pierre Gressens (ESPR, Silke Mader (EFCNI, Manuel Sánchez Luna (UENPS, Miklós Szabó (Hungarian Society of Perinatology, Luc Zimmermann (ESPR Session “Circulation, O2 Transport and Haematology”ABS 1. TRANSITIONAL CHANGES IN CEREBRAL BLOOD VOLUME OF TERM AND PRETERM INFANTS WITH AND WITHOUT RESPIRATORY SUPPORT AFTER BIRTH • B. Schwaberger, G. Pichler, A. Avian, C. Binder-Heschl, N. Baik, B. UrlesbergerABS 2. HEMATOLOGIC ABNORMALITIES IN THE FIRST 72 HOURS OF LIFE IN SMALL-FOR-GESTATIONAL-AGE PRETERM NEWBORNS • A. Matic, A. RistivojevicABS 3. THE ANTICOAGULANT ACTION OF ACTIVATED PROTEIN C IN VERY PRETERM INFANTS • E. Neary, N. McCallion, B. Kevane, K. Egan, M. Cotter, F. Ni AinleABS 4. SURVIVAL AFTER CARDIAC ARREST IN THE NEONATAL INTENSIVE CARE UNIT • E. Foglia, R. Langeveld, L. Heimall, A. Deveney, A. Ades, E. JensenABS 5. A PATENT DUCTUS ARTERIOSUS SEVERITY SCORE INCORPORATING MARKERS OF HAEMODYNAMIC SIGNIFICANCE AND LEFT VENTRICLE DIASTOLIC FUNCTION PREDICTS CHRONIC LUNG DISEASE • A.T. James, J.D. Corcoran, P. Dicker, O. Franklin, Y.N. Elsayed, J. Ting, A. Sehgal, A. Malikawi, A. Harabor, A.S. Soraisham, P.J. McNamaraABS 6. A STUDY TO VALIDATE THE DURATION OF ASSESSMENT OF BASELINE NIRS VALUES IN PRETERM BABIES WITH ECHOCARDIOGRAPHICALLY

  16. Engineering surveying

    CERN Document Server

    Schofield, W

    2001-01-01

    The aim of Engineering Surveying has always been to impart and develop a clear understanding of the basic topics of the subject. The author has fully revised the book to make it the most up-to-date and relevant textbook available on the subject.The book also contains the latest information on trigonometric levelling, total stations and one-person measuring systems. A new chapter on satellites ensures a firm grasp of this vitally important topic.The text covers engineering surveying modules for civil engineering students on degree courses and forms a reference for the engineering surveying module in land surveying courses. It will also prove to be a valuable reference for practitioners.* Simple clear introduction to surveying for engineers* Explains key techniques and methods* Details reading systems and satellite position fixing

  17. The Outer Solar System Origins Survey (OSSOS): Survey Status and Highlights

    Science.gov (United States)

    Kavelaars, J. J.; Bannister, Michele T.; Alexandersen, Mike; Chen, Ying-Tung; Gladman, Brett; Gwyn, Stephen; Petit, Jean-Marc; Volk, Kathryn; OSSOS Collaboration

    2016-10-01

    We report the discovery, tracking and detection circumstances for 562 trans- Neptunian objects (TNOs) from the first 128 deg2 of the Outer Solar System Origins Survey (OSSOS). This ongoing r-band Solar System survey uses the ~1 deg2 field-of-view MegaPrime camera on the 3.6 m Canada-France-Hawaii Telescope. The orbital elements for these TNOs are precise to a fractional semi-major axis uncertainty of between 0.1 - 0.01%. We achieve this precision in just two oppositions, as compared to the normal 3--5 oppositions, via a dense observing cadence and innovative astrometric technique. These discoveries are free of ephemeris bias, a first for large trans-Neptunian surveys. Using the current OSSOS sample we confirm the existence of a cold "kernel" of objects within the main cold classical Kuiper belt, and infer the existence of an extension of the "stirred" cold classical Kuiper belt to at least several AU beyond the 2 :1 mean motion resonance with Neptune. We find that the population model of Petit et al. (2011) provides a plausible 1st order representation of the Kuiper belt, but more detailed structure has begun to emerged. The full survey, to be completed in 2017, will provide an exquisitely characterized sample of important resonant TNO populations, ideal for testing models of giant planet migration during the early history of the Solar System.

  18. 1st September 2010 - British Vice-Chancellor, Liverpool University Sir Newby and Lady Newby signing the Guest Book with Head of International Relations F. Pauss; visiting the LHC superconducting magnet test hall with P. Cruikshank; accompanied by Beams Department Head P. Collier and Liverpool University T. Bowcock and P. Allport.

    CERN Multimedia

    Maximilien Brice

    2010-01-01

    1st September 2010 - British Vice-Chancellor, Liverpool University Sir Newby and Lady Newby signing the Guest Book with Head of International Relations F. Pauss; visiting the LHC superconducting magnet test hall with P. Cruikshank; accompanied by Beams Department Head P. Collier and Liverpool University T. Bowcock and P. Allport.

  19. Bathymetric survey of the Brandon Road Dam Spillway, Joliet, Illinois

    Science.gov (United States)

    Engel, Frank; Krahulik, Justin

    2016-01-01

    Bathymetric survey data of the Brandon Road Dam spillway was collected on May 27 and May 28, 2015 by the US Geological Survey (USGS) using Trimble Real-Time Kinematic Global Positioning System (RTK-GPS) equipment. The base station was set up over a temporarily installed survey pin on both days. This pin was surveyed into an existing NGS benchmark (PID: BBCN12) within the Brandon Road Lock property. In wadeable sections, a GPS rover with 2.0 meter range pole and flat-foot was deployed. In sections unable to be waded, a 2.0 meter range pole was fix-mounted to a jon boat, and a boat-mounted Acoustic Doppler Current Profiler (ADCP) was used to collect the depth data. ADCP depth data were reviewed in the WinRiver II software and exported for processing with the Velocity Mapping Toolbox (Parsons and others, 2013). The RTK-GPS survey points of the water surface elevations were used to convert ADCP-measured depths into bed elevations. An InSitu Level Troll collected 1-minute water level data throughout the two day survey. These data were used to verify that a flat-pool assumption was reasonable for the conversion of the ADCP data to bed elevations given the measurement precision of the ADCP. An OPUS solution was acquired for each survey day.Parsons, D. R., Jackson, P. R., Czuba, J. A., Engel, F. L., Rhoads, B. L., Oberg, K. A., Best, J. L., Mueller, D. S., Johnson, K. K. and Riley, J. D. (2013), Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements. Earth Surf. Process. Landforms, 38: 1244–1260. doi: 10.1002/esp.3367

  20. Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards.

    Science.gov (United States)

    Baptista, Paula; Reis, Francisca; Pereira, Eric; Tavares, Rui M; Santos, Pedro M; Richard, Franck; Selosse, Marc-André; Lino-Neto, Teresa

    2015-12-01

    Fungal diversity in Mediterranean forest soils is poorly documented, particularly when considering saprobic and pathogenic organisms. Next-generation sequencing (NGS) methods applied to soil fungi provide the opportunity to unveil the most inconspicuous functional guilds (e.g. saprobes) and life forms (e.g. Corticiaceae) of this tremendous diversity. We used fruitbody surveys over 2 years and soil 454 metabarcoding in Castanea sativa orchards to evaluate respectively the reproductive (fruitbodies) and vegetative (mycelia) parts of fungal communities in three 100-year-old stands. Analysis of 839 fruitbodies and 210 291 ITS1 reads revealed high fungal diversity, mainly shown by belowground analysis, with high (dominant) abundance of mycorrhizal fruitbodies and reads. Both methods displayed contrasted composition and structure of fungal communities, with Basidio- and Ascomycetes dominating above- and belowground, respectively. For the two dominant fungal guilds (i.e. ectomycorrhizal and saprobic), diversity above- and belowground overlapped weakly. This study is the first assessment of the complementarity of fruitbody surveys and NGS for analysing fungal diversity in Mediterranean ecosystems and shows that belowground methods still need to be completed by fruiting diversity to provide a comprehensive overview of the different fungal guilds. The results shed light on chestnut soil biodiversity and question the spatial distribution and synergies among fungal guilds.