Sample records for reverse genetic applications

  1. Flavivirus reverse genetic systems, construction techniques and applications: a historical perspective.

    PubMed

    Aubry, Fabien; Nougairède, Antoine; Gould, Ernest A; de Lamballerie, Xavier

    2015-02-01

    The study of flaviviruses, which cause some of the most important emerging tropical and sub-tropical human arbovirus diseases, has greatly benefited from the use of reverse genetic systems since its first development for yellow fever virus in 1989. Reverse genetics technology has completely revolutionized the study of these viruses, making it possible to manipulate their genomes and evaluate the direct effects of these changes on their biology and pathogenesis. The most commonly used reverse genetics system is the infectious clone technology. Whilst flavivirus infectious clones provide a powerful tool, their construction as full-length cDNA molecules in bacterial vectors can be problematic, laborious and time consuming, because they are often unstable, contain unwanted induced substitutions and may be toxic for bacteria due to viral protein expression. The incredible technological advances that have been made during the past 30years, such as the use of PCR or new sequencing methods, have allowed the development of new approaches to improve preexisting systems or elaborate new strategies that overcome these problems. This review summarizes the evolution and major technical breakthroughs in the development of flavivirus reverse genetics technologies and their application to the further understanding and control of these viruses and their diseases. PMID:25512228

  2. Application of Reverse Genetics for Producing Attenuated Vaccine Strains against Highly Pathogenic Avian Influenza Viruses

    PubMed Central

    UCHIDA, Yuko; TAKEMAE, Nobuhiro; SAITO, Takehiko

    2014-01-01

    ABSTRACT In this study, reverse genetics was applied to produce vaccine candidate strains against highly pathogenic avian influenza viruses (HPAIVs) of the H5N1 subtype. The H5 subtype vaccine strains were generated by a reverse genetics method in a biosafety level 2 facility. The strain contained the HA gene from the H5N1 subtype HPAIV attenuated by genetic modification at the cleavage site, the NA gene derived from the H5N1 subtype HPAI or the H5N3 subtype of avian influenza virus and internal genes from A/Puerto Rico/8/34. Vaccination with an inactivated recombinant virus with oil-emulsion completely protected chickens from a homologous viral challenge with a 640 HAU or 3,200 HAU/vaccination dose. Vaccination with a higher dose of antigen, 3,200 HAU, was effective at increasing survival and efficiently reduced viral shedding even when challenged by a virus of a different HA clade. The feasibility of differentiation of infected from vaccinated animals (DIVA) was demonstrated against a challenge with H5N1 HPAIVs when the recombinant H5N3 subtype viruses were used as the antigens of the vaccine. Our study demonstrated that the use of reverse genetics would be an option to promptly produce an inactivated vaccine with better matching of antigenicity to a circulating strain. PMID:24805906

  3. RNA Virus Reverse Genetics and Vaccine Design

    PubMed Central

    Stobart, Christopher C.; Moore, Martin L.

    2014-01-01

    RNA viruses are capable of rapid spread and severe or potentially lethal disease in both animals and humans. The development of reverse genetics systems for manipulation and study of RNA virus genomes has provided platforms for designing and optimizing viral mutants for vaccine development. Here, we review the impact of RNA virus reverse genetics systems on past and current efforts to design effective and safe viral therapeutics and vaccines. PMID:24967693

  4. Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals

    PubMed Central

    Barkley, N.A; Wang, M.L

    2008-01-01

    With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed. PMID:19452039

  5. Establishment of Canine RNA Polymerase I-Driven Reverse Genetics for Influenza A Virus: Its Application for H5N1 Vaccine Production

    Microsoft Academic Search

    Shin Murakami; Taisuke Horimoto; Shinya Yamada; Satoshi Kakugawa; Hideo Goto; Yoshihiro Kawaoka

    2008-01-01

    In the event of a new influenza pandemic, vaccines whose antigenicities match those of circulating strains must be rapidly produced. Here, we established an alternative reverse genetics system for influenza virus using the canine polymerase I (PolI) promoter sequence that works efficiently in the Madin-Darby canine kidney cell line, a cell line approved for human vaccine production. Using this system,

  6. Biomimetic Evolutionary Reverse Engineering of Genetic Regulatory Networks

    Microsoft Academic Search

    Daniel Marbach; Claudio Mattiussi; Dario Floreano

    2007-01-01

    The eective reverse engineering of biochemical networks is one of the great challenges of systems biology. The contribution of this paper is two-fold: 1) We introduce a new method for reverse engineering genetic regulatory networks from gene expression data; 2) We demon- strate how nonlinear gene networks can be inferred from steady-state data alone. The reverse engineering method is based

  7. Time Reversing Waves For Biomedical Applications

    Microsoft Academic Search

    Mickael Tanter; Mathias Fink

    Time reversal is a concept that always fascinated the majority of scientists. In fact, this fundamental symmetry of physics, the time reversal invariance, can be exploited in the domain of wave physics, in acoustics and more recently in electromagnetism, leading to a huge variety of experiments and instruments both for fundamental physics and applications. Today, these applications go from medical

  8. Revolution, Revision or Reversal: Genetics - Ethics Curriculum.

    ERIC Educational Resources Information Center

    Blake, Deborah D.

    1994-01-01

    Reviews three pioneer programs that attempt to integrate genetic science and ethics in the classroom. Concludes by suggesting that the basic goal of integrating science and ethics is undermined in each program by a lack of correspondence between the articulated pedagogical goals and the unarticulated theoretical framework. (LZ)

  9. Reverse genetics through random mutagenesis in Histoplasma capsulatum

    Microsoft Academic Search

    Brian H Youseff; Julie A Dougherty; Chad A Rappleye

    2009-01-01

    BACKGROUND: The dimorphic fungal pathogen Histoplasma capsulatum causes respiratory and systemic disease in humans and other mammals. Progress in understanding the mechanisms underlying the biology and the pathogenesis of Histoplasma has been hindered by a shortage of methodologies for mutating a gene of interest. RESULTS: We describe a reverse genetics process that combines the random mutagenesis of Agrobacterium-mediated transformation with

  10. REVERSE ENGINEERING AND AUTOMATIC SYNTHESIS OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING

    E-print Network

    Fernandez, Thomas

    REVERSE ENGINEERING AND AUTOMATIC SYNTHESIS OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC of Medicine Department of Electrical Engineering Stanford University, Stanford, California, koza (reverse engineer) a network of chemical reactions from observed time-domain data. Genetic programming

  11. Forward and reverse genetics of rapid-cycling Brassica oleracea

    Microsoft Academic Search

    Edward Himelblau; Erin J. Gilchrist; Kelly Buono; Colleen Bizzell; Laurie Mentzer; Robert Vogelzang; Thomas Osborn; Richard M. Amasino; Isobel A. P. Parkin; George W. Haughn

    2009-01-01

    Seeds of rapid-cycling Brassica oleracea were mutagenized with the chemical mutagen, ethylmethane sulfonate. The reverse genetics technique, TILLING, was used on\\u000a a sample population of 1,000 plants, to determine the mutation profile. The spectrum and frequency of mutations induced by\\u000a ethylmethane sulfonate was similar to that seen in other diploid species such as Arabidopsis thaliana. These data indicate that the

  12. see reverse side for application timeline Robinson Scholarship Application Instructions

    E-print Network

    Hayes, Jane E.

    see reverse side for application timeline Robinson Scholarship Application Instructions Application, room and board, and book allowance is available for each of the 29 counties services by the Robinson service and school involvement, participation in Robinson Scholars enrichment activities, writing ability

  13. Chloroquine Susceptibility and Reversibility in a Plasmodium falciparum Genetic Cross

    PubMed Central

    Patel, Jigar J.; Thacker, Drew; Tan, John C.; Pleeter, Perri; Checkley, Lisa; Gonzales, Joseph M.; Deng, Bingbing; Roepe, Paul D.; Cooper, Roland A.; Ferdig, Michael T.

    2011-01-01

    Summary Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT), are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 × Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the Southeast Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute with the pfcrt and pfmdr1 loci to influence CQR levels. Chemoreversal via a wide range of chemical structures operates through a direct pfcrt-based mechanism. Direct inhibition of parasite growth by these reversal agents is influenced by pfcrt mutations and additional loci. Direct labeling of purified recombinant PfMDR1 protein with a highly specific photoaffinity CQ analogue, and lack of competition for photolabeling by VP, supports our QTL predictions. We find no evidence that pfmdr1 copy number affects CQ response in the progeny, however, inheritance patterns indicate that an allele-specific interaction between pfmdr1 and pfcrt is part of the complex genetic background of CQR. PMID:20807203

  14. Reverse Engineering iOS Mobile Applications Mona Erfani Joorabchi

    E-print Network

    Mesbah, Ali

    Reverse Engineering iOS Mobile Applications Mona Erfani Joorabchi University of British Columbia that automatically (1) hooks into, dynamically runs, and analyzes a given iOS mobile application, (2) exercises its mobile application. Keywords-reverse engineering; mobile applications; iOS; model generation II

  15. A Genetic Approach with a Simple Fitness Function for Sorting Unsigned Permutations by Reversals

    E-print Network

    Ayala-Rincón, Mauricio

    A Genetic Approach with a Simple Fitness Function for Sorting Unsigned Permutations by Reversals proposed. In this paper we propose a new genetic algorithm approach that uses modified crossover and mutation operators adapted to the problem. Instead previous genetic algorithmic approaches, the proposed

  16. Deletion-Based Reverse Genetics in Medicago truncatula1[W][OA

    PubMed Central

    Rogers, Christian; Wen, Jiangqi; Chen, Rujin; Oldroyd, Giles

    2009-01-01

    The primary goal of reverse genetics, the identification of null mutations in targeted genes, is achieved through screening large populations of randomly mutagenized plants. T-DNA and transposon-based mutagenesis has been widely employed but is limited to species in which transformation and tissue culture are efficient. In other species, TILLING (for Targeting Induced Local Lesions IN Genomes), based on chemical mutagenesis, has provided an efficient method for the identification of single base pair mutations, only 5% of which will be null mutations. Furthermore, the efficiency of inducing point mutations, like insertion-based mutations, is dependent on target size. Here, we describe an alternative reverse genetic strategy based on physically induced genomic deletions that, independent of target size, exclusively recovers knockout mutants. Deletion TILLING (De-TILLING) employs fast neutron mutagenesis and a sensitive polymerase chain reaction-based detection. A population of 156,000 Medicago truncatula plants has been structured as 13 towers each representing 12,000 M2 plants. The De-TILLING strategy allows a single tower to be screened using just four polymerase chain reaction reactions. Dual screening and three-dimensional pooling allows efficient location of mutants from within the towers. With this method, we have demonstrated the detection of mutants from this population at a rate of 29% using five targets per gene. This De-TILLING reverse genetic strategy is independent of tissue culture and efficient plant transformation and therefore applicable to any plant species. De-TILLING mutants offer advantages for crop improvement as they possess relatively few background mutations and no exogenous DNA. PMID:19759346

  17. Reverse genetics of rabies virus: new strategies to attenuate virus virulence for vaccine development.

    PubMed

    Zhu, Shimao; Li, Hui; Wang, Chunhua; Luo, Farui; Guo, Caiping

    2015-08-01

    Rabies is an ancient neurological disease that is almost invariably fatal once the clinical symptoms develop. Currently, prompt wound cleansing after exposing to a potentially rabid animal and vaccination using rabies vaccine combined with administration of rabies immune globulin are the only effective methods for post-exposure prophylaxis against rabies. Reverse genetic technique is a novel approach to investigate the function of a specific gene by analyzing the phenotypic effects through directly manipulating the gene sequences. It has revolutionized and provided a powerful tool to study the molecular biology of RNA viruses and has been widely used in rabies virus research. The attenuation of rabies virus virulence is the prerequisite for rabies vaccine development. Given the current challenge that sufficient and affordable high-quality vaccines are limited and lacking for global rabies prevention and control, highly cell-adapted, stable, and attenuated rabies viruses with broad cross-reactivity against different viral variants are ideal candidates for consideration to meet the need for human rabies control in the future. A number of approaches have been pursued to reduce the virulence of the virus and improve the safety of rabies vaccines. The application of reverse genetic technique has greatly advanced the engineering of rabies virus and paves the avenue for utilizing rabies virus for vaccine against rabies, viral vectors for exogenous antigen expression, and gene therapy in the future. PMID:25994916

  18. A Reverse Logistics Network Design Method Using Genetic Algorithm

    Microsoft Academic Search

    Jun Li; Jirong Wang

    2006-01-01

    Driven by ever growing concern to environments, legislative regulation and economic profitability, more and more firms pay attentions to physical design of reverse logistics networks. This paper considers the problem of determining the numbers and locations of centralized return centers (i.e., reverse consolidation points) where returned products from retailers or end-customers were collected, sorted and consolidated into a large shipment

  19. Reverse genetics systems as tools for the development of novel therapies against filoviruses.

    PubMed

    Hoenen, Thomas; Feldmann, Heinz

    2014-10-01

    Filoviruses cause severe hemorrhagic fevers with case fatality rates of up to 90%, for which no antivirals are currently available. Their categorization as biosafety level 4 agents restricts work with infectious viruses to a few maximum containment laboratories worldwide, which constitutes a significant obstacle for the development of countermeasures. Reverse genetics facilitates the generation of recombinant filoviruses, including reporter-expressing viruses, which have been increasingly used for drug screening and development in recent years. Further, reverse-genetics based lifecycle modeling systems allow modeling of the filovirus lifecycle without the need for a maximum containment laboratory and have recently been optimized for use in high-throughput assays. The availability of these reverse genetics-based tools will significantly improve our ability to find novel antivirals against filoviruses. PMID:25169588

  20. Analysis of photoregulation in a cyanobacterium through reverse genetics 

    E-print Network

    Cogdell, David Earl

    1997-01-01

    . As determined by the genetic interruption, the cloned response regulator srrB, is not involved in the transcriptional induction of the psbAII gene encoding the photosystem 11 reaction center protein DI under high-light conditions. No phenotype is known for srr...

  1. Reverse Genetics System for Mouse Hepatitis Virus Strain 1

    E-print Network

    Carter, Kristen

    2011-04-19

    fragments, which had been previously generated by the Baric lab. Once all seven genomic fragments are cloned, this work will allow for the genetic modification of the entire genome and will make it possible to identify and study the genes that have been...

  2. A TILLING Reverse Genetics Tool and a Web-Accessible Collection of Mutants of the Legume Lotus japonicus

    Microsoft Academic Search

    Jillian A. Perry; Trevor L. Wang; Tracey J. Welham; Sarah Gardner; Jodie M. Pike; Satoko Yoshida; Martin Parniske

    2003-01-01

    Reverse genetics aims to identify the function of a gene with known sequence by phenotypic analysis of cells or organisms in which the function of this gene is impaired. Commonly used strategies for reverse genetics encompass transposon mutagenesis (Tissier et al., 1999) and RNA-mediated gene silencing or RNA interference (Voinnet, 2002). We adopted a complementary strategy to set up a

  3. Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipe sh

    E-print Network

    Avise, John

    Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipe sh Adam G, USA Due to the phenomenon of male pregnancy, the ¢sh family Syngnathidae (seahorses and pipe¢shes) has assemblage of pipe¢shes or seahorses in order to demonstrate conclusively that sexual selection acts most

  4. Rapid Genetic Diagnosis With the Transcription—Reverse Transcription Concerted Reaction System for Cancer Micrometastasis

    Microsoft Academic Search

    Takaaki Ishii; Yoshiyuki Fujiwara; Satoru Ohnaka; Toshinori Hayashi; Hirokazu Taniguchi; Shuji Takiguchi; Takushi Yasuda; Masahiko Yano; Morito Monden

    2004-01-01

    Background: Detection of cancer micrometastases is required for improvement of cancer therapy. The aim of this study was to establish a rapid and practical genetic assay to detect micrometastasis in gastric cancer and to assess its clinical significance with respect to prognosis. Methods: A novel RNA amplification system with transcription–reverse transcription concerted reaction (TRC) was introduced for quantitative detection of

  5. Pharmacological or Genetic Inactivation of the Serotonin Transporter Improves Reversal Learning in Mice

    PubMed Central

    Mathur, Poonam; Harvey-White, Judith; Izquierdo, Alicia; Saksida, Lisa M.; Bussey, Timothy J.; Fox, Stephanie; Deneris, Evan; Murphy, Dennis L.; Holmes, Andrew

    2010-01-01

    Growing evidence supports a major contribution of cortical serotonin (5-hydroxytryptamine, 5-HT) to the modulation of cognitive flexibility and the cognitive inflexibility evident in neuropsychiatric disorders. The precise role of 5-HT and the influence of 5-HT gene variation in mediating this process is not fully understood. Using a touch screen–based operant system, we assessed reversal of a pairwise visual discrimination as an assay for cognitive flexibility. Effects of constitutive genetic or pharmacological inactivation of the 5-HT transporter (5-HTT) on reversal were examined by testing 5-HTT null mice and chronic fluoxetine-treated C57BL/6J mice, respectively. Effects of constitutive genetic loss or acute pharmacological depletion of 5-HT were assessed by testing Pet-1 null mice and para-chlorophenylalanine (PCPA)–treated C57BL/6J mice, respectively. Fluoxetine-treated C57BL/6J mice made fewer errors than controls during the early phase of reversal when perseverative behavior is relatively high. 5-HTT null mice made fewer errors than controls in completing the reversal task. However, reversal in Pet-1 null and PCPA-treated C57BL/6J mice was not different from controls. These data further support an important role for 5-HT in modulating reversal learning and provide novel evidence that inactivating the 5-HTT improves this process. These findings could have important implications for understanding and treating cognitive inflexibility in neuropsychiatric disease. PMID:20032063

  6. THE FUTURE AND APPLICATIONS OF GENETIC ALGORITHMS

    Microsoft Academic Search

    Marcus Randall

    This paper presents a method of producing solutions to difficult problems based on the laws of natural selection. The method, known as the genetic algorithm, is described in detail and applied to the c art pole c ontrol problem. The future of genetic algorithms is discussed in terms of potential commercial application.

  7. Potato genetics, genomics, and applications

    PubMed Central

    Watanabe, Kazuo

    2015-01-01

    Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding. PMID:25931980

  8. Modeling of Flux Reversal Machines for direct drive applications

    Microsoft Academic Search

    Gianmario Pellegrino; Chris Gerada

    2011-01-01

    Flux Reversal Machines can be easy to manufacture, are reliable and well suited for direct-drive applications. They also have the advantage that they can be controlled as standard synchronous PM machines. As for most of doubly salient machines, the machine design is relatively complicated due to the highly non-linear magnetic behavior that makes it difficult to device a general optimal

  9. Reversible vectorisation of 3D digital planar curves and applications

    E-print Network

    Sivignon, Isabelle

    Reversible vectorisation of 3D digital planar curves and applications Isabelle Sivignon a,, Florent modelling exactly the digital surface. Key words: discrete polygon, 3D, vectorisation, modelling. 1 (called pixels in 2D, voxels in 3D). Corresponding Author. E-mail: isabelle.sivignon@liris.cnrs.fr - Tel

  10. Boron removal by reverse osmosis membranes in seawater desalination applications

    Microsoft Academic Search

    Kha L. Tu; Long D. Nghiem; Allan R. Chivas

    2010-01-01

    Rapid development of seawater desalination applications using membrane technology in recent years has reignited the issue of boron in drinking water. This is reflected by an increasing number of scientific investigations on the removal of boron by reverse osmosis (RO) and to a lesser extent by nanofiltration (NF) membranes over the last decade. This review provides a summary of the

  11. Sex reversal triggers the rapid transition from genetic to temperature-dependent sex.

    PubMed

    Holleley, Clare E; O'Meally, Denis; Sarre, Stephen D; Marshall Graves, Jennifer A; Ezaz, Tariq; Matsubara, Kazumi; Azad, Bhumika; Zhang, Xiuwen; Georges, Arthur

    2015-07-01

    Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination). Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene-environment interactions. Most mechanistic models of transitions invoke a role for sex reversal. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish and rarely in amphibians. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change. PMID:26135451

  12. Large-scale reverse docking profiles and their applications

    PubMed Central

    2012-01-01

    Background Reverse docking approaches have been explored in previous studies on drug discovery to overcome some problems in traditional virtual screening. However, current reverse docking approaches are problematic in that the target spaces of those studies were rather small, and their applications were limited to identifying new drug targets. In this study, we expanded the scope of target space to a set of all protein structures currently available and developed several new applications of reverse docking method. Results We generated 2D Matrix of docking scores among all the possible protein structures in yeast and human and 35 famous drugs. By clustering the docking profile data and then comparing them with fingerprint-based clustering of drugs, we first showed that our data contained accurate information on their chemical properties. Next, we showed that our method could be used to predict the druggability of target proteins. We also showed that a combination of sequence similarity and docking profile similarity could predict the enzyme EC numbers more accurately than sequence similarity alone. In two case studies, 5-flurouracil and cycloheximide, we showed that our method can successfully find identifying target proteins. Conclusions By using a large number of protein structures, we improved the sensitivity of reverse docking and showed that using as many protein structure as possible was important in finding real binding targets. PMID:23282219

  13. Reverse genetics for peste-des-petits-ruminants virus (PPRV): Promoter and protein specificities

    Microsoft Academic Search

    Dalan Bailey; Louisa S. Chard; Pradyot Dash; Tom Barrett; Ashley C. Banyard

    2007-01-01

    Peste-des-petits-ruminants virus (PPRV) (family Paramyxoviridae, genus Morbillivirus) causes an acute febrile illness in sheep and goats resulting in significant morbidity and mortality in infected herds. The paramyxoviruses all have negative sense, non-segmented RNA genomes and their host range and pathogenic determinants have been extensively studied using reverse genetics. This technology also enables a more rational approach to be taken with

  14. The genetic mating system of a sex-role-reversed pipefish ( Syngnathus typhle ): a molecular inquiry

    Microsoft Academic Search

    Adam G. Jones; Gunilla Rosenqvist; Anders Berglund; John C. Avise

    1999-01-01

    In the pipefish Syngnathus typhle as in other species of Syngnathidae, developing embryos are reared on the male's ventral surface. Although much laboratory\\u000a research has been directed toward understanding sexual selection in this sex-role-reversed species, few studies have addressed\\u000a the mating behavior of S. typhle in the wild, and none has capitalized upon the power of molecular genetic assays. Here

  15. Genetic engineering applications in animal breeding

    Microsoft Academic Search

    Hugo H. Montaldo

    2006-01-01

    Abbreviations: ES: embryonic stem cells ESR: estrogen receptor locus IGF-I: insulin-like growth factor I MAS: Marker-assisted selection QTL: quantitative trait loci This paper discusses the use of genetic engineering applications in animal breeding, including a description of the methods, their potential and current uses and ethical issues. Genetic engineering is the name of a group of techniques used to identify,

  16. Mouse models of cancer: Sleeping Beauty transposons for insertional mutagenesis screens and reverse genetic studies.

    PubMed

    Tschida, Barbara R; Largaespada, David A; Keng, Vincent W

    2014-03-01

    The genetic complexity and heterogeneity of cancer has posed a problem in designing rationally targeted therapies effective in a large proportion of human cancer. Genomic characterization of many cancer types has provided a staggering amount of data that needs to be interpreted to further our understanding of this disease. Forward genetic screening in mice using Sleeping Beauty (SB) based insertional mutagenesis is an effective method for candidate cancer gene discovery that can aid in distinguishing driver from passenger mutations in human cancer. This system has been adapted for unbiased screens to identify drivers of multiple cancer types. These screens have already identified hundreds of candidate cancer-promoting mutations. These can be used to develop new mouse models for further study, which may prove useful for therapeutic testing. SB technology may also hold the key for rapid generation of reverse genetic mouse models of cancer, and has already been used to model glioblastoma and liver cancer. PMID:24468652

  17. Forward and reverse mouse genetics through derivation of haploid embryonic stem cells

    PubMed Central

    Elling, Ulrich; Taubenschmid, Jasmin; Wirnsberger, Gerald; O'Malley, Ronan; Demers, Simon; Vanhaelen, Quentin; Shukalyuk, Andrey I.; Schmauss, Gerald; Schramek, Daniel; Schnuetgen, Frank; von Melchner, Harald; Ecker, Joseph R.; Stanford, William L.; Zuber, Johannes; Stark, Alexander; Penninger, Josef M.

    2014-01-01

    All somatic mammalian cells carry two copies of chromosomes (diploidy), whereas organisms with a single copy of their genome such as yeast provide a basis for recessive genetics. Here we report the generation of haploid mouse ES cell lines from parthenogenetic embryos. These cells carry 20 chromosomes, express stem cell markers, and develop into all germ-layers in vitro and in vivo. We also developed a reversible mutagenesis protocol that allows saturated genetic recessive screens and results in homozygous alleles. This system allowed us to generate the first knock-out cell line for the microRNA processing enzyme Drosha. In a forward genetic screen, we identified Gpr107 as a molecule essential for killing by ricin, a toxin being used as bioweapon. Our results open the possibility to combine the power of a haploid genome with pluripotency of embryonic stem cells to uncover fundamental biological processes in defined cell types at a genomic scale. PMID:22136931

  18. Mouse Models of Cancer: Sleeping Beauty Transposons for Insertional Mutagenesis Screens and Reverse Genetic Studies

    PubMed Central

    Tschida, Barbara R.; Largaespada, David A.; Keng, Vincent W.

    2014-01-01

    The genetic complexity and heterogeneity of cancer has posed a problem in designing rationally targeted therapies effective in a large proportion of human cancer. Genomic characterization of many cancer types has provided a staggering amount of data that needs to be interpreted to further our understanding of this disease. Forward genetic screening in mice using Sleeping Beauty (SB) based insertional mutagenesis is an effective method for candidate cancer gene discovery that can aid in distinguishing driver from passenger mutations in human cancer. This system has been adapted for unbiased screens to identify drivers of multiple cancer types. These screens have already identified hundreds of candidate cancer-promoting mutations. These can be used to develop new mouse models for further study, which may prove useful for therapeutic testing. SB technology may also hold the key for rapid generation of reverse genetic mouse models of cancer, and has already been used to model glioblastoma and liver cancer. PMID:24468652

  19. Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity on Arabidopsis Revealed by Association and Reverse Genetics

    PubMed Central

    Guy, Endrick; Genissel, Anne; Hajri, Ahmed; Chabannes, Matthieu; David, Perrine; Carrere, Sébastien; Lautier, Martine; Roux, Brice; Boureau, Tristan; Arlat, Matthieu; Poussier, Stéphane; Noël, Laurent D.

    2013-01-01

    ABSTRACT The pathogenic bacterium Xanthomonas campestris pv. campestris, the causal agent of black rot of Brassicaceae, manipulates the physiology and the innate immunity of its hosts. Association genetic and reverse-genetic analyses of a world panel of 45 X. campestris pv. campestris strains were used to gain understanding of the genetic basis of the bacterium’s pathogenicity to Arabidopsis thaliana. We found that the compositions of the minimal predicted type III secretome varied extensively, with 18 to 28 proteins per strain. There were clear differences in aggressiveness of those X. campestris pv. campestris strains on two Arabidopsis natural accessions. We identified 3 effector genes (xopAC, xopJ5, and xopAL2) and 67 amplified fragment length polymorphism (AFLP) markers that were associated with variations in disease symptoms. The nature and distribution of the AFLP markers remain to be determined, but we observed a low linkage disequilibrium level between predicted effectors and other significant markers, suggesting that additional genetic factors make a meaningful contribution to pathogenicity. Mutagenesis of type III effectors in X. campestris pv. campestris confirmed that xopAC functions as both a virulence and an avirulence gene in Arabidopsis and that xopAM functions as a second avirulence gene on plants of the Col-0 ecotype. However, we did not detect the effect of any other effector in the X. campestris pv. campestris 8004 strain, likely due to other genetic background effects. These results highlight the complex genetic basis of pathogenicity at the pathovar level and encourage us to challenge the agronomical relevance of some virulence determinants identified solely in model strains. PMID:23736288

  20. Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-Citrate Lyase in Arabidopsis W

    E-print Network

    Wurtele, Eve Syrkin

    Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-Citrate Lyase in Arabidopsis W Beth L. Fatland,a,b Basil J. Nikolau,b and Eve Syrkin Wurtelea,1 aDepartment of Genetics alterations associated with reduced ACL expression, indicating that the observed metabolic alterations

  1. Statistical Applications in Genetics and Molecular Biology

    E-print Network

    Babu, M. Madan

    Statistical Applications in Genetics and Molecular Biology Volume 5, Issue 1 2006 Article 5.gilks@mrc-bsu.cam.ac.uk Medical Research Council Laboratory of Molecular Biology, madanm@mrc-lmb.cam.ac.uk Medical Research Council Laboratory of Molecular Biology, sat@mrc-lmb.cam.ac.uk Copyright c 2006 The Berkeley Electronic

  2. Statistical Applications in Genetics and Molecular Biology

    E-print Network

    Spirtes, Peter

    Statistical Applications in Genetics and Molecular Biology Volume 3, Issue 1 2004 Article 25 of these sources of unreliability intrinsic to cDNA microarray design and use. KEYWORDS: Cross in their laboratories. This type of microarray is used extensively in nearly all areas of life sciences and biomedical

  3. Introduction to Genetic Engineering and Its Applications

    NSDL National Science Digital Library

    National Science Foundation GK-12 and Research Experience for Teachers (RET) Programs,

    Students learn how engineers apply their understanding of DNA to manipulate specific genes to produce desired traits, and how engineers have used this practice to address current problems facing humanity. They learn what genetic engineering means and examples of its applications, as well as moral and ethical problems related to its implementation. Students fill out a flow chart to list the methods to modify genes to create GMOs and example applications of bacteria, plant and animal GMOs.

  4. A Multi-Stage Reverse Logistics Network Problem by Using Hybrid Priority-Based Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Lee, Jeong-Eun; Gen, Mitsuo; Rhee, Kyong-Gu

    Today remanufacturing problem is one of the most important problems regarding to the environmental aspects of the recovery of used products and materials. Therefore, the reverse logistics is gaining become power and great potential for winning consumers in a more competitive context in the future. This paper considers the multi-stage reverse Logistics Network Problem (m-rLNP) while minimizing the total cost, which involves reverse logistics shipping cost and fixed cost of opening the disassembly centers and processing centers. In this study, we first formulate the m-rLNP model as a three-stage logistics network model. Following for solving this problem, we propose a Genetic Algorithm pri (GA) with priority-based encoding method consisting of two stages, and introduce a new crossover operator called Weight Mapping Crossover (WMX). Additionally also a heuristic approach is applied in the 3rd stage to ship of materials from processing center to manufacturer. Finally numerical experiments with various scales of the m-rLNP models demonstrate the effectiveness and efficiency of our approach by comparing with the recent researches.

  5. DNA marker technologies and their applications in aquaculture genetics

    Microsoft Academic Search

    Z. J. Liu; J. F. Cordes

    2004-01-01

    The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

  6. Randomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse Engineering of Protein and

    E-print Network

    Sontag, Eduardo

    in the reverse engineering of protein and gene networks. Our contributions are as follows: · We abstract problems investigated in this paper that arise out of reverse engineering of gene and protein networks canRandomized Approximation Algorithms for Set Multicover Problems with Applications to Reverse

  7. Applications of Time-Reversal Processing for Planetary Surface Communications

    NASA Technical Reports Server (NTRS)

    Barton, Richard J.

    2007-01-01

    Due to the power constraints imposed on wireless sensor and communication networks deployed on a planetary surface during exploration, energy efficient transfer of data becomes a critical issue. In situations where groups of nodes within a network are located in relatively close proximity, cooperative communication techniques can be utilized to improve the range, data rate, power efficiency, and lifetime of the network. In particular, if the point-to-point communication channels on the network are well modeled as frequency non-selective, distributed or cooperative beamforming can employed. For frequency-selective channels, beamforming itself is not generally appropriate, but a natural generalization of it, time-reversal communication (TRC), can still be effective. Time-reversal processing has been proposed and studied previously for other applications, including acoustical imaging, electromagnetic imaging, underwater acoustic communication, and wireless communication channels. In this paper, we study both the theoretical advantages and the experimental performance of cooperative TRC for wireless communication on planetary surfaces. We give a brief introduction to TRC and present several scenarios where TRC could be profitably employed during planetary exploration. We also present simulation results illustrating the performance of cooperative TRC employed in a complex multipath environment and discuss the optimality of cooperative TRC for data aggregation in wireless sensor networks

  8. Genetic Counseling Graduate Program Webinar: Preparing your GC Program Application

    E-print Network

    Finley Jr., Russell L.

    Genetic Counseling Graduate Program Webinar: Preparing your GC Program Application Friday, October 31st, 2014 1:00-2:30 PM EDT Are you applying to genetic counseling programs for fall 2015 admission for an interactive webinar where we will: · Review the genetic counseling program application and admission process

  9. Application of Genetic Algorithms in Seismic Tomography

    NASA Astrophysics Data System (ADS)

    Soupios, Pantelis; Akca, Irfan; Mpogiatzis, Petros; Basokur, Ahmet; Papazachos, Constantinos

    2010-05-01

    In the earth sciences several inverse problems that require data fitting and parameter estimation are nonlinear and can involve a large number of unknown parameters. Consequently, the application of analytical inversion or optimization techniques may be quite restrictive. In practice, most analytical methods are local in nature and rely on a linearized form of the problem in question, adopting an iterative procedure using partial derivatives to improve an initial model. This approach can lead to a dependence of the final model solution on the starting model and is prone to entrapment in local misfit minima. Moreover, the calculation of derivatives can be computationally inefficient and create instabilities when numerical approximations are used. In contrast to these local minimization methods, global techniques that do not rely on partial derivatives, are independent of the form of the data misfit criterion, and are computationally robust. Such methods often use random processes to sample a selected wider span of the model space. In this situation, randomly generated models are assessed in terms of their data-fitting quality and the process may be stopped after a certain number of acceptable models is identified or continued until a satisfactory data fit is achieved. A new class of methods known as genetic algorithms achieves the aforementioned approximation through novel model representation and manipulations. Genetic algorithms (GAs) were originally developed in the field of artificial intelligence by John Holland more than 20 years ago, but even in this field it is less than a decade that the methodology has been more generally applied and only recently did the methodology attract the attention of the earth sciences community. Applications have been generally concentrated in geophysics and in particular seismology. As awareness of genetic algorithms grows there surely will be many more and varied applications to earth science problems. In the present work, the application of hybrid genetic algorithms in seismic tomography is examined and the efficiency of least squares and genetic methods as representative of the local and global optimization, respectively, is presented and evaluated. The robustness of both optimization methods has been tested and compared for the same source-receiver geometry and characteristics of the model structure (anomalies, etc.). A set of seismic refraction synthetic (noise free) data was used for modeling. Specifically, cross-well, down-hole and typical refraction studies using 24 geophones and 5 shoots were used to confirm the applicability of the genetic algorithms in seismic tomography. To solve the forward modeling and estimate the traveltimes, the revisited ray bending method was used supplemented by an approximate computation of the first Fresnel volume. The root mean square (rms) error as the misfit function was used and calculated for the entire random velocity model for each generation. After the end of each generation and based on the misfit of the individuals (velocity models), the selection, crossover and mutation (typical process steps of genetic algorithms) were selected continuing the evolution theory and coding the new generation. To optimize the computation time, since the whole procedure is quite time consuming, the Matlab Distributed Computing Environment (MDCE) was used in a multicore engine. During the tests, we noticed that the fast convergence that the algorithm initially exhibits (first 5 generations) is followed by progressively slower improvements of the reconstructed velocity models. Thus, to improve the final tomographic models, a hybrid genetic algorithm (GA) approach was adopted by combining the GAs with a local optimization method after several generations, on the basis of the convergence of the resulting models. This approach is shown to be efficient, as it directs the solution search towards a model region close to the global minimum solution.

  10. Genome-Wide Association Mapping Combined with Reverse Genetics Identifies New Effectors of Low Water Potential-Induced Proline Accumulation in Arabidopsis1[W][OPEN

    PubMed Central

    Verslues, Paul E.; Lasky, Jesse R.; Juenger, Thomas E.; Liu, Tzu-Wen; Kumar, M. Nagaraj

    2014-01-01

    Arabidopsis (Arabidopsis thaliana) exhibits natural genetic variation in drought response, including varying levels of proline (Pro) accumulation under low water potential. As Pro accumulation is potentially important for stress tolerance and cellular redox control, we conducted a genome-wide association (GWAS) study of low water potential-induced Pro accumulation using a panel of natural accessions and publicly available single-nucleotide polymorphism (SNP) data sets. Candidate genomic regions were prioritized for subsequent study using metrics considering both the strength and spatial clustering of the association signal. These analyses found many candidate regions likely containing gene(s) influencing Pro accumulation. Reverse genetic analysis of several candidates identified new Pro effector genes, including thioredoxins and several genes encoding Universal Stress Protein A domain proteins. These new Pro effector genes further link Pro accumulation to cellular redox and energy status. Additional new Pro effector genes found include the mitochondrial protease LON1, ribosomal protein RPL24A, protein phosphatase 2A subunit A3, a MADS box protein, and a nucleoside triphosphate hydrolase. Several of these new Pro effector genes were from regions with multiple SNPs, each having moderate association with Pro accumulation. This pattern supports the use of summary approaches that incorporate clusters of SNP associations in addition to consideration of individual SNP probability values. Further GWAS-guided reverse genetics promises to find additional effectors of Pro accumulation. The combination of GWAS and reverse genetics to efficiently identify new effector genes may be especially applicable for traits difficult to analyze by other genetic screening methods. PMID:24218491

  11. All-in-One Bacmids: an Efficient Reverse Genetics Strategy for Influenza A Virus Vaccines

    PubMed Central

    Chen, Hongjun; Angel, Matthew; Li, Weizhong; Finch, Courtney; Gonzalez, Ana Silvia; Sutton, Troy; Santos, Jefferson

    2014-01-01

    ABSTRACT Vaccination is the first line of defense against influenza virus infection, yet influenza vaccine production methods are slow, antiquated, and expensive as a means to effectively reduce the virus burden during epidemic or pandemic periods. There is a great need for alternative influenza vaccines and vaccination methods with a global scale of impact. We demonstrate here a strategy to generate influenza A virus in vivo by using bacmid DNAs. Compared to the classical reverse genetics system, the “eight-in-one” bacmids (bcmd-RGFlu) showed higher efficiency of virus rescue in various cell types. Using a transfection-based inoculation (TBI) system, intranasal delivery to DBA/2J and BALB/c mice of bcmd-RGFlu plus 293T cells led to the generation of lethal PR8 virus in vivo. A prime-boost intranasal vaccination strategy using TBI in the context of a bcmd-RGFlu carrying a temperature-sensitive H1N1 virus resulted in protection of mice against lethal challenge with the PR8 strain. Taken together, these studies provide proof of principle to highlight the potential of vaccination against influenza virus by using in vivo reverse genetics. IMPORTANCE Vaccination is the first line of defense against influenza virus infections. A major drawback in the preparation of influenza vaccines is that production relies on a heavily time-consuming process of growing the viruses in eggs. We propose a radical change in the way influenza vaccination is approached, in which a recombinant bacmid, a shuttle vector that can be propagated in both Escherichia coli and insect cells, carries an influenza virus infectious clone (bcmd-RGFlu). Using a surrogate cell system, we found that intranasal delivery of bcmd-RGFlu resulted in generation of influenza virus in mice. Furthermore, mice vaccinated with this system were protected against lethal influenza virus challenge. The study serves as a proof of principle of a potentially universal vaccine platform against influenza virus and other pathogens. PMID:24942589

  12. Voltage shift phenomena introduced by reverse-bias application in multilayer organic light emitting diodes

    Microsoft Academic Search

    Dechun Zou; Tetsuo Tsutsui

    2000-01-01

    The effects of reverse-bias on the current-voltage (I-V) and luminance-voltage (L-V) properties of organic light-emitting diodes (OLEDs) were systematically measured. Shifts toward lower voltage both in I-V and L-V curves were observed for the OLEDs treated by reverse-bias application. The voltage-shift phenomena were discussed based on the effective drive voltage change induced by reverse bias application and the voltage-shift process

  13. Development of a Reverse Genetics System to Produce Live, Attenuated Infectious Salmon Anemia Virus (ISAV) Vaccine Candidates

    E-print Network

    1 Development of a Reverse Genetics System to Produce Live, Attenuated Infectious Salmon Anemia Grant Number: NA03NMF4270132 March 29, 2006 Abstract Infectious salmon anemia (ISA), induced by the viral causative agent infectious salmon anemia virus (ISAV), has had a large, negative economic impact

  14. Reverse Genetics Demonstrates that Proteolytic Processing of the Ebola Virus Glycoprotein Is Not Essential for Replication in Cell Culture

    Microsoft Academic Search

    Gabriele Neumann; Heinz Feldmann; Shinji Watanabe; Igor Lukashevich; Yoshihiro Kawaoka

    2002-01-01

    Ebola virus, a prime example of an emerging pathogen, causes fatal hemorrhagic fever in humans and in nonhuman primates. Identification of major determinants of Ebola virus pathogenicity has been hampered by the lack of effective strategies for experimental mutagenesis. Here we exploit a reverse genetics system that allows the generation of Ebola virus from cloned cDNA to engineer a mutant

  15. Universal Influenza B Virus Genomic Amplification Facilitates Sequencing, Diagnostics, and Reverse Genetics

    PubMed Central

    Zhou, Bin; Lin, Xudong; Wang, Wei; Halpin, Rebecca A.; Bera, Jayati; Stockwell, Timothy B.; Barr, Ian G.

    2014-01-01

    Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock. PMID:24501036

  16. A tunable and reversible platform for the intracellular formation of genetically engineered protein microdomains

    PubMed Central

    Pastuszka, Martha K.; Janib, Siti M.; Weitzhandler, Isaac; Okamoto, Curtis T.; Hamm-Alvarez, Sarah; MacKay, J. Andrew

    2012-01-01

    From mitochondria to the nuclear envelope, the controlled assembly of micro and nanostructures is essential for life; however, the level at which we can deliberately engineer the assembly of microstructures within intracellular environments remains primitive. To overcome this obstacle, we present a platform to reversibly assemble genetically-engineered protein microdomains (GEPMs) on the time scale of minutes within living cells. Biologically inspired from the human protein tropoelastin, these protein polymers form a secondary aqueous phase above a tunable transition temperature. This assembly process is easily manipulated to occur at or near physiological temperature by adjusting molecular weight and hydrophobicity. We fused protein polymers to green fluorescent protein (GFP) to visualize their behavior within the cytoplasm. While soluble, these polymers have a similar intracellular diffusion constant as cytosolic proteins at 7.4 ?m2/s; however, above their phase transition temperature, the proteins form distinct microdomains (0.1–2 ?m) with a reduced diffusion coefficient of 1.1 ?m2/s. Microdomain assembly and disassembly are both rapid processes with half-lives of 3.8 and 1.0 min respectively. Via selection of the protein polymer, the assembly temperature is tunable between 20 and 40 °C. This approach may be useful to control intracellular formation of genetically engineered proteins and protein complexes into concentrated microdomains. PMID:23088632

  17. Genetically modified plants for tactical systems applications

    NASA Astrophysics Data System (ADS)

    Stewart, C. Neal, Jr.

    2002-08-01

    Plants are ubiquitous in the environment and have the ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green light when excited by blue or UV light. In addition, my group and collaborators have developed methods to detect GFP in plants by contact instruments and at a standoff. There are several tactical uses for this technology. Some obvious applications are using plants as sentinels for detecting biological and chemical warfare agents or their derivatives from a remote platform, as well as detecting explosives. Another tactical application is covert monitoring using individual plants. Different methods to detect GFP in transgenic plants will be discussed.

  18. MULTIOBJECTIVES GENETIC SNAKES: APPLICATION ON AUDIO-VISUAL SPEECH RECOGNITION

    E-print Network

    Coello, Carlos A. Coello

    MULTIOBJECTIVES GENETIC SNAKES: APPLICATION ON AUDIO-VISUAL SPEECH RECOGNITION Renaud Séguier.Seguier@supelec.fr, Nicolas.Cladel@supelec.fr Abstract: We propose in this article a new optimization of Genetic Snakes (GS): Multiobjectives Genetics Snakes (MGS) faster and simpler to implement. They enable us to make converge two snakes

  19. Static Performance of Six Innovative Thrust Reverser Concepts for Subsonic Transport Applications: Summary of the NASA Langley Innovative Thrust Reverser Test Program

    NASA Technical Reports Server (NTRS)

    Asbury, Scott C.; Yetter, Jeffrey A.

    2000-01-01

    The NASA Langley Configuration Aerodynamics Branch has conducted an experimental investigation to study the static performance of innovative thrust reverser concepts applicable to high-bypass-ratio turbofan engines. Testing was conducted on a conventional separate-flow exhaust system configuration, a conventional cascade thrust reverser configuration, and six innovative thrust reverser configurations. The innovative thrust reverser configurations consisted of a cascade thrust reverser with porous fan-duct blocker, a blockerless thrust reverser, two core-mounted target thrust reversers, a multi-door crocodile thrust reverser, and a wing-mounted thrust reverser. Each of the innovative thrust reverser concepts offer potential weight savings and/or design simplifications over a conventional cascade thrust reverser design. Testing was conducted in the Jet-Exit Test Facility at NASA Langley Research Center using a 7.9%-scale exhaust system model with a fan-to-core bypass ratio of approximately 9.0. All tests were conducted with no external flow and cold, high-pressure air was used to simulate core and fan exhaust flows. Results show that the innovative thrust reverser concepts achieved thrust reverser performance levels which, when taking into account the potential for system simplification and reduced weight, may make them competitive with, or potentially more cost effective than current state-of-the-art thrust reverser systems.

  20. Development of a Cucumis sativus TILLinG Platform for Forward and Reverse Genetics

    PubMed Central

    Troadec, Christelle; Audigier, Pascal; Kumar, Anish P. K.; Chatterjee, Manash; Alsadon, Abdullah A.; Sadder, Monther T.; Wahb-Allah, Mahmoud A.; Al-Doss, Abdullah A.; Bendahmane, Abdelhafid

    2014-01-01

    Background Cucumber (Cucumis sativus) belongs to the Cucurbitaceae family that includes more than 800 species. The cucumber genome has been recently sequenced and annotated. Transcriptomics and genome sequencing of many plant genomes are providing information on candidate genes potentially related to agronomically important traits. To accelerate functional characterization of these genes in cucumber we have generated an EMS mutant population that can be used as a TILLinG platform for reverse genetics. Principal Findings A population of 3,331 M2 mutant seed families was generated using two EMS concentrations (0.5% and 0.75%). Genomic DNA was extracted from M2 families and eight-fold pooled for mutation detection by ENDO1 nuclease. To assess the quality of the mutant collection, we screened for induced mutations in five genes and identified 26 mutations. The average mutation rate was calculated as 1/1147?Kb giving rise to approximately 320 mutations per genome. We focused our characterization on three missense mutations, G33C, S238F and S249F identified in the CsACS2 sex determination gene. Protein modeling and crystallography studies predicted that mutation at G33 may affect the protein function, whereas mutations at S238 and S249 may not impair the protein function. As predicted, detailed phenotypic evaluation showed that the S238F and the S249F mutant lines had no sexual phenotype. In contrast, plants homozygous for the G33C mutation showed a complete sexual transition from monoecy to andromonoecy. This result demonstrates that TILLinG is a valuable tool for functional validation of gene function in crops recalcitrant to transgenic transformation. Conclusions We have developed a cucumber mutant population that can be used as an efficient reverse genetics tool. The cucumber TILLinG collection as well as the previously described melon TILLinG collection will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in cucurbits in general. PMID:24835852

  1. A Genetic Toolbox for Creating Reversible Ca2+-Sensitive Materials Shana Topp,, V. Prasad, Gianguido C. Cianci, Eric R. Weeks, and Justin P. Gallivan*,,

    E-print Network

    Weeks, Eric R.

    A Genetic Toolbox for Creating Reversible Ca2+-Sensitive Materials Shana Topp,,§ V. Prasad Here, we describe a genetic toolbox of natural and engineered protein modules that can be rationally anticipated that a fully genetic approach would provide several important advantages to creating

  2. A Reverse Engineering Methodology For Data Processing Applications

    Microsoft Academic Search

    Kit Kamper; Spencer Rugaber

    1994-01-01

    mfReverse engineering produces a high-level representation of a software systerom a low-level one. This paper describes a methodology for reverse engineeringddthat constructs an architectural design for a system from its source code and relateocumentation. The methodology makes use of several techniques normally used durcing the forward software development process as well as a new technique called SynhronizedRefinement. Synchronized Refinement is

  3. Theory and applications of time reversal and interferometric imaging

    Microsoft Academic Search

    Liliana Borcea; George Papanicolaou; Chrysoula Tsogka

    2003-01-01

    In time reversal, an array of transducers receives the signal emitted by a localized source, time reverses it and re-emits it into the medium. The emitted waves back-propagate to the source and tend to focus near it. In a homogeneous medium, the cross-range resolution of the refocused field at the source location is lgr0L\\/a, where lgr0 is the carrier wavelength,

  4. Application of time reverse modeling on ultrasonic non-destructive testing of concrete

    Microsoft Academic Search

    Erik H. Saenger; Georg Karl Kocur; Roman Jud; Manuel Torrilhon

    2011-01-01

    Time reverse modeling (TRM) is applied to localize and characterize acoustic emission using a numerical concrete model. Aim is to transform a method within exploration geophysics to non-destructive testing. In contrast to previous time reverse applications, no single event or first onset time identification is applied. The method is described from a mathematical point of view. So-called source TRM with

  5. Tradeoffs in the Application of Time-Reversed Acoustics to Tactile Stimulation

    E-print Network

    Hartmann, Mitra J. Z.

    Tradeoffs in the Application of Time-Reversed Acoustics to Tactile Stimulation Charles Hudin1 , Jos problem. We describe here the appli- cation of time-reversed acoustics to the creation of deformations and engineering tradeoffs of this approach and describe the results obtained from an experimental mock-up device

  6. Establishment of a Reverse Genetics System for Studying Human Bocavirus in Human Airway Epithelia

    PubMed Central

    Cheng, Fang; Luo, Yong; Shen, Weiran; Lei-Butters, Diana C. M.; Chen, Aaron Yun; Li, Yi; Tang, Liang; Söderlund-Venermo, Maria; Engelhardt, John F.; Qiu, Jianming

    2012-01-01

    Human bocavirus 1 (HBoV1) has been identified as one of the etiological agents of wheezing in young children with acute respiratory-tract infections. In this study, we have obtained the sequence of a full-length HBoV1 genome (including both termini) using viral DNA extracted from a nasopharyngeal aspirate of an infected patient, cloned the full-length HBoV1 genome, and demonstrated DNA replication, encapsidation of the ssDNA genome, and release of the HBoV1 virions from human embryonic kidney 293 cells. The HBoV1 virions generated from this cell line-based production system exhibits a typical icosahedral structure of approximately 26 nm in diameter, and is capable of productively infecting polarized primary human airway epithelia (HAE) from the apical surface. Infected HAE showed hallmarks of lung airway-tract injury, including disruption of the tight junction barrier, loss of cilia and epithelial cell hypertrophy. Notably, polarized HAE cultured from an immortalized airway epithelial cell line, CuFi-8 (originally derived from a cystic fibrosis patient), also supported productive infection of HBoV1. Thus, we have established a reverse genetics system and generated the first cell line-based culture system for the study of HBoV1 infection, which will significantly advance the study of HBoV1 replication and pathogenesis. PMID:22956907

  7. Development of reverse genetics for Ibaraki virus to produce viable VP6-tagged IBAV

    PubMed Central

    Matsuo, Eiko; Saeki, Keiichi; Roy, Polly; Kawano, Junichi

    2015-01-01

    Ibaraki virus (IBAV) is a member of the epizootic hemorrhagic disease virus (EHDV) serogroup, which belongs to the Orbivirus genus of the Reoviridae family. Although EHDV, including IBAV, represents an ongoing threat to livestock in the world, molecular mechanisms of EHDV replication and pathogenesis have been unclear. The reverse genetics (RG) system is one of the strong tools to understand molecular mechanisms of virus replication. Here, we developed a RG system for IBAV to identify the nonessential region of a minor structural protein, VP6, by generating VP6-truncated IBAV. Moreover, several tags were inserted into the truncated region to produce VP6-tagged IBAV. We demonstrated that all VP6-tagged IBAV could replicate in BHK cells in the absence of any helper VP6 protein. Further, tagged-VP6 proteins were first assembled into puncta in cells infected with VP6-tagged IBAV. Our data suggests that, in order to initiate primary replication, IBAV VP6 is likely to accumulate in some parts of infected cells to assemble efficiently into the primary replication complex (subcore).

  8. A plasmid-based reverse genetics system for influenza A virus.

    PubMed Central

    Pleschka, S; Jaskunas, R; Engelhardt, O G; Zürcher, T; Palese, P; García-Sastre, A

    1996-01-01

    A reverse genetics system for negative-strand RNA viruses was first successfully developed for influenza viruses. This technology involved the transfection of in vitro-reconstituted ribonucleoprotein (RNP) complexes into influenza virus-infected cells. We have now developed a method that allows intracellular reconstitution of RNP complexes from plasmid-based expression vectors. Expression of a viral RNA-like transcript is achieved from a plasmid containing a truncated human polymerase I (polI) promoter and a ribozyme sequence that generates the desired 3' end by autocatalytic cleavage. The polI-driven plasmid is cotransfected into human 293 cells with polII-responsive plasmids that express the viral PB1, PB2, PA, and NP proteins. This exclusively plasmid-driven system results in the efficient transcription and replication of the viral RNA-like reporter and allows the study of cis- and trans-acting signals involved in the transcription and replication of influenza virus RNAs. Using this system, we have also been able to rescue a synthetic neuraminidase gene into a recombinant influenza virus. This method represents a convenient alternative to the previously established RNP transfection system. PMID:8648766

  9. Time Reversed Acoustics and applications to earthquake location and salt dome flank imaging

    E-print Network

    Lu, Rongrong

    2008-01-01

    The objective of this thesis is to investigate the applications of Time Reversed Acoustics (TRA) to locate seismic sources and image subsurface structures. The back-propagation process of the TRA experiment can be divided ...

  10. Applications of Competitor RNA in Diagnostic Reverse Transcription-PCR

    Microsoft Academic Search

    Steven B. Kleiboeker

    2003-01-01

    Detection of RNA viruses by reverse transcription (RT)-PCR has proven to be a useful approach for the diagnosis of infections caused by many viral pathogens. However, adequate controls are required for each step of the RT-PCR protocol to ensure the accuracies of diagnostic test results. Heterologous competitor RNA can be used as a control for a number of different aspects

  11. Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia

    PubMed Central

    Vallat, Laurent; Kemper, Corey A.; Jung, Nicolas; Maumy-Bertrand, Myriam; Bertrand, Frédéric; Meyer, Nicolas; Pocheville, Arnaud; Fisher, John W.; Gribben, John G.; Bahram, Seiamak

    2013-01-01

    Cellular behavior is sustained by genetic programs that are progressively disrupted in pathological conditions—notably, cancer. High-throughput gene expression profiling has been used to infer statistical models describing these cellular programs, and development is now needed to guide orientated modulation of these systems. Here we develop a regression-based model to reverse-engineer a temporal genetic program, based on relevant patterns of gene expression after cell stimulation. This method integrates the temporal dimension of biological rewiring of genetic programs and enables the prediction of the effect of targeted gene disruption at the system level. We tested the performance accuracy of this model on synthetic data before reverse-engineering the response of primary cancer cells to a proliferative (protumorigenic) stimulation in a multistate leukemia biological model (i.e., chronic lymphocytic leukemia). To validate the ability of our method to predict the effects of gene modulation on the global program, we performed an intervention experiment on a targeted gene. Comparison of the predicted and observed gene expression changes demonstrates the possibility of predicting the effects of a perturbation in a gene regulatory network, a first step toward an orientated intervention in a cancer cell genetic program. PMID:23267079

  12. The genetic matrix of Mayan applicative acquisition

    E-print Network

    Pye, Clifton

    2007-07-01

    Groups Child Measure 2;0 2;6 3;0 3;6 Al Tiyaan Age 2;1 2;7 2;10 MLU 1.3 2.1 2.8 No. of Utts. 1811 844 1026 Al Chaay Age 2;9 3;0 3;6 MLU 1.6 2.7 3.5 No. of Utts. 945 2356 1770 A Carlos Age 3;1 3;4 3;8 MLU 1.8 2.8 3.3 No. of Utts. 735 3032 1508 The genetic... addressee 1 (25) Tzeltal children’s use of the applicative su‰x -b’e (derived from Brown, in press) Lus 2;0 2;6 3;0 3;6 dative 1/3 dative 1/6 dative 1/13 dative 1/13 benefactive 4 benefactive 4 benefactive 4 benefactive 4 malefactive 1 malefactive 1...

  13. Reverse Genetics in Eukaryotes1 Serge Hardy1,2, Vincent Legagneux1,2, Yann Audic 1,2, Luc Paillard1,26

    E-print Network

    Boyer, Edmond

    1 Reverse Genetics in Eukaryotes1 2 3 4 5 Serge Hardy1,2, Vincent Legagneux1,2, Yann Audic 1,2, Luc;102(10):561-80" DOI : 10.1042/BC20100038 #12;2 Abstract23 Reverse genetics consists in the modification this goal and will be25 explained in this review. Two of them are centered on genome alterations. Mutations

  14. Using Genetic Algorithms in Secured Business Intelligence Mobile Applications

    Microsoft Academic Search

    Silvia TRIF

    2011-01-01

    The paper aims to assess the use of genetic algorithms for training neural networks used in secured Business Intelligence Mobile Applications. A comparison is made between classic back-propagation method and a genetic algorithm based training. The design of these algorithms is presented. A comparative study is realized for determining the better way of training neural networks, from the point of

  15. Applications of terpene analysis in forest genetics

    Microsoft Academic Search

    James W. Hanover

    1992-01-01

    Terpenoid substances in forest trees are versatile biochemical systems for use as genetic markers and for studying genetic regulation at the biochemical level. Univariate, multivariate and correlative data analyses from numerous studies on different coniferous species are presented. These data indicate that fitness values for most terpenes examined are probably so low as to be unmeasurable except in long evolutionary

  16. A reversible Rotman lens useful in short, linear, array applications

    NASA Astrophysics Data System (ADS)

    Monser, George J.

    1995-01-01

    The Gent lens was first demonstrated in 1956, and applied to early warning radar in 1958. This paper describes a small printed lens on Duroid substrate, and is unique in that it is reversible; that is, either side can be used to feed the array with the other side acting as beamports. Performance data are given for an eight-element linear array at 14 GHz.

  17. Application of genetic diversityecosystem function research to ecological restoration

    E-print Network

    REVIEW Application of genetic diversity­ecosystem function research to ecological restoration Karin) long-term plant persistence and (iii) restoration of functioning ecosystems. Restoration practitioners for local environmental conditions. Restoring functioning ecosystems is considered a loftier goal

  18. Application of Genetic Programming to High Energy Physics Event Selection

    E-print Network

    Link, J M; Anjos, J C; Bediaga, I; Castromonte, C; Göbel, C; Machado, A A; Magnin, J; Massafferri, A; De Miranda, J M; Pepe, I M; Polycarpo, E; Dos Reis, A C; Carrillo, S; Casimiro, E; Cuautle, E; Sánchez-Hernández, A; Uribe, C; Vázquez, F; Agostino, L; Cinquini, L; Cumalat, J P; O'Reilly, B; Segoni, I; Stenson, K; Butler, J N; Cheung, H W K; Chiodini, G; Gaines, I; Garbincius, P H; Garren, L A; Gottschalk, E; Kasper, P H; Kreymer, A E; Kutschke, R; Wang, M; Benussi, L; Bertani, M; Bianco, S; Fabbri, Franco Luigi; Pacetti, S; Zallo, A; Reyes, M; Cawlfield, C; Kim, D Y; Rahimi, A; Wiss, J; Gardner, R; Kryemadhi, A; Chung, Y S; Kang, J S; Ko, B R; Kwak, J W; Lee, K B; Cho, K; Park, H; Alimonti, G; Barberis, S; Boschini, M; Cerutti, A; D'Angelo, P; Di Corato, M; Dini, P; Edera, L; Erba, S; Inzani, P; Leveraro, F; Malvezzi, S; Menasce, D; Mezzadri, M; Moroni, L; Pedrini, D; Pontoglio, C; Prelz, F; Rovere, M; Sala, S; Davenport, T F; Arena, V; Boca, G; Bonomi, G; Gianini, G; Liguori, G; Lopes-Pegna, D; Merlo, M M; Pantea, D; Ratti, S P; Riccardi, C; Vitulo, P; Hernández, H; López, A M; Méndez, H; Paris, A; Quinones, J; Ramírez, J E; Zhang, Y; Wilson, J R; Handler, T; Mitchell, R; Engh, D; Hosack, M; Johns, W E; Luiggi, E; Moore, J E; Nehring, M; Sheldon, P D; Vaandering, E W; Webster, M; Sheaff, M

    2005-01-01

    We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.

  19. Application of Genetic Programming to High Energy Physics Event Selection

    E-print Network

    The FOCUS Collaboration; J. M. Link

    2005-05-12

    We review genetic programming principles, their application to FOCUS data samples, and use the method to study the doubly Cabibbo suppressed decay D+ -> K+ pi+ pi- relative to its Cabibbo favored counterpart, D+ -> K- pi+ pi+. We find that this technique is able to improve upon more traditional analysis methods. To our knowledge, this is the first application of the genetic programming technique to High Energy Physics data.

  20. Polyglot programming in applications used for genetic data analysis.

    PubMed

    Nowak, Robert M

    2014-01-01

    Applications used for the analysis of genetic data process large volumes of data with complex algorithms. High performance, flexibility, and a user interface with a web browser are required by these solutions, which can be achieved by using multiple programming languages. In this study, I developed a freely available framework for building software to analyze genetic data, which uses C++, Python, JavaScript, and several libraries. This system was used to build a number of genetic data processing applications and it reduced the time and costs of development. PMID:25197633

  1. Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps and

    E-print Network

    California at Berkeley. University of

    PWP-073 Stochastic Models of Energy Commodity Prices and Their Applications: Mean of the Program on Workable Energy Regulation (POWER). POWER is a program of the University of California Energy.ucei.berkeley.edu/ucei #12;Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps

  2. Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses

    PubMed Central

    Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nuntawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

    2012-01-01

    Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate (A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby Canine Kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 29 HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. PMID:22230579

  3. Performance of a model cascade thrust reverser for short-haul applications

    NASA Technical Reports Server (NTRS)

    Dietrich, D. A.; Gutierrez, O. A.

    1974-01-01

    Aerodynamic and acoustic characteristics are presented for a cowl-mounted, model cascade thrust reverser suitable for short-haul aircraft. Thrust reverser efficiency and the influence on fan performance were determined from isolated fan-driven models under static and forward velocity conditions. Cascade reverser noise characteristics were determined statically in an isolated pipe-flow test, while aerodynamic installation effects were determined with a wind-tunnel, fan-powered airplane model. Application of test results to short-haul aircraft calculations demonstrate that such a cascade thrust reverser may be able to meet both the performance and noise requirements for short-haul aircraft operation. However, aircraft installation effects can be quite significant.

  4. Performance of a model cascade thrust reverser for short-haul applications

    NASA Technical Reports Server (NTRS)

    Dietrich, D. A.; Gutierrez, O. A.

    1974-01-01

    Aerodynamic and acoustic characteristics are presented for a cowlmounted, model cascade thrust reverser suitable for short-haul aircraft. Thrust reverser efficiency and the influence on fan performance were determined from isolated fan-driven models under static and forward velocity conditions. Cascade reverser noise characteristics were determined statically in an isolated pipe-flow test, while aerodynamic installation effects were determined with a wind-tunnel, fan-powered airplane model. Application of test results to short-haul aircraft calculations demonstrated that such a cascade thrust reverser may be able to meet both the performance and noise requirements for short-haul aircraft operation. However, aircraft installation effects can be quite significant.

  5. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis

    Microsoft Academic Search

    Jose M. Alonso; Joseph R. Ecker

    2006-01-01

    Genome sequencing, in combination with various computational and empirical approaches to sequence annotation, has made possible the identification of more than 30,000 genes in Arabidopsis thaliana. Increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of these genes gives rise to a complex organism. The combination of classical forward genetics with recently

  6. Applications of graph theory to landscape genetics

    Microsoft Academic Search

    Colin J. Garroway; Jeff Bowman; Denis Carr; Paul J. Wilson

    2008-01-01

    We investigated the relationships among landscape quality, gene flow, and pop- ulation genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a net- work node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a

  7. Genetically modified plants for law enforcement applications

    Microsoft Academic Search

    C. Neal Stewart

    2002-01-01

    Plants are ubiquitous in the environment and have the unique ability to respond to their environment physiologically and through altered gene expression profiles (they cannot walk away). In addition, plant genetic transformation techniques and genomic information in plants are becoming increasingly advanced. We have been performing research to express the jellyfish green fluorescent protein (GFP) in plants. GFP emits green

  8. Genetic Patterns as a Function of Landscape Process: Applications of Neutral Genetic Markers for Predictive Modeling in Landscape Ecology

    Microsoft Academic Search

    Melanie A. Murphy; Jeffrey S. Evans

    \\u000a Integrating landscape ecology and population genetics (Manel et al. 2003), landscape genetics1 aims to link observed patterns of genetic variation to underlying landscape process(es) (Storfer et al. 2007). Landscape\\u000a genetics is a useful, emerging approach with the potential to develop new understanding of ecological theory and improve management\\u000a decisions (Balkenhol et al. 2009). Current applications that incorporate both genetic data

  9. High volume molecular genetic identification of single nucleotide polymorphisms using Genetic Bit Analysis Application to human genetic diagnosis

    SciTech Connect

    Boyce-Jacino, M.T.; Reynolds, J.; Nikiforov, T. [Molecular Tool, Inc., Baltimore, MD (United States)] [and others

    1994-09-01

    The most common type of genetic disease-associated mutation is the single nucleotide polymorphism (SNP). Because most genetic diseases can be caused by multiple SNPs in the same gene, effective routine diagnosis of complex genetic diseases is dependent on a simple and reliable method of interrogating SNP sites. Molecular Tool`s solid phase assay capable of direct genotyping (single base sequencing) of SNP sites, Genetic Bit Analysis (GBA), involves hybridization-capture of a single-stranded PCR product to a sequence-specific, microtiter plate-bound oligonucleotide primer. The captured PCR product then acts as template for single-base extension of the capture primer across the polymorphic site, enabling direct determination of the base composition of the polymorphism through a simple colormetric assay. Genotyping in a high volume, semi-automated, processing system with a current capacity of 100 SNP interrogations per technician per day enables the screening of candidate mutations rapidly and cost-effectively, critically important to comprehensive genetic diagnosis. Using this gel-free technology, we have developed prototype diagnostic tests for CFTR and ApoE polymorphisms which enable direct sequencing of the polymorphic base at each site of interest. Routine clinical diagnosis of genetically complex diseases such as cystic fibrosis is dependent on this combination of robust biochemistry and simple format. Additionally, the ability to transfer the format and biochemistry to any disease gene of interest enables the broad application of this technology to clinical diagnostics, especially for genetically complex diseases.

  10. Applications of Genetic Programming in Cancer Research

    PubMed Central

    Worzel, William P.; Yu, Jianjun; Almal, Arpit A.; Chinnaiyan, Arul M.

    2012-01-01

    The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allows scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future. PMID:18929677

  11. Preimplantation genetic diagnosis: technology and clinical applications.

    PubMed

    Swanson, Amy; Strawn, Estil; Lau, Eduardo; Bick, David

    2007-05-01

    Preimplantation genetic diagnosis (PGD) is a method by which embryos formed through in vitro fertilization (IVF) can be tested for single-gene disorders or chromosome abnormalities prior to embryo transfer. This enables couples to significantly improve their chances of having a healthy child. PGD is an important addition to conventional prenatal diagnosis for genetic disorders. PGD is a complex combination of various technologies that requires close collaboration of a team of specialists for optimal patient care. This review article will cover patient management, assisted reproductive technologies including IVF and PGD as well as indications for PGD. Clinical vignettes from The Froedtert Hospital and Medical College of Wisconsin Reproductive Medicine Clinic PGD Program will be presented, including the first single-gene disorder PGD performed in Wisconsin. These vignettes highlight the importance of a detailed family history, use of PGD for cases of recurrent miscarriage, and the use of PGD for spinal muscular atrophy. PMID:17642353

  12. A linear model of reversible metabolism and its application to bioavailability assessment

    Microsoft Academic Search

    S. Hwang; K. C. Kwan; K. S. Albert

    1981-01-01

    A theoretical basis has been established for the bioavailability assessment of drug and metabolite wherein the biotransformation of one to the other is reversible. The method is applicable to linear systems and requires knowledge of drug and metabolite clearance rates as well as the rate of their interconversion. While not necessary, an unconventional definition of plasma clearance appears desirable and

  13. Reversible Polygonalization of a 3D Planar Discrete Curve: Application on Discrete Surfaces

    E-print Network

    Dupont, Florent

    composing the discrete object. This approach simply needs an efficient convex hull algorithm, which of the transformation is desired. A first naive method consists in computing the convex hull of the discrete pointsReversible Polygonalization of a 3D Planar Discrete Curve: Application on Discrete Surfaces

  14. Reverse genetics in the tide pool: knock-down of target gene expression via RNA interference in the copepod Tigriopus californicus.

    PubMed

    Barreto, Felipe S; Schoville, Sean D; Burton, Ronald S

    2015-07-01

    Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are susceptible to RNAi-mediated gene knock-down, we developed a simple method for delivery of gene-specific double-stranded RNA that results in significant suppression of target gene transcription levels. The protocol was examined on five genes of interest, and for each, at least 50% knock-down in expression was achieved. While knock-down levels did not reach 100% in any trial, a well-controlled experiment with one heat-shock gene showed unambiguously that such partial gene suppression may cause dramatic changes in phenotype. Copepods with suppressed expression of heat-shock protein beta 1 (hspb1) exhibited dramatically decreased tolerance to high temperatures, validating the importance of this gene during thermal stress, as proposed by a previous study. The application of this RNAi protocol in T. californicus will be invaluable for examining the role of genes putatively involved in reproductive isolation, mitochondrial function and local adaptation. PMID:25487181

  15. Effect of Host Genetic Variation on the Pharmacokinetics and Clinical Response of Non-nucleoside Reverse Transcriptase Inhibitors

    PubMed Central

    Saitoh, Akihiko; Spector, Stephen A.

    2010-01-01

    Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have been used widely for treating human immunodeficiency virus type 1 (HIV-1) infected patients as a component of highly active antiretroviral therapy (HAART) and for the prevention of mother-to-child transmission (MTCT). Cytochrome P450 (CYP) 2B6 is an important hepatic isoenzyme responsible for the metabolism of NNRTIs including efavirenz and nevirapine. Recent pharmacogenetic studies have shown that CYP2B6 genetic variants alter hepatic CYP2B6 protein expression and function, and the pharmacokinetics of several CYP2B6 substrates. In particular, the CYP2B6-G516T polymorphism in exon 4 affects the pharmacokinetics of efavirenz. Other studies have shown associations of the CYP2B6-G516T genotype with nevirapine pharmacokinetics and central nervous system adverse effects related to efavirenz use. In total, CYP2B6 genetic variants are important determinants of efavirenz and nevirapine pharmacokinetics . Further studies are needed to identify the associations of CYP2B6 genetic variants with the development of NNRTI resistant viruses. PMID:21197270

  16. Image reversal photoresist for small molecule organic light-emitting diode applications

    Microsoft Academic Search

    Seungjun Yi; Chul Gyu Jhun; Woo Young Kim; Kyung-Hee Choi

    2011-01-01

    We have developed an image reversal photoresist with high thermal stability and electric insulating properties for small molecule organic light-emitting diode (SMOLED) applications. The thermal stability and electric insulating properties were investigated and compared to those of the conventional insulation layer and cathode separator materials of SMOLEDs. Moreover, to verify its applicability and reliability, 1.17? 96×RGB (red, green, and blue

  17. Applications of graph theory to landscape genetics

    PubMed Central

    Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

    2008-01-01

    We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

  18. Applications of graph theory to landscape genetics.

    PubMed

    Garroway, Colin J; Bowman, Jeff; Carr, Denis; Wilson, Paul J

    2008-11-01

    We investigated the relationships among landscape quality, gene flow, and population genetic structure of fishers (Martes pennanti) in ON, Canada. We used graph theory as an analytical framework considering each landscape as a network node. The 34 nodes were connected by 93 edges. Network structure was characterized by a higher level of clustering than expected by chance, a short mean path length connecting all pairs of nodes, and a resiliency to the loss of highly connected nodes. This suggests that alleles can be efficiently spread through the system and that extirpations and conservative harvest are not likely to affect their spread. Two measures of node centrality were negatively related to both the proportion of immigrants in a node and node snow depth. This suggests that central nodes are producers of emigrants, contain high-quality habitat (i.e., deep snow can make locomotion energetically costly) and that fishers were migrating from high to low quality habitat. A method of community detection on networks delineated five genetic clusters of nodes suggesting cryptic population structure. Our analyses showed that network models can provide system-level insight into the process of gene flow with implications for understanding how landscape alterations might affect population fitness and evolutionary potential. PMID:25567802

  19. Genetic algorithm application in optimization of wireless sensor networks.

    PubMed

    Norouzi, Ali; Zaim, A Halim

    2014-01-01

    There are several applications known for wireless sensor networks (WSN), and such variety demands improvement of the currently available protocols and the specific parameters. Some notable parameters are lifetime of network and energy consumption for routing which play key role in every application. Genetic algorithm is one of the nonlinear optimization methods and relatively better option thanks to its efficiency for large scale applications and that the final formula can be modified by operators. The present survey tries to exert a comprehensive improvement in all operational stages of a WSN including node placement, network coverage, clustering, and data aggregation and achieve an ideal set of parameters of routing and application based WSN. Using genetic algorithm and based on the results of simulations in NS, a specific fitness function was achieved, optimized, and customized for all the operational stages of WSNs. PMID:24693235

  20. Network Model and Optimization of Medical Waste Reverse Logistics by Improved Genetic Algorithm

    Microsoft Academic Search

    Lihong Shi; Houming Fan; Pingquan Gao; Hanyu Zhang

    2009-01-01

    The medical waste management is of great importance because of the potential environmental hazards and public health risks.\\u000a Manufacturers have to collect the medical waste and control its recovery or disposal. Medical waste recovery, which encompasses\\u000a reusing, remanufacturing and materials recycling, requires a specially structured reverse logistics network in order to collect\\u000a the medical waste efficiently. This paper presents a

  1. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle.

    PubMed

    Daniels, Tyler F; Wu, Xiao-Lin; Pan, Zengxiang; Michal, Jennifer J; Wright, Raymond W; Killinger, Karen M; MacNeil, Michael D; Jiang, Zhihua

    2010-01-01

    In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F(1) bulls, 113 F(1) dams, and 246 F(2) progeny. A total of 37 amplicons were used to screen single nucleotide polymorphisms (SNPs) on 6 F(1) bulls. Among 36 SNPs detected in 11 of these 13 genes, 19 were selected for genotyping by the Sequenom assay design on all F(2) progeny. Single-marker analysis revealed seven SNPs in ATP binding cassette A1, apolipoproteins A1, B and E, phospholipid transfer protein and paraoxinase 1 genes significantly associated with nine phenotypes (P<0.05). Previously, we reported genetic networks associated with 19 complex phenotypes based on a total of 138 genetic polymorphisms derived from 71 known functional genes. Therefore, after Bonferroni correction, these significant (adjusted P<0.05) and suggestive (adjusted P<0.10) associations were then used to identify genetic networks related to the RCT pathway. Multiple-marker analysis suggested possible genetic networks involving the RCT pathway for kidney-pelvic-heart fat percentage, rib-eye area, and subcutaneous fat depth phenotypes with markers derived from paraoxinase 1, apolipoproteins A1 and E, respectively. The present study confirmed that genes involved in cholesterol homeostasis are useful targets for investigating obesity in humans as well as for improving meat quality phenotypes in a livestock production. PMID:21151936

  2. An Experimental Application of Learnable Evolution Model and Genetic Algorithms

    E-print Network

    Michalski, Ryszard S.

    an application of LEM1, a preliminary implementation of Learnable Evolution Model (LEM), and two canonical genetic algorithms, GA1 and GA2, to parameter estimation in digital signal filter design. LEM1 alternates of a population has not improved sufficiently during one mode, LEM1 switches to another mode. LEM1 alternates

  3. Genetic algorithms and their applications in accelerator physics

    SciTech Connect

    Hofler, Alicia S. [JLAB

    2013-12-01

    Multi-objective optimization techniques are widely used in an extremely broad range of fields. Genetic optimization for multi-objective optimization was introduced in the accelerator community in relatively recent times and quickly spread becoming a fundamental tool in multi-dimensional optimization problems. This discussion introduces the basics of the technique and reviews applications in accelerator problems.

  4. Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

    Microsoft Academic Search

    Chris Duran; Nikki Appleby; David Edwards; Jacqueline Batley

    2009-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in

  5. The social and genetic mating system in flickers linked to partially reversed sex roles

    Microsoft Academic Search

    Karen L. Wiebe; Bart Kempenaers

    2009-01-01

    The type of social and genetic mating system observed in birds is influenced by the need of both sexes to provide parental care. In woodpeckers, unlike most birds, females are partially emancipated as males provide most of the care including nocturnal incubation. We analyzed the mating system of northern flickers Colaptes auratus and used microsatellite markers to assess parentage of

  6. Reverse genetic engineering of the human rhinovirus serotype 16 genome to introduce an antibody-detectable tag.

    PubMed

    Walker, Erin J; Jensen, Lora M; Ghildyal, Reena

    2015-01-01

    The ability to accurately detect viral proteins during infection is essential for virology research, and the lack of specific antibodies can make this detection difficult. Reverse genetic engineering of virus genomes to alter the wild-type genome is a powerful technique to introduce a detectable tag onto a viral protein. Here we outline a method to incorporate an influenza hemagglutinin epitope tag onto the 2A protease of HRV16. The method uses site-directed mutagenesis PCR to introduce the sequence for the HA antigen onto either the C or N termini of 2A protease while keeping the relevant internal cleavage sites intact. The new viral product is then cloned into a wild-type HRV16 plasmid and transfected into Ohio Hela cells to produce recombinant virus. PMID:25261314

  7. A High Through-Put Reverse Genetic Screen Identifies Two Genes Involved in Remote Memory in Mice

    PubMed Central

    Matynia, Anna; Anagnostaras, Stephan G.; Wiltgen, Brian J.; Lacuesta, Maress; Fanselow, Michael S.; Silva, Alcino J.

    2008-01-01

    Previous studies have revealed that the initial stages of memory formation require several genes involved in synaptic, transcriptional and translational mechanisms. In contrast, very little is known about the molecular and cellular mechanisms underlying later stages of memory, including remote memory (i.e. 7-day memory). To identify genes required for remote memory, we screened randomly selected mouse strains harboring known mutations. In our primary reverse genetic screen, we identified 4 putative remote memory mutant strains out of a total of 54 lines analyzed. Additionally, we found 11 other mutant strains with other abnormal profiles. Secondary screens confirmed that mutations of integrin ?2 (Itg?2) and steryl-O-acyl transferase 1 (Soat1) specifically disrupted remote memory. This study identifies some of the first genes required for remote memory, and suggests that screens of targeted mutants may be an efficient strategy to identify molecular requirements for this process. PMID:18464936

  8. Quantitative genetic versions of Hamilton's rule with empirical applications.

    PubMed

    McGlothlin, Joel W; Wolf, Jason B; Brodie, Edmund D; Moore, Allen J

    2014-05-19

    Hamilton's theory of inclusive fitness revolutionized our understanding of the evolution of social interactions. Surprisingly, an incorporation of Hamilton's perspective into the quantitative genetic theory of phenotypic evolution has been slow, despite the popularity of quantitative genetics in evolutionary studies. Here, we discuss several versions of Hamilton's rule for social evolution from a quantitative genetic perspective, emphasizing its utility in empirical applications. Although evolutionary quantitative genetics offers methods to measure each of the critical parameters of Hamilton's rule, empirical work has lagged behind theory. In particular, we lack studies of selection on altruistic traits in the wild. Fitness costs and benefits of altruism can be estimated using a simple extension of phenotypic selection analysis that incorporates the traits of social interactants. We also discuss the importance of considering the genetic influence of the social environment, or indirect genetic effects (IGEs), in the context of Hamilton's rule. Research in social evolution has generated an extensive body of empirical work focusing--with good reason--almost solely on relatedness. We argue that quantifying the roles of social and non-social components of selection and IGEs, in addition to relatedness, is now timely and should provide unique additional insights into social evolution. PMID:24686930

  9. Sex-Role Reversal and "Dominance Genes" in African Cichlid Fish The broad scope of my research aims to understand the genetic basis of behavior from an

    E-print Network

    Renn, Susan C.P.

    1 Sex-Role Reversal and "Dominance Genes" in African Cichlid Fish The broad scope of my research the genetic basis of species-specific "sex-role" behaviors, and how these behaviors relate to environmental specific aims designed to test the hypothesis that species- specific "sex-role" behaviors, imposed

  10. SEQUENCE ANALYSIS OF THE COMPLETE GENOME OF AVIAN METAPNEUMOVIRUS SUBGROUP C COLORADO STRAIN: DEVELOPMENT OF A REVERSE GENETICS SYSTEM FOR THIS VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The availability of the complete genome information is essential for development of a reverse genetics system to study the molecular biology and rescue infectious avian metapneumovirus from cloned DNA. Therefore, we determined the nucleotide (nt) sequence of the complete genome of aMPV-C Colorado s...

  11. Blue light- and genetically-reversed gravitropic response in protonemata of the moss Ceratodon purpureus.

    PubMed

    Lamparter, T; Hughes, J; Hartmann, E

    1998-09-01

    In darkness, protonemal filaments of Ceratodon purpureus (Brid.) grow negatively gravitropically (upwards). Red light induces a positive phototropic response mediated by the photoreceptor phytochrome. A red light treatment also has an inhibitory effect on the gravitropic response, an effect also mediated by phytochrome. In this study the effects of blue light on phototropism and on gravitropism were analysed. Unilateral blue light resulted in only a weak phototropic response, but markedly randomised growth direction. Blue light given together with a gravitropic stimulus reversed the gravitropism, changing it from negative to positive (filaments grow downward). The effect of blue light was also analysed with the mutant ptr116, which is defective in the biosynthesis of the phytochrome chromophore, and in a newly isolated mutant wwr2, which is positively gravitropic in darkness. Blue light induced the same reversal of gravitropism in ptrll6 as in the wild type, indicating that phytochrome is not involved in this process. In wwr2 the direction of gravitropism was unaltered by the blue light treatment. Light also affects chlorophyll content and the size of plastids, potential statoliths for gravitropism. Red light induced an increase in plastid size and chlorophyll content in the wild type but not in ptr116. Blue light induced a similar change in wild type plastids. It seems as though light-induced alterations of gravitropism are not simply mediated by alterations in plastid properties, and that red light and blue light evoke fundamentally different responses. PMID:11536885

  12. The Identification of Candidate Genes for a Reverse Genetic Analysis of Development and Function in the Arabidopsis Gynoecium1

    PubMed Central

    Scutt, Charles P.; Vinauger-Douard, Marion; Fourquin, Chloé; Ailhas, Jérôme; Kuno, Norihito; Uchida, Kenko; Gaude, Thierry; Furuya, Masaki; Dumas, Christian

    2003-01-01

    The screening for mutants and their subsequent molecular analysis has permitted the identification of a number of genes of Arabidopsis involved in the development and functions of the gynoecium. However, these processes remain far from completely understood. It is clear that in many cases, genetic redundancy and other factors can limit the efficiency of classical mutant screening. We have taken the alternative approach of a reverse genetic analysis of gene function in the Arabidopsis gynoecium. A high-throughput fluorescent differential display screen performed between two Arabidopsis floral homeotic mutants has permitted the identification of a number of genes that are specifically or preferentially expressed in the gynoecium. Here, we present the results of this screen and a detailed characterization of the expression profiles of the genes identified. Our expression analysis makes novel use of several Arabidopsis floral homeotic mutants to provide floral organ-specific gene expression profiles. The results of these studies permit the efficient targeting of effort into a functional analysis of gynoecium-expressed genes. PMID:12805595

  13. [The genetic control of mouse coat color and its applications in genetics teaching].

    PubMed

    Xing, Wanjin; Morigen, Morigen

    2014-10-01

    Mice are the most commonly used mammalian model. The coat colors of mice are typical Mendelian traits, which have various colors such as white, black, yellow and agouti. The inheritance of mouse coat color is usually stated as an example only in teaching the knowledge of recessive lethal alleles. After searched the related literatures and summarized the molecular mechanisms of mouse coat color inheritance, we further expanded the application of this example into the introduction of the basic concepts of alleles and Mendelian laws, demonstration of the gene structure and function, regulation of gene expression, gene interaction, epigenetic modification, quantitative genetics, as well as evolutionary genetics. By running this example through the whole genetics-teaching lectures, we help the student to form a systemic and developmental view of genetic analysis. At the same time, this teaching approach not only highlights the advancement and integrity of genetics, but also results in a good teaching effect on inspiring the students' interest and attracting students' attention. PMID:25406255

  14. SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement

    PubMed Central

    2013-01-01

    Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

  15. Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen

    PubMed Central

    Liakath-Ali, Kifayathullah; Vancollie, Valerie E.; Heath, Emma; Smedley, Damian P.; Estabel, Jeanne; Sunter, David; DiTommaso, Tia; White, Jacqueline K.; Ramirez-Solis, Ramiro; Smyth, Ian; Steel, Karen P.; Watt, Fiona M.

    2014-01-01

    Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous gland and interfollicular epidermal abnormalities using ontology terms from the Mammalian Phenotype Ontology. Of the 50 mutants with an epidermal phenotype, 9 map to human genetic conditions with skin abnormalities. Some mutant genes are expressed in the skin, whereas others are not, indicating systemic effects. One phenotype is affected by diet and several are incompletely penetrant. In-depth analysis of three mutants, Krt76, Myo5a (a model of human Griscelli syndrome) and Mysm1, provides validation of the screen. Our study is the first large-scale genome-wide tissue phenotype screen from the International Knockout Mouse Consortium and provides an open access resource for the scientific community. PMID:24721909

  16. Pathogenicity study in sheep using reverse-genetics-based reassortant bluetongue viruses

    PubMed Central

    Celma, Cristina C.; Bhattacharya, Bishnupriya; Eschbaumer, Michael; Wernike, Kerstin; Beer, Martin; Roy, Polly

    2014-01-01

    Bluetongue (BT) disease, caused by the non-enveloped bluetongue virus (BTV) belonging to the Reoviridae family, is an economically important disease that affects a wide range of wild and domestic ruminants. Currently, 26 different serotypes of BTV are recognized in the world, of which BTV-8 has been found to exhibit one of the most virulent manifestations of BT disease in livestock. In recent years incursions of BTV-8 in Europe have resulted in significant morbidity and mortality not only in sheep but also in cattle. The molecular and genetic basis of BTV-8 pathogenesis is not known. To understand the genetic basis of BTV-8 pathogenicity, we generated reassortant viruses by replacing the 3 most variable genes, S2, S6 and S10 of a recent isolate of BTV-8, in different combinations into the backbone of an attenuated strain of BTV-1. The growth profiles of these reassortant viruses were then analyzed in two different ovine cell lines derived from different organs, kidney and thymus. Distinct patterns for each reassortant virus in these two cell lines were observed. To determine the pathogenicity of these reassortant viruses, groups of BTV-susceptible sheep were infected with each of these viruses. The data suggested that the clinical manifestations of these two different serotypes, BTV-1 and BTV-8, were slightly distinct and BTV-1, when comprising all 3 genome segments of BTV-8, behaved differently to BTV-1. Our results also suggested that the molecular basis of BT disease is highly complex. PMID:25307940

  17. Cross flow filtration for radwaste applications reverse osmosis demonstration case studies

    SciTech Connect

    Malkmus, D. [VECTRA Technologies, Inc., Columbia, SC (United States)

    1995-05-01

    Today`s radwaste economic and regulatory scenarios signify the importance in the improvement of operational practices to reduce generator liabilities. This action is largely due to the rising cost dealing with burial sites and the imposed waste volume restriction. To control the economical burdens associated with waste burial and to comply with stricter environmental regulations, NPP`s are attempting to modify their radwaste system(s) design and operating philosophy by placing a major emphasis on waste volume reduction and processing techniques. The utilization of reverse osmosis technology as a means for treatment of process and wastewater streams in the nuclear power industry has been investigated for many years. This paper will outline reverse osmosis theory and highlight performance data for process and waste stream purification applications. Case studies performed at 5 nuclear plants have been outlined. The demonstrations were performed on a widely variety of process stream for both a PWR and BWR application. The data provided by the pilot systems, the equipment design, and the economical impact a reverse osmosis unit will have on producing treated (high purity) are as follows.

  18. Novel and potential application of cryopreservation to plant genetic transformation.

    PubMed

    Wang, Biao; Zhang, Zhibo; Yin, Zhenfang; Feng, Chaohong; Wang, Qiaochun

    2012-01-01

    The world population now is 6.7 billion and is predicted to reach 9 billion by 2050. Such a rapid growing population has tremendously increased the challenge for food security. Obviously, it is impossible for traditional agriculture to ensure the food security, while plant biotechnology offers considerable potential to realize this goal. Over the last 15 years, great benefits have been brought to sustainable agriculture by commercial cultivation of genetically modified (GM) crops. Further development of new GM crops will with no doubt contribute to meeting the requirements for food by the increasing population. The present article provides updated comprehensive information on novel and potential application of cryopreservation to genetic transformation. The major progresses that have been achieved in this subject include (1), long-term storage of a large number of valuable plant genes, which offers a good potential for further development of novel cultivars by genetic transformation; (2), retention of regenerative capacity of embryogenic tissues and protoplasts, which ensures efficient plant regeneration system for genetic transformation; (3), improvement of transformation efficiency and plant regeneration of transformed cells; (4), long-term preservation of transgenic materials with stable expression of transgenes and productive ability of recombinant proteins, which allows transgenic materials to be stored in a safe manner before being analyzed and evaluated, and allows establishment of stable seed stocks for commercial production of homologous proteins. Data provided in this article clearly demonstrate that cryo-technique has an important role to play in the whole chain of genetic transformation. Further studies coupling cryotechnique and genetic transformation are expected to significantly improve development of new GM crops. PMID:22079800

  19. Time reversal for radiative transport with applications to inverse and control problems

    E-print Network

    Sebastian Acosta

    2013-08-03

    In this paper we develop a time reversal method for the radiative transport equation to solve two problems: an inverse problem for the recovery of an initial condition from boundary measurements, and the exact boundary controllability of the transport field with finite steering time. Absorbing and scattering effects, modeled by coefficients with low regularity, are incorporated in the formulation of these problems. This time reversal approach leads to a convergent iterative procedure to reconstruct the initial condition provided that the scattering coefficient is sufficiently small in the $L^{\\infty}$ norm. Then, using duality arguments, we show that the solvability of the inverse problem leads to exact controllability of the transport field with minimum-norm control obtained constructively. The solution approach to both of these problems may have medical applications in areas such as optical imaging and optimization of radiation delivery for cancer therapy.

  20. Application of genetic algorithms to tuning fuzzy control systems

    NASA Technical Reports Server (NTRS)

    Espy, Todd; Vombrack, Endre; Aldridge, Jack

    1993-01-01

    Real number genetic algorithms (GA) were applied for tuning fuzzy membership functions of three controller applications. The first application is our 'Fuzzy Pong' demonstration, a controller that controls a very responsive system. The performance of the automatically tuned membership functions exceeded that of manually tuned membership functions both when the algorithm started with randomly generated functions and with the best manually-tuned functions. The second GA tunes input membership functions to achieve a specified control surface. The third application is a practical one, a motor controller for a printed circuit manufacturing system. The GA alters the positions and overlaps of the membership functions to accomplish the tuning. The applications, the real number GA approach, the fitness function and population parameters, and the performance improvements achieved are discussed. Directions for further research in tuning input and output membership functions and in tuning fuzzy rules are described.

  1. Application of Genetic Algorithms to Molecular Biology: Locating Putative Protein Signal Sequences

    E-print Network

    Levin, Michael

    Application of Genetic Algorithms to Molecular Biology: Locating Putative Protein Signal Sequences-7758 mlevin@husc.harvard.edu #12;Summary This paper presents an application of genetic algorithms to a problem difficult task. No good algorithm currently exists for locating brand new signals. A genetic algorithm

  2. Improvement of Current-Voltage Characteristics in Organic Light Emitting Diodes by Application of Reversed-Bias Voltage

    Microsoft Academic Search

    Dechun Zou; Masayuki Yahiro; Tetsuo Tsutsui

    1998-01-01

    The effects of reversed-bias application on current-voltage and luminance-voltage characteristics of standard-type double-layer organic light emitting diodes [OLEDs], ITO\\/TPD(50 nm)\\/Alq3(50 nm)\\/Mg:Ag, were investigated. Both the magnitude of reversed-bias and the duration of reversed-bias application were systematically changed. Evident voltage shifts towards the lower voltage side in current-voltage and luminance-voltage characteristics were observed in the diodes which were treated under various

  3. Investigating CNS synaptogenesis at single-synapse resolution by combining reverse genetics with correlative light and electron microscopy.

    PubMed

    Urwyler, Olivier; Izadifar, Azadeh; Dascenco, Dan; Petrovic, Milan; He, Haihuai; Ayaz, Derya; Kremer, Anna; Lippens, Saskia; Baatsen, Pieter; Guérin, Christopher J; Schmucker, Dietmar

    2015-01-15

    Determining direct synaptic connections of specific neurons in the central nervous system (CNS) is a major technical challenge in neuroscience. As a corollary, molecular pathways controlling developmental synaptogenesis in vivo remain difficult to address. Here, we present genetic tools for efficient and versatile labeling of organelles, cytoskeletal components and proteins at single-neuron and single-synapse resolution in Drosophila mechanosensory (ms) neurons. We extended the imaging analysis to the ultrastructural level by developing a protocol for correlative light and 3D electron microscopy (3D CLEM). We show that in ms neurons, synaptic puncta revealed by genetically encoded markers serve as a reliable indicator of individual active zones. Block-face scanning electron microscopy analysis of ms axons revealed T-bar-shaped dense bodies and other characteristic ultrastructural features of CNS synapses. For a mechanistic analysis, we directly combined the single-neuron labeling approach with cell-specific gene disruption techniques. In proof-of-principle experiments we found evidence for a highly similar requirement for the scaffolding molecule Liprin-? and its interactors Lar and DSyd-1 (RhoGAP100F) in synaptic vesicle recruitment. This suggests that these important synapse regulators might serve a shared role at presynaptic sites within the CNS. In principle, our CLEM approach is broadly applicable to the developmental and ultrastructural analysis of any cell type that can be targeted with genetically encoded markers. PMID:25503410

  4. REVERSE ENGINEERING RECENT ADVANCES

    E-print Network

    Telea, Alexandru C.

    #12;REVERSE ENGINEERING ­ RECENT ADVANCES AND APPLICATIONS Edited by Alexandru C. Telea #12;Reverse;#12;Contents Preface IX Part 1 Software Reverse Engineering 1 Chapter 1 Software Reverse Engineering GUIsurfer: A Reverse Engineering Framework for User Interface Software 31 José Creissac Campos, João Saraiva

  5. High-throughput, luciferase-based reverse genetics systems for identifying inhibitors of Marburg and Ebola viruses.

    PubMed

    Uebelhoer, Luke S; Albariño, César G; McMullan, Laura K; Chakrabarti, Ayan K; Vincent, Joel P; Nichol, Stuart T; Towner, Jonathan S

    2014-06-01

    Marburg virus (MARV) and Ebola virus (EBOV), members of the family Filoviridae, represent a significant challenge to global public health. Currently, no licensed therapies exist to treat filovirus infections, which cause up to 90% mortality in human cases. To facilitate development of antivirals against these viruses, we established two distinct screening platforms based on MARV and EBOV reverse genetics systems that express secreted Gaussia luciferase (gLuc). The first platform is a mini-genome replicon to screen viral replication inhibitors using gLuc quantification in a BSL-2 setting. The second platform is complementary to the first and expresses gLuc as a reporter gene product encoded in recombinant infectious MARV and EBOV, thereby allowing for rapid quantification of viral growth during treatment with antiviral compounds. We characterized these viruses by comparing luciferase activity to virus production, and validated luciferase activity as an authentic real-time measure of viral growth. As proof of concept, we adapt both mini-genome and infectious virus platforms to high-throughput formats, and demonstrate efficacy of several antiviral compounds. We anticipate that both approaches will prove highly useful in the development of anti-filovirus therapies, as well as in basic research on the filovirus life cycle. PMID:24713118

  6. A Novel Application of Time Reversed Acoustics: Salt Dome Flank Imaging Using Walk Away VSP Surveys

    E-print Network

    Hoop, Martijn de

    2005-01-01

    In the past few years, there has been considerable research and interest in a topic known by various names, such as Time Reverse Acoustics (TRA), Time Reverse Mirrors (TRM), and Time Reverse Cavities (TRC), which exploits ...

  7. Application of Ionic Liquids in High Performance Reversed-Phase Chromatography

    PubMed Central

    Wang, Ye; Tian, Minglei; Bi, Wentao; Row, Kyung Ho

    2009-01-01

    Ionic liquids, considered “green” chemicals, are widely used in many areas of analytical chemistry due to their unique properties. Recently, ionic liquids have been used as a kind of novel additive in separation and combined with silica to synthesize new stationary phase as separation media. This review will focus on the properties and mechanisms of ionic liquids and their potential applications as mobile phase modifier and surface-bonded stationary phase in reversed-phase high performance liquid chromatography (RP-HPLC). Ionic liquids demonstrate advantages and potential in chromatographic field. PMID:19582220

  8. Applications of a formal approach to decipher discrete genetic networks

    PubMed Central

    2010-01-01

    Background A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. Results In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach, offers a wide variety of functionalities, going beyond simple simulations, such as proof of consistency, model revision, prediction of properties, search for minimal models relatively to specified criteria. Conclusions The formal approach proposed here deeply changes the way to proceed in the exploration of genetic and biochemical networks, first by avoiding the usual trial-and-error procedure, and second by placing the emphasis on sets of solutions, rather than a single solution arbitrarily chosen among many others. Last, the constraint approach promotes an integration of model and experimental data in a single framework. PMID:20646302

  9. Trends in genetic patent applications: the commercialization of academic intellectual property

    PubMed Central

    Kers, Jannigje G; Van Burg, Elco; Stoop, Tom; Cornel, Martina C

    2014-01-01

    We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications data from the PATSTAT database from 1990 until 2009 were analyzed for time trends and regional distribution. Overall, the number of patent applications has been growing. In 2009, 152?000 patent applications were submitted under the Patent Cooperation Treaty (PCT) and within the EP (European Patent) system of the European Patent Office (EPO). The number of genetic patent applications increased until a peak was reached in the year 2000, with >8000 applications, after which it declined by almost 50%. Continents show different patterns over time, with the global peak in 2000 mainly explained by the USA and Europe, while Asia shows a stable number of >1000 per year. Nine countries together account for 98.9% of the total number of genetic patent applications. In The Netherlands, 26.7% of the genetic patent applications originate from public research institutions. After the year 2000, the number of genetic patent applications dropped significantly. Academic leadership and policy as well as patent regulations seem to have an important role in the trend differences. The ongoing investment in genetic research in the past decade is not reflected by an increase of patent applications. PMID:24448546

  10. Molecular scissors and their application in genetically modified farm animals.

    PubMed

    Petersen, Bjoern; Niemann, Heiner

    2015-06-01

    Molecular scissors (MS), incl. Zinc Finger Nucleases (ZFN), Transcription-activator like endoncleases (TALENS) and meganucleases possess long recognition sites and are thus capable of cutting DNA in a very specific manner. These molecular scissors mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site. Compared to conventional homologous recombination based gene targeting, MS can increase the targeting rate 10,000-fold, and gene disruption via mutagenic DNA repair is stimulated at a similar frequency. The successful application of different MS has been shown in different organisms, including insects, amphibians, plants, nematodes, and mammals, including humans. Recently, another novel class of molecular scissors was described that uses RNAs to target a specific genomic site. The CRISPR/Cas9 system is capable of targeting even multiple genomic sites in one shot and thus could be superior to ZFNs or TALEN, especially by its easy design. MS can be successfully employed for improving the understanding of complex physiological systems, producing transgenic animals, incl. creating large animal models for human diseases, creating specific cell lines, and plants, and even for treating human genetic diseases. This review provides an update on molecular scissors, their underlying mechanism and focuses on new opportunities for generating genetically modified farm animals. PMID:25603988

  11. Ultrasonic beam focusing through tissue inhomogeneities with a time reversal mirror: application to transskull therapy

    Microsoft Academic Search

    Jean-Louis Thomas; Mathias A. Fink

    1996-01-01

    Time reversal of ultrasonic fields allows a very efficient approach to focus pulsed ultrasonic waves through lossless inhomogeneous media. Time reversal mirrors (TRMs) are made of large transducer arrays, allowing the incident field to be sampled, time reversed, and reemitted. Time reversal method corrects for phase, amplitude, and even shape aberration and thus, is more efficient than time shift compensation

  12. The Breeder Genetic Algorithm and its application to optimization problems

    SciTech Connect

    Muehlenbein, H.

    1994-12-31

    The Breeder Genetic Algorithm BGA models artificial selection as performed by human breeders. The science of breeding is based on advanced statistical methods. The well known response to selection equation and the concept of heritability have been used to predict the behavior of the BGA. Selection, recombination and mutation have been analyzed within this framework. The theoretical results have been obtained under the assumption of additive gene effects. For general fitness landscapes regression techniques for estimating the heritability are used to analyze and control the BGA. The BGA has been applied to a number of optimization problems, ranging from the optimization of multimodal continuous functions to the breeding of neural networks. In the talk we will describe the first application in some detail and summarize some combinatorial applications e.g. transport optimization, job shop scheduling, autocorrelation.

  13. New applications of the genetic algorithm for the interpretation of high-resolution spectra1

    E-print Network

    Nijmegen, University of

    804 New applications of the genetic algorithm for the interpretation of high-resolution spectra1 W. An alternative approach is unassigned fits of the spectra using genetic algorithms (GAs) with special cost, genetic algorithm, biomolecules, structure, van der Waals clusters. Résumé : La spectroscopie électronique

  14. Graph Classification Using Genetic Algorithm and Graph Probing Application to Symbol Recognition

    E-print Network

    Paris-Sud XI, Université de

    Graph Classification Using Genetic Algorithm and Graph Probing Application to Symbol Recognition classification approach using genetic algorithm and a fast dissimilarity measure between graphs called graph this learning set, a graph based Genetic Algorithm (GA) is applied. Its aim is to generate a set of K graph

  15. Application of genetic algorithm to the calculation of bound states and local density approximations

    E-print Network

    Zeiri, Yehuda

    Application of genetic algorithm to the calculation of bound states and local density; accepted 16 November 1994 A novel method, based on genetic algorithms, has been developed and applied. © 1995 American Institute of Physics. I. INTRODUCTION Genetic algorithms GA are global optimization meth

  16. Gene Prioritization through genomic data fusion Methods and applications in human genetics

    E-print Network

    Gene Prioritization through genomic data fusion Methods and applications in human genetics L mathematics and machine learning to biology and human genetics). I would also like to express my gratitude a clearer picture of human genetics problematics; the introduction of the present thesis is mainly based

  17. Analyzing the Application of a Reverse Engineering Process to a Real Situation Fabio Abbattista (*), Gregorio M.G. Fatone (**), Filippo Lanubile (*), Giuseppe Visaggio (*)

    E-print Network

    Lanubile, Filippo

    Analyzing the Application of a Reverse Engineering Process to a Real Situation Fabio Abbattista, University of Bari, Italy (**) Basica S.p.A., Potenza, Italy Abstract A reverse engineering process model. The experience enabled modifications to be introduced connecting the reverse engineering process more closely

  18. Application of chromosomal microdissection, polymerase chain reaction (PCR), and reverse chromosome painting in prenatal diagnosis

    SciTech Connect

    Wang, N.; Xu, J.; Cedrone, E. [Univ. of Rochester School of Medicine, Rochester, NY (United States)

    1994-09-01

    De novo marker chromosomes have been found in about 0.04% of amniotic fluid cultures. The origin of these marker chromosomes is difficult to identify by routine chromosome banding analysis. In the present study, we applied microdissection, PCR, and reverse chromosome painting to two amniotic fluid cases with a karyotype of 47,XX,+mar, and 47,XX,+?i(9p), respectively. Fluorescence in situ hybridization of the biotin-labeled DNA probe generated from 5 copies of the dissected marker chromosomes was applied to the normal metaphase spreads and revealed that the marker originated from the p arm of chromosomes 14 and 22, while the ?i(9p) was actually i(4p). Reverse painting of the same probe to the metaphase spreads of the patients completely painted the marker chromosomes in question, which confirms the accuracy of the analysis. Our study provides an example of the application of chromosome microdissection and molecular cytogenetics in prenatal diagnosis for the identification of marker chromosomes unidentifiable by routine analysis.

  19. Genetic Characterization of a Mammalian Protein-Protein Interaction Domain by Using a Yeast Reverse Two-Hybrid System

    Microsoft Academic Search

    Marc Vidal; Pascal Braun; Elbert Chen; Jef D. Boeke; Ed Harlow

    1996-01-01

    Many biological processes rely upon protein-protein interactions. Hence, detailed analysis of these interactions is critical for their understanding. Due to the complexities involved, genetic approaches are often needed. In yeast and phage, genetic characterizations of protein complexes are possible. However, in multicellular organisms, such characterizations are limited by the lack of powerful selection systems. Herein we describe genetic selections that

  20. Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis

    PubMed Central

    2014-01-01

    Mobile group II introns are bacterial retrotransposons that combine the activities of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase to insert site-specifically into DNA. They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. Algorithms have been developed to program the DNA target site specificity of several mobile group II introns, allowing them to be made into ‘targetrons.’ Targetrons function for gene targeting in a wide variety of bacteria and typically integrate at efficiencies high enough to be screened easily by colony PCR, without the need for selectable markers. Targetrons have found wide application in microbiological research, enabling gene targeting and genetic engineering of bacteria that had been intractable to other methods. Recently, a thermostable targetron has been developed for use in bacterial thermophiles, and new methods have been developed for using targetrons to position recombinase recognition sites, enabling large-scale genome-editing operations, such as deletions, inversions, insertions, and ‘cut-and-pastes’ (that is, translocation of large DNA segments), in a wide range of bacteria at high efficiency. Using targetrons in eukaryotes presents challenges due to the difficulties of nuclear localization and sub-optimal magnesium concentrations, although supplementation with magnesium can increase integration efficiency, and directed evolution is being employed to overcome these barriers. Finally, spurred by new methods for expressing group II intron reverse transcriptases that yield large amounts of highly active protein, thermostable group II intron reverse transcriptases from bacterial thermophiles are being used as research tools for a variety of applications, including qRT-PCR and next-generation RNA sequencing (RNA-seq). The high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology. PMID:24410776

  1. The multi-niche crowding genetic algorithm: Analysis and applications

    SciTech Connect

    Cedeno, W.

    1995-09-01

    The ability of organisms to evolve and adapt to the environment has provided mother nature with a rich and diverse set of species. Only organisms well adapted to their environment can survive from one generation to the next, transferring on the traits, that made them successful, to their offspring. Competition for resources and the ever changing environment drives some species to extinction and at the same time others evolve to maintain the delicate balance in nature. In this disertation we present the multi-niche crowding genetic algorithm, a computational metaphor to the survival of species in ecological niches in the face of competition. The multi-niche crowding genetic algorithm maintains stable subpopulations of solutions in multiple niches in multimodal landscapes. The algorithm introduces the concept of crowding selection to promote mating among members with qirnilar traits while allowing many members of the population to participate in mating. The algorithm uses worst among most similar replacement policy to promote competition among members with similar traits while allowing competition among members of different niches as well. We present empirical and theoretical results for the success of the multiniche crowding genetic algorithm for multimodal function optimization. The properties of the algorithm using different parameters are examined. We test the performance of the algorithm on problems of DNA Mapping, Aquifer Management, and the File Design Problem. Applications that combine the use of heuristics and special operators to solve problems in the areas of combinatorial optimization, grouping, and multi-objective optimization. We conclude by presenting the advantages and disadvantages of the algorithm and describing avenues for future investigation to answer other questions raised by this study.

  2. Genetics

    MedlinePLUS

    Homozygous; Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  3. Innovative Applications of Genetic Algorithms to Problems in Accelerator Physics

    SciTech Connect

    Hofler, Alicia [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Terzic, Balsa [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States) and Old Dominion University, Norfolk, VA (United States); Kramer, Matthew [University of California, Berkeley, CA (United States); Zvezdin, Anton [Stony Brook University, Stony Brook, NY (United States); Morozov, Vasiliy [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Roblin, Yves [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Lin, Fanglei [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Jarvis, Colin [Macalester College, Saint Paul, MN (United States)

    2013-01-01

    The genetic algorithm (GA) is a relatively new technique that implements the principles nature uses in biological evolution in order to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others) fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing CEBAF facility, the proposed MEIC at Jefferson Lab, and a radio frequency (RF) gun based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, including a newly devised enhancement, which leads to improved convergence to the optimum and make recommendations for future GA developments and accelerator applications.

  4. Interdependence of Hemagglutinin Glycosylation and Neuraminidase as Regulators of Influenza Virus Growth: a Study by Reverse Genetics

    PubMed Central

    Wagner, Ralf; Wolff, Thorsten; Herwig, Astrid; Pleschka, Stephan; Klenk, Hans-Dieter

    2000-01-01

    The hemagglutinin (HA) of fowl plague virus A/FPV/Rostock/34 (H7N1) carries two N-linked oligosaccharides attached to Asn123 and Asn149 in close vicinity to the receptor-binding pocket. In previous studies in which HA mutants lacking either one (mutants G1 and G2) or both (mutant G1,2) glycosylation sites had been expressed from a simian virus 40 vector, we showed that these glycans regulate receptor binding affinity (M. Ohuchi, R. Ohuchi, A. Feldmann, and H. D. Klenk, J. Virol. 71:8377–8384, 1997). We have now investigated the effect of these mutations on virus growth using recombinant viruses generated by an RNA polymerase I-based reverse genetics system. Two reassortants of influenza virus strain A/WSN/33 were used as helper viruses to obtain two series of HA mutant viruses differing only in the neuraminidase (NA). Studies using N1 NA viruses revealed that loss of the oligosaccharide from Asn149 (mutant G2) or loss of both oligosaccharides (mutant G1,2) has a pronounced effect on virus growth in MDCK cells. Growth of virus lacking both oligosaccharides from infected cells was retarded, and virus yields in the medium were decreased about 20-fold. Likewise, there was a reduction in plaque size that was distinct with G1,2 and less pronounced with G2. These effects could be attributed to a highly impaired release of mutant progeny viruses from host cells. In contrast, with recombinant viruses containing N2 NA, these restrictions were much less apparent. N1 recombinants showed lower neuraminidase activity than N2 recombinants, indicating that N2 NA is able to partly overrule the high-affinity binding of mutant HA to the receptor. These results demonstrate that N-glycans flanking the receptor-binding site of the HA molecule are potent regulators of influenza virus growth, with the glycan at Asn149 being dominant and that at Asn123 being less effective. In addition, we show here that HA and NA activities need to be highly balanced in order to allow productive influenza virus infection. PMID:10864641

  5. Genetic algorithms and their applications to the design of neural networks. Antonia J. Jones

    E-print Network

    Jones, Antonia J.

    Genetic algorithms and their applications to the design of neural networks. Antonia J. Jones & Applications, 1(1):32-45, 1993. Copyright © 1991. Antonia J. Jones. #12;Antonia J. Jones - Version 12 October. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 #12;Antonia J. Jones - Version 12 October 2002 2 Figure 1 Generic model for a GA. Genetic

  6. Time reversal and phase conjugation with acoustic waves: industrial and medical applications

    Microsoft Academic Search

    M. Fink

    2005-01-01

    Time-reversal invariance, a fundamental symmetry that holds nearly everywhere in microscopic physics, can be exploited in a unique way in acoustics, to create a variety of useful instruments. In the past years, taking advantage of the reversibility of the acoustic propagation that holds in many situations (to the extent that everything is adiabatic) time reversal mirrors (TRMs) have been developed

  7. Application of a hybrid model of neural networks and genetic algorithms to evaluate landslide susceptibility

    NASA Astrophysics Data System (ADS)

    Wang, H. B.; Li, J. W.; Zhou, B.; Yuan, Z. Q.; Chen, Y. P.

    2013-03-01

    In the last few decades, the development of Geographical Information Systems (GIS) technology has provided a method for the evaluation of landslide susceptibility and hazard. Slope units were found to be appropriate for the fundamental morphological elements in landslide susceptibility evaluation. Following the DEM construction in a loess area susceptible to landslides, the direct-reverse DEM technology was employed to generate 216 slope units in the studied area. After a detailed investigation, the landslide inventory was mapped in which 39 landslides, including paleo-landslides, old landslides and recent landslides, were present. Of the 216 slope units, 123 involved landslides. To analyze the mechanism of these landslides, six environmental factors were selected to evaluate landslide occurrence: slope angle, aspect, the height and shape of the slope, distance to river and human activities. These factors were extracted in terms of the slope unit within the ArcGIS software. The spatial analysis demonstrates that most of the landslides are located on convex slopes at an elevation of 100-150 m with slope angles from 135°-225° and 40°-60°. Landslide occurrence was then checked according to these environmental factors using an artificial neural network with back propagation, optimized by genetic algorithms. A dataset of 120 slope units was chosen for training the neural network model, i.e., 80 units with landslide presence and 40 units without landslide presence. The parameters of genetic algorithms and neural networks were then set: population size of 100, crossover probability of 0.65, mutation probability of 0.01, momentum factor of 0.60, learning rate of 0.7, max learning number of 10 000, and target error of 0.000001. After training on the datasets, the susceptibility of landslides was mapped for the land-use plan and hazard mitigation. Comparing the susceptibility map with landslide inventory, it was noted that the prediction accuracy of landslide occurrence is 93.02%, whereas units without landslide occurrence are predicted with an accuracy of 81.13%. To sum up, the verification shows satisfactory agreement with an accuracy of 86.46% between the susceptibility map and the landslide locations. In the landslide susceptibility assessment, ten new slopes were predicted to show potential for failure, which can be confirmed by the engineering geological conditions of these slopes. It was also observed that some disadvantages could be overcome in the application of the neural networks with back propagation, for example, the low convergence rate and local minimum, after the network was optimized using genetic algorithms. To conclude, neural networks with back propagation that are optimized by genetic algorithms are an effective method to predict landslide susceptibility with high accuracy.

  8. Application of immersed MF (IMF) followed by reverse osmosis (RO) membrane for wastewater reclamation: A case study in Malaysia

    Microsoft Academic Search

    Z. Ujang; K. S. Ng; Tg Hazmin Tg Hamzah; P. Roger; M. R. Ismail; S. M. Shahabudin; M. H. Abdul Hamid

    2007-01-01

    A pilot scale membrane plant was constructed and monitored in Shah Alam, Malaysia for municipal wastewater reclamation for industrial application purposes. The aim of this study was to verify its suitability under the local conditions and environmental constraints for secondary wastewater reclamation. Immersed-type crossflow microfiltration (IMF) was selected as the pretreatment step before reverse osmosis filtration. Secondary wastewater after chlorine

  9. Ormosil approach toward developing a completely reversible hydrogen sensor for aerospace applications

    NASA Astrophysics Data System (ADS)

    Kazemi, Alex A.; Goswami, Kisholoy; Sampathkumaran, Uma

    2006-08-01

    Optical hydrogen sensors are intrinsically safe since they produce no arc or spark in an explosive environment caused by the leakage of hydrogen. Safety remains a top priority since leakage of hydrogen in air during production, storage, transfer and distribution creates an explosive atmosphere for concentrations between 4% (v/v) - the lower explosive limit (LEL) and 74.5% (v/v) - the upper explosive limit (UEL) at room temperature and pressure. Being a very small molecule, hydrogen is prone to leakage through seals and micro-cracks. Hydrogen detection in space application is very challenging; public acceptance of hydrogen fuel would require the integration of a reliable hydrogen safety sensor. For detecting leakage of cryogenic fluids in spaceport facilities, Launch vehicle industry and NASA are currently relying heavily on the bulky mass spectrometers, which fill one or more equipment racks, and weigh several hundred kilograms. An optical sensor system can decrease pay load while monitoring multiple leak locations in situ and in real time. In this paper design of ormsoil approach for developing a completely reversible optical hydrogen sensors for aerospace application is being discussed.

  10. Examination of time-reversal acoustics in shallow water and applications to noncoherent underwater communications.

    PubMed

    Smith, Kevin B; Abrantes, Antonio A M; Larraza, Andres

    2003-06-01

    The shallow water acoustic communication channel is characterized by strong signal degradation caused by multipath propagation and high spatial and temporal variability of the channel conditions. At the receiver, multipath propagation causes intersymbol interference and is considered the most important of the channel distortions. This paper examines the application of time-reversal acoustic (TRA) arrays, i.e., phase-conjugated arrays (PCAs), that generate a spatio-temporal focus of acoustic energy at the receiver location, eliminating distortions introduced by channel propagation. This technique is self-adaptive and automatically compensates for environmental effects and array imperfections without the need to explicitly characterize the environment. An attempt is made to characterize the influences of a PCA design on its focusing properties with particular attention given to applications in noncoherent underwater acoustic communication systems. Due to the PCA spatial diversity focusing properties, PC arrays may have an important role in an acoustic local area network. Each array is able to simultaneously transmit different messages that will focus only at the destination receiver node. PMID:12822782

  11. Genetics and psychiatry: a proposal for the application of the precautionary principle.

    PubMed

    Porteri, Corinna

    2013-08-01

    The paper suggests an application of the precautionary principle to the use of genetics in psychiatry focusing on scientific uncertainty. Different levels of uncertainty are taken into consideration--from the acknowledgement that the genetic paradigm is only one of the possible ways to explain psychiatric disorders, via the difficulties related to the diagnostic path and genetic methods, to the value of the results of studies carried out in this field. Considering those uncertainties, some measures for the use of genetics in psychiatry are suggested. Some of those measures are related to the conceptual limits of the genetic paradigm; others are related to present knowledge and should be re-evaluated. PMID:22460929

  12. Applications of hybrid genetic algorithms in seismic tomography

    NASA Astrophysics Data System (ADS)

    Soupios, Pantelis; Akca, Irfan; Mpogiatzis, Petros; Basokur, Ahmet T.; Papazachos, Constantinos

    2011-11-01

    Almost all earth sciences inverse problems are nonlinear and involve a large number of unknown parameters, making the application of analytical inversion methods quite restrictive. In practice, most analytical methods are local in nature and rely on a linearized form of the problem equations, adopting an iterative procedure which typically employs partial derivatives in order to optimize the starting (initial) model by minimizing a misfit (penalty) function. Unfortunately, especially for highly non-linear cases, the final model strongly depends on the initial model, hence it is prone to solution-entrapment in local minima of the misfit function, while the derivative calculation is often computationally inefficient and creates instabilities when numerical approximations are used. An alternative is to employ global techniques which do not rely on partial derivatives, are independent of the misfit form and are computationally robust. Such methods employ pseudo-randomly generated models (sampling an appropriately selected section of the model space) which are assessed in terms of their data-fit. A typical example is the class of methods known as genetic algorithms (GA), which achieves the aforementioned approximation through model representation and manipulations, and has attracted the attention of the earth sciences community during the last decade, with several applications already presented for several geophysical problems. In this paper, we examine the efficiency of the combination of the typical regularized least-squares and genetic methods for a typical seismic tomography problem. The proposed approach combines a local (LOM) and a global (GOM) optimization method, in an attempt to overcome the limitations of each individual approach, such as local minima and slow convergence, respectively. The potential of both optimization methods is tested and compared, both independently and jointly, using the several test models and synthetic refraction travel-time date sets that employ the same experimental geometry, wavelength and geometrical characteristics of the model anomalies. Moreover, real data from a crosswell tomographic project for the subsurface mapping of an ancient wall foundation are used for testing the efficiency of the proposed algorithm. The results show that the combined use of both methods can exploit the benefits of each approach, leading to improved final models and producing realistic velocity models, without significantly increasing the required computation time.

  13. Polarization Reversal Over Flooded Regions and Applications to Large-Scale Flood Mapping with Spaceborne Scatterometers

    NASA Technical Reports Server (NTRS)

    Nghiem, Son V.; Liu, W. Timothy; Xie, Xiao-Su

    1999-01-01

    We present the polarization reversal in backscatter over flooded land regions, and demonstrate for the first time the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. Scatterometer data were collected over the globe by the NASA Scatterometer (NSCAT) operated at 14 GHz on the Japanese ADEOS spacecraft from September 1996 to June 1997. During this time span, several severe floods occurred. Over most land surface, vertical polarization backscatter (Sigma(sub upsilon(upsilon)) is larger than horizontal polarization backscatter (sigma(sub hh)). Such polarization characteristics is reversed and sigma(sub upsilon(upsilon)) is smaller than sigma(sub hh) over flooded regions, except under a dense forest canopy. The total backscatter from the flooded landscape consists of direct backscatter and boundary-interaction backscatter. The direct term is contributed by direct backscattering from objects protruding above the water surface, and by backscattering from waves on the water surface. The boundary-interaction term is contributed by the forward scattering from the protruding objects and then reflected from the water surface, and also by the forward scattering from these objects after the water-surface reflection. Over flooded regions, the boundary-interaction term is dominant at large incidence angles and the strong water-surface reflection is much larger for horizontal polarization than the vertical one due to the Brewster effect in transverse-magnetic waves. These scattering mechanisms cause the polarization reversal over flooded regions. An example obtained with the Analytic Wave Theory is used to illustrate the scattering mechanisms leading to the polarization reversal. We then demonstrate the utility of spaceborne Ku-band scatterometer for large-scale flood mapping. We process NSCAT data to obtain the polarization ratio sigma(sub hh)/sigma(sub upsilon(upsilon)) with colocated data at incidence angles larger than 40 deg. The results over Asian summer monsoon regions in September-October 1996 indicate flooded areas in many countries such as Bangladesh, India, Lao, Vietnam, Cambodia, and China. Reports documented by the United Nation Department of Humanitarian Affairs (now called UN Office for the Coordination of Humanitarian Affairs) show loss of many lives and severe flood related damages which affected many million people in the corresponding flooded areas. We also map the NSCAT polarization ratio over the same regions in the "dry season" in January 1997 as a reference to confirm our results. Furthermore, we obtain concurrent ocean wind fields also derived from NSCAT data, and Asia topographic data (USGS GTOPO30) to investigate the flooded area. The results show that winds during summer monsoon season blowing inland, which perplex flood problems. Overlaying the topographic map over NSCAT results reveals an excellent correspondence between the confinement of flooded area within the relevant topographic features, which very well illustrates the value of topographic wetness index. Finally, we discuss the applications of future spaceborne scatterometers, including QuikSCAT and Seawinds, for flood mapping over the globe.

  14. From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding

    Microsoft Academic Search

    Haja N. Kadarmideen; Peter von Rohr; Luc L. G. Janss

    2006-01-01

    This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics\\u000a in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative\\u000a genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and\\u000a key findings in this research are reviewed. Various

  15. Second-law analysis and optimization of reverse brayton cycles of different configurations for cryogenic applications

    NASA Astrophysics Data System (ADS)

    Streit, James Ryder; Razani, Arsalan

    2012-06-01

    Second-law of thermodynamics (2nd law) and exergy analyses and optimization offour Reverse Brayton Refrigeration (RBR) cryogenic cycle configurations: Conventional 1-stage compression cycle; Conventional 2-stage compression cycle; 1-stage compressionModified cycle with intermediate cooling of the recuperator using an auxiliary cooler; andan Integrated 2-stage expansion RBR cycle are performed. The conventional RBR cyclesare analyzed for low and high pressure ratio applications using multistage compressorswith intercooling. Analytical solutions for the conventional cycles are developed includingthermal and fluid flow irreversibilities of the recuperators and all heat exchangers inaddition to the compression and expansion processes. Analytical solutions are used to findthe thermodynamic bounds for the performance of the cycles. Exergy irreversibilitydiagrams of the cycles are developed and the effects of important system parameters onRBR cycle performance are investigated. 2nd law/exergy analyses, and optimization of thecycles with intermediate cooling of the recuperator, considering the cooling temperatureand the recuperator effectiveness and pressure drop, are included. The effect of the 2ndlaw/exergy efficiency of the auxiliary cooler on the total system efficiencies is presented.

  16. Controlled reversal of Co/Pt Dots for nanomagnetic logic applications

    SciTech Connect

    Breitkreutz, Stephan; Kiermaier, Josef; Schmitt-Landsiedel, Doris; Becherer, Markus [Lehrstuhl fuer Technische Elektronik, Technische Universitaet Muenchen, Arcisstrasse 21, 80333 Munich (Germany); Vijay Karthik, Sankar; Csaba, Gyorgy [Center for Nano Science and Technology, University of Notre Dame, Notre Dame, Indiana 46556 (United States)

    2012-04-01

    Domain reversal in perpendicular multilayer films is governed by an intrinsic distribution of anisotropy. However, control of the switching field distribution (SFD) of field-coupled, single domain Co/Pt dots is the key to building large integrated systems for nanomagnetic logic applications. In this work, partial Ga{sup +} focused ion beam (FIB) irradiation of single-domain Co/Pt dots is employed which locally reduces the anisotropy and renders the film-inherent SFD ineffective. Controlled reduction in the switching field compared to non-irradiated dots is achieved, depending on size and dose of irradiation. TEM images of an as-grown and irradiated Co/Pt stack show a change in morphology from distinct Co/Pt interfaces to intermixed and randomly oriented grains due to the Ga{sup +} ion impact. The presented method is highly suitable to control the switching behavior in field-coupled logic devices. Experimental results are used to demonstrate a nanomagnetic fanout operation.

  17. FAR FIELD MODELLING OF ELECTROMAGNETIC TIME-REVERSAL AND APPLICATION TO SELECTIVE FOCUSING

    E-print Network

    Paris-Sud XI, Université de

    , 45A05, 74J20,78M35 1. Introduction. In the last decade, acoustic time reversal has definitely demon Emission/Reception/Time-Reversal. If the propagation medium is non dissipative, the operator T is hermitian for the acoustic scattering problem by small scatterers in the free space in [19] and in a two-dimensional straight

  18. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

    Microsoft Academic Search

    William W Lockwood; Raj Chari; Bryan Chi; Wan L Lam

    2006-01-01

    Array comparative genomic hybridization (array CGH) is a method used to detect segmental DNA copy number alterations. Recently, advances in this technology have enabled high-resolution examination for identifying genetic alterations and copy number variations on a genome-wide scale. This review describes the current genomic array platforms and CGH methodologies, highlights their applications for studying cancer genetics, constitutional disease and human

  19. Comparative application of artificial neural networks and genetic algorithms for multivariate time-series modelling

    E-print Network

    Fernandez, Thomas

    Comparative application of artificial neural networks and genetic algorithms for multivariate time of artificial neural networks and genetic algorithms in terms of forecasting and understanding of algal blooms algorithms not only perform better in seven-days-ahead predictions of algal blooms than artificial neural

  20. Stock Portfolio Evaluation: An Application of Genetic-Programming-Based Technical Analysis

    E-print Network

    Fernandez, Thomas

    Stock Portfolio Evaluation: An Application of Genetic- Programming-Based Technical Analysis Liad to predictability of stock. When attempting to create an efficient portfolio of stocks, there are numerous factors approximations to go off track. This paper presents a genetic programming approach to portfolio evaluation

  1. The reverse cholesterol transport pathway improves understanding of genetic networks for fat deposition and muscle growth in beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the present study, thirteen genes involved in the reverse cholesterol transport (RCT) pathway were investigated for their associations with three fat depositions, eight fatty acid compositions and two growth-related phenotypes in a Wagyu x Limousin reference population, including 6 F1 bulls, 113 ...

  2. Identification of Encephalomyocarditis Virus in Clinical Samples by Reverse Transcription-PCR Followed by Genetic Typing Using Sequence Analysis

    Microsoft Academic Search

    H. VANDERHALLEN; F. KOENEN

    1998-01-01

    The objective of the present study was to gain a better understanding of the epidemiology of encephalomyo- carditis virus (EMCV) infections in pigs by applying molecular techniques. The diagnostic potential of a reverse transcription-PCR (RT-PCR) targeting 286 nucleotides at the 3* end of the gene which encodes the viral polymerase was assessed with experimental and field samples. In addition, the

  3. Thermally responsive polymer systems for self-healing, reversible adhesion and shape memory applications

    NASA Astrophysics Data System (ADS)

    Luo, Xiaofan

    Responsive polymers are "smart" materials that are capable of performing prescribed, dynamic functions under an applied stimulus. In this dissertation, we explore several novel design strategies to develop thermally responsive polymers and polymer composites for self-healing, reversible adhesion and shape memory applications. In the first case described in Chapters 2 and 3, a thermally triggered self-healing material was prepared by blending a high-temperature epoxy resin with a thermoplastic polymer, poly(epsilon-caprolactone) (PCL). The initially miscible system undergoes polymerization induced phase separation (PIPS) during the curing of epoxy and yields a variety of compositionally dependent morphologies. At a particular PCL loading, the cured blend displays a "bricks-and-mortar" morphology in which epoxy exists as interconnected spheres ("bricks") within a continuous PCL matrix ("mortar"). A heat induced "bleeding" phenomenon was observed in the form of spontaneous wetting of all free surfaces by the molten PCL, and is attributed to the volumetric thermal expansion of PCL above its melting point in excess of epoxy brick expansion, which we term differential expansive bleeding (DEB). This DEB is capable of healing damage such as cracks. In controlled self-healing experiments, heating of a cracked specimen led to PCL bleeding from the bulk that yields a liquid layer bridging the crack gap. Upon cooling, a "scar" composed of PCL crystals was formed at the site of the crack, restoring a significant portion of mechanical strength. We further utilized DEB to enable strong and thermally-reversible adhesion of the material to itself and to metallic substrates, without any requirement for macroscopic softening or flow. After that, Chapters 4--6 present a novel composite strategy for the design and fabrication of shape memory polymer composites. The basic approach involves physically combining two or more functional components into an interpenetrating fiber/matrix structure, allowing them to function in a synergistic fashion yet remain physically separated. This latter aspect is critical since it enables the control of overall composite properties and functions by separately tuning each component. Utilizing the intrinsic versatility of this approach, composites with novel properties and functions (in addition to "regular" shape memory) have been developed, including (1) shape memory elastomeric composites (SMECs; Chapter 4), (2) triple-shape polymeric composites (TSPCs; Chapter 5), and (3) electrically conductive nanocomposites (Chapter 6). Then in Chapter 7, by combining the success in both thermoplastic based self-healing and shape memory polymer composites, we demonstrate a thermally triggered self-healing coating. This coating features a unique "shape memory assisted self-healing" mechanism in which crack closure (via shape memory) and crack re-bonding (via melting and diffusion of the thermoplastic healing agent) are achieved simultaneously upon a single heating step, leading to both structural and functional (corrosion resistance) recovery. Finally, Chapter 8 presents for the first time the preparation of functionally graded shape memory polymers (SMPs) that, unlike conventional SMPs, have a range of glass transition temperatures that are spatially graded. This was achieved using a temperature gradient curing method that imposes different vitrification limits at different positions along the gradient. The resulting material is capable of responding to a wide range of thermal triggers and a good candidate for low-cost, material based temperature sensors. All the aforementioned materials and methods show great potential for practical applications due to their high performance, low cost and broad applicability. Some recommendations for future research and development are given in Chapter 9.

  4. Genetic reference materials and their application to haematology

    Microsoft Academic Search

    J. R. Hawkins; M. Hawkins; J. Boyle; E. Gray; P. Matejtschuk; P. Metcalfe

    2010-01-01

    Genetic investigations are becoming increasingly useful and widespread in many areas of human health. However, there is a worldwide lack of certified reference materials for use in genetic testing, meaning that tests are being run without well validated controls and new assays are more difficult to develop and validate. We have responded to this challenge by starting a programme of

  5. Recent identity by descent in human genetic data - methods and applications 

    E-print Network

    Glodzik, Dominik

    2014-11-28

    The thesis describes algorithms for detecting regions of recent identity by descent (IBD) from human genetic data and its applications in optimising resequencing studies, genomic predictions and detecting Mendelian ...

  6. Integration of Multi-objective and Interactive Genetic Algorithms and its Application to Animation Design

    E-print Network

    Coello, Carlos A. Coello

    Integration of Multi-objective and Interactive Genetic Algorithms and its Application to Animation and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute human like motions in animation by computer graphics is a difficult task. Currently, motions

  7. Designing a multistage supply chain in cross-stage reverse logistics environments: application of particle swarm optimization algorithms.

    PubMed

    Chiang, Tzu-An; Che, Z H; Cui, Zhihua

    2014-01-01

    This study designed a cross-stage reverse logistics course for defective products so that damaged products generated in downstream partners can be directly returned to upstream partners throughout the stages of a supply chain for rework and maintenance. To solve this reverse supply chain design problem, an optimal cross-stage reverse logistics mathematical model was developed. In addition, we developed a genetic algorithm (GA) and three particle swarm optimization (PSO) algorithms: the inertia weight method (PSOA_IWM), V(Max) method (PSOA_VMM), and constriction factor method (PSOA_CFM), which we employed to find solutions to support this mathematical model. Finally, a real case and five simulative cases with different scopes were used to compare the execution times, convergence times, and objective function values of the four algorithms used to validate the model proposed in this study. Regarding system execution time, the GA consumed more time than the other three PSOs did. Regarding objective function value, the GA, PSOA_IWM, and PSOA_CFM could obtain a lower convergence value than PSOA_VMM could. Finally, PSOA_IWM demonstrated a faster convergence speed than PSOA_VMM, PSOA_CFM, and the GA did. PMID:24772026

  8. Reversal of Aggregation Using ?-Breaker Dipeptide Containing Peptides: Application to A?(1–40) Self-Assembly and Its Inhibition

    PubMed Central

    2014-01-01

    Reversion of protein or peptide aggregation is a formidable task, important in various domains of research at the interface of chemistry, medicine, and nanoscience. A novel class of dipeptides, termed as ?-breaker dipeptides (BBDPs), is identified, which can be incorporated into the self-recognizing sequences to generate a novel class of conformational switch which forms ?-sheet at an initial stage and then converts in a controlled manner to random coil at specific conditions. Incorporation of BBDPs in a well designed amyloidogenic peptides generates a special class of ?-sheet breaker peptides those undergo a chemical change at physiological condition generating a breaker element in situ. These ?-breaker peptides are shown to first incorporate into the amyloid and then disrupt it. Such conformational switches may be used to study agrregation/disaggregation process and may find many biomedical applications relevant to aggregation related disorders. Such strategy for reversion of peptide aggregation using chemical tricks may find application in material chemistry as well. PMID:24661180

  9. Speciation in reverse: morphological and genetic evidence of the collapse of a three-spined stickleback (Gasterosteus aculeatus) species pair.

    PubMed

    Taylor, E B; Boughman, J W; Groenenboom, M; Sniatynski, M; Schluter, D; Gow, J L

    2006-02-01

    Historically, six small lakes in southwestern British Columbia each contained a sympatric species pair of three-spined sticklebacks (Gasterosteus aculeatus). These pairs consisted of a 'benthic' and 'limnetic' species that had arisen postglacially and, in four of the lakes, independently. Sympatric sticklebacks are considered biological species because they are morphologically, ecologically and genetically distinct and because they are strongly reproductively isolated from one another. The restricted range of the species pairs places them at risk of extinction, and one of the pairs has gone extinct after the introduction of an exotic catfish. In another lake, Enos Lake, southeastern Vancouver Island, an earlier report suggested that its species pair is at risk from elevated levels of hybridization. We conducted a detailed morphological analysis, as well as genetic analysis of variation at five microsatellite loci for samples spanning a time frame of 1977 to 2002 to test the hypothesis that the pair in Enos Lake is collapsing into a hybrid swarm. Our morphological analysis showed a clear breakdown between benthics and limnetics. Bayesian model-based clustering indicated that two morphological clusters were evident in 1977 and 1988, which were replaced by 1997 by a single highly variable cluster. The most recent 2000 and 2002 samples confirm the breakdown. Microsatellite analysis corroborated the morphological results. Bayesian analyses of population structure in a sample collected in 1994 indicated two genetically distinct populations in Enos Lake, but only a single genetic population was evident in 1997, 2000, and 2002. In addition, genetic analyses of samples collected in 1997, 2000, and 2002 showed strong signals of 'hybrids'; they were genetically intermediate to parental genotypes. Our results support the idea that the Enos Lake species pair is collapsing into a hybrid swarm. Although the precise mechanism(s) responsible for elevated hybridization in the lake is unknown, the demise of the Enos Lake species pair follows the appearance of an exotic crayfish, Pascifasticus lenisculus, in the early 1990s. PMID:16448405

  10. Applications of Real-time Reverse Transcription Polymerase Chain Reaction in Clinical Virology Laboratories for the Diagnosis of Human Diseases

    Microsoft Academic Search

    R. Manojkumar; V. Mrudula

    2006-01-01

    Early diagnosis that prevents further expansion of the causative agent and thereby aids control and eradication of infectious agents is critical for countries trying to obtain a particular disease free status. In these diagnostics speed is paramount, including the assay's applicability, sensitivity, specificity, cost effectiveness and patentability. Real-time Reverse Transcription PCR (rRT-PCR) has revolutionized the field of molecular biology and

  11. Cystic fibrosis genetics: from molecular understanding to clinical application

    PubMed Central

    Cutting, Garry R.

    2015-01-01

    The availability of the human genome sequence and tools for interrogating individual genomes provide an unprecedented opportunity to apply genetics to medicine. Mendelian conditions, which are caused by dysfunction of a single gene, offer powerful examples that illustrate how genetics can provide insights into disease. Cystic fibrosis, one of the more common lethalautosomal recessive Mendelian disorders, is presented here as an example. Recent progress in elucidating disease mechanism and causes of phenotypic variation, as well as in the development of treatments, demonstrates that genetics continues to play an important part in cystic fibrosis research 25 years after the d iscove1y of the disease-causing gene. PMID:25404111

  12. A reverse osmosis treatment process for produced water: optimization, process control, and renewable energy application 

    E-print Network

    Mareth, Brett

    2009-06-02

    osmosis membranes were considered for demineralizing and desalinizing the water. Organo-clay adsorbant was found to be the most effective method for de-oiling, while reverse osmosis membranes were chosen over nanofiltration membranes due to superior...

  13. A Novel Application of Time Reversed Acoustics: Salt Dome Flank Imaging Using Walkaway VSP surveys

    E-print Network

    deHoop, Maarten V.

    2006-03-01

    In this paper we present initial results of applying Time-Reversed Acoustics (TRA) technology to saltdome flank, seismic imaging. We created a set of synthetic traces representing a multilevel, walkaway VSP for a model ...

  14. A reverse osmosis treatment process for produced water: optimization, process control, and renewable energy application

    E-print Network

    Mareth, Brett

    2009-06-02

    osmosis membranes were considered for demineralizing and desalinizing the water. Organo-clay adsorbant was found to be the most effective method for de-oiling, while reverse osmosis membranes were chosen over nanofiltration membranes due to superior...

  15. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

    Microsoft Academic Search

    Pierre Hilson; Joke Allemeersch; Thomas Altmann; Sébastien Aubourg; Alexandra Avon; Jim Beynon; Rishikesh P. Bhalerao; Frédérique Bitton; Michel Caboche; Bernard Cannoot; Vasil Chardakov; Cécile Cognet-Holliger; Vincent Colot; Mark Crowe; Caroline Darimont; Steffen Durinck; Holger Eickhoff; Andéol Falcon de Longuevialle; Edward E. Farmer; Murray Grant; Martin T. R. Kuiper; Hans Lehrach; Céline Léon; Antonio Leyva; Joakim Lundeberg; Claire Lurin; Yves Moreau; Wilfried Nietfeld; Javier Paz-Ares; Philippe Reymond; Pierre Rouzé; Goran Sandberg; Maria Dolores Segura; Carine Serizet; Alexandra Tabrett; Ludivine Taconnat; Vincent Thareau; Paul Van Hummelen; Steven Vercruysse; Marnik Vuylsteke; Magdalena Weingartner; Peter J. Weisbeek; Valtteri Wirta; Floyd R. A. Wittink; Marc Zabeau; Ian Small

    2004-01-01

    Abstract: Microarray transcript profiling and RNA interference are two new technologies crucial forlarge-scale gene function studies in multicellular eukaryotes. Both rely onsequence-specific hybridization between complementary nucleic acid strands, inciting us tocreate a collection of gene-specific sequence tags (GSTs) representing at least 21,500Arabidopsis genes and which are compatible with both approaches. The GSTs werecarefully selected to ensure that each of them

  16. Reverse time migration: A seismic processing application on the connection machine

    NASA Technical Reports Server (NTRS)

    Fiebrich, Rolf-Dieter

    1987-01-01

    The implementation of a reverse time migration algorithm on the Connection Machine, a massively parallel computer is described. Essential architectural features of this machine as well as programming concepts are presented. The data structures and parallel operations for the implementation of the reverse time migration algorithm are described. The algorithm matches the Connection Machine architecture closely and executes almost at the peak performance of this machine.

  17. Reverse Correlation in Neurophysiology

    ERIC Educational Resources Information Center

    Ringach, Dario; Shapley, Robert

    2004-01-01

    This article presents a review of reverse correlation in neurophysiology. We discuss the basis of reverse correlation in linear transducers and in spiking neurons. The application of reverse correlation to measure the receptive fields of visual neurons using white noise and m-sequences, and classical findings about spatial and color processing in…

  18. Ultrasonic Time Reversal Mirrors

    Microsoft Academic Search

    Mathias Fink; Gabriel Montaldo; Mickael Tanter

    2004-01-01

    For more than ten years, time reversal techniques have been developed in many different fields of applications including detection of defects in solids, underwater acoustics, room acoustics and also ultrasound medical imaging and therapy. The essential property that makes time reversed acoustics possible is that the underlying physical process of wave propagation would be unchanged if time were reversed. In

  19. Genetically engineered phage fibers and coatings for antibacterial applications

    E-print Network

    Mao, Joan Y

    2009-01-01

    Multifunctionality can be imparted to protein-based fibers and coatings via either synthetic or biological approaches. Here, we demonstrate potent antimicrobial functionality of genetically engineered, phage-based fibers ...

  20. Application of Bayesian Hierarchical Models in Genetic Data Analysis 

    E-print Network

    Zhang, Lin

    2012-08-15

    . This dissertation focuses on several important issues in genetic data analysis, graphical network modeling, feature selection, and covariance estimation. First, we develop a gene network modeling method for discrete gene expression data, produced by technologies...

  1. Genetic Algorithms applications to optimization and system identification

    E-print Network

    Lin, Yun-Jeng

    1998-01-01

    Genetic Algorithms (GA) are very different from the traditional optimization techniques. GA is a new generation of artificial intelligence and its principles mimic the behavior of the biologic genes in the natural world. Its execution is simple...

  2. The Application of Genetic Markers to Landscape Management

    Microsoft Academic Search

    Paul Sunnucks; Andrea C Taylor

    There is great concern about how landscape change will affect the persistence of native biota, and the services they provide\\u000a to human wellbeing. Of fundamental concern is the effect on population processes — birth and death rates, migration and genetic\\u000a exchange. Molecular ecology and landscape genetics make contributions to the analysis and monitoring of landscape change that\\u000a are otherwise inaccessible.

  3. Production of novel ebola virus-like particles from cDNAs: an alternative to ebola virus generation by reverse genetics.

    PubMed

    Watanabe, Shinji; Watanabe, Tokiko; Noda, Takeshi; Takada, Ayato; Feldmann, Heinz; Jasenosky, Luke D; Kawaoka, Yoshihiro

    2004-01-01

    We established a plasmid-based system for generating infectious Ebola virus-like particles (VLPs), which contain an Ebola virus-like minigenome consisting of a negative-sense copy of the green fluorescent protein gene. This system produced nearly 10(3) infectious particles per ml of supernatant, equivalent to the titer of Ebola virus generated by a reverse genetics system. Interestingly, infectious Ebola VLPs were generated, even without expression of VP24. Transmission and scanning electron microscopic analyses showed that the morphology of the Ebola VLPs was indistinguishable from that of authentic Ebola virus. Thus, this system allows us to study Ebola virus entry, replication, and assembly without biosafety level 4 containment. Furthermore, it may be useful in vaccine production against this highly pathogenic agent. PMID:14694131

  4. Implementing reverse genetics in Rosaceae: analysis of T-DNA flanking sequences of insertional mutant lines in the diploid strawberry, Fragaria vesca.

    PubMed

    Oosumi, Teruko; Ruiz-Rojas, Juan Jairo; Veilleux, Richard E; Dickerman, Allan; Shulaev, Vladimir

    2010-09-01

    Reverse genetics is used for functional genomics research in model plants. To establish a model system for the systematic reverse genetics research in the Rosaceae family, we analyzed genomic DNA flanking the T-DNA insertions in 191 transgenic plants of the diploid strawberry, Fragaria vesca. One hundred and seventy-six T-DNA flanking sequences were amplified from the right border (RB) and 37 from the left border (LB) by thermal asymmetric interlaced PCR. Analysis of the T-DNA nick positions revealed that T-DNA was most frequently nicked at the cleavage sites. Analysis of 11 T-DNA integration sites indicated that T-DNA was integrated into the F. vesca genome by illegitimate recombination, as reported in other model plants: Arabidopsis, rice and tobacco. First, deletion of DNA was found at T-DNA integration target sites in all transgenic plants tested. Second, microsimilarities of a few base pairs between the left and/or right ends of the T-DNA and genomic sites were found in all transgenic plants tested. Finally, filler DNA was identified in four break-points. Out of 191 transgenic plants, T-DNA flanking sequences of 79 plants (41%) showed significant similarity to genes, elements or proteins of other plant species and 67 (35%) of the sequences are still unknown strawberry gene fragments. T-DNA flanking sequences of 126 plants (66%) showed homology to plant ESTs. This is the first report of T-DNA integration in a sizeable population of a rosaceous species. We have shown in this paper that T-DNA integration in strawberry is not random but directed by sequence microsimilarities in the host genome. PMID:20444194

  5. Enhanced auditory reversal learning by genetic activation of protein kinase C in small groups of rat hippocampal neurons.

    PubMed

    Neill, J C; Sarkisian, M R; Wang, Y; Liu, Z; Yu, L; Tandon, P; Zhang, G; Holmes, G L; Geller, A I

    2001-09-30

    The hippocampus has a central role in specific types of learning, but there is only limited evidence identifying the requisite molecular changes in ensembles of hippocampal neurons. To investigate the role of protein kinase C (PKC) pathways in hippocampal mediated learning, a constitutively active, catalytic domain of rat PKC betaII was delivered into hippocampal dentate granule neurons using a Herpes Simplex Virus (HSV-1) vector. This PKC causes a long-lasting, activation-dependent increase in neurotransmitter release from cultured cells. Activation of PKC pathways in a small percentage (< or =0.26%) of dentate granule neurons was sufficient to enhance rat auditory discrimination reversal learning. The affected neurons altered hippocampal physiology as revealed by elevated NMDA receptor densities in specific hippocampal areas. Thus, these results directly suggest that activation of PKC pathways in a specific hippocampal area alters rat auditory discrimination reversal learning. Because each rat may contain a unique pattern of affected neurons, there appears to be considerable flexibility and/or redundancy in the groups of neurons that can modify learning. PMID:11589990

  6. An analytical application of a time-reversal mirror in a sensor with solid cylindrical waveguides

    NASA Astrophysics Data System (ADS)

    Puckett, Anthony D.; Peterson, M. L.

    2002-05-01

    A solid cylindrical waveguide or buffer rod is commonly used to isolate piezoelectric transducers from high temperature and pressure. Due to constraints on the waveguide dimensions, multiple longitudinal modes are often propagated. Dispersion and the existence of the multiple modes make it difficult to perform standard ultrasonic measurements. To simplify the measurements an analytical model was developed to model the dispersion in the multimode waveguide. This model was used to calculate the time-reversed signal required to reconstruct a pulse in the waveguide. The time-reversed signal was used in experiments to demonstrate the ability of the calculated time-reversed signal to construct a pulse. The experiments also showed the ability of the analytical model to represent the dispersion in the waveguide. Results are presented and the limitations of the analytical model presented are discussed. [Research sponsored by the Ballistic Missile Defense Organization through the ONR, Science Officer Dr. Y. D. S. Rajapakse.

  7. New genetic operators in the Fly algorithm: application to medical PET image reconstruction

    E-print Network

    Boyer, Edmond

    through the human body using methods similar to those used in conventional X-ray computed tomography [7New genetic operators in the Fly algorithm: application to medical PET image reconstruction Franck Processing, EvoApplications 2010 6024 (2010)" #12;medicine, this method makes use of a gamma emitter as radio

  8. Genetics

    NSDL National Science Digital Library

    Jennifer Doherty

    This activity helps students to understand basic principles of genetics, including relationships of genotype to phenotype, concepts of recessive and dominant alleles, and how understanding meiosis and fertilization provides the basis for understanding inheritance, as summarized in Punnett squares. The Student Handout includes an analysis of the inheritance of albinism that teaches all of these concepts, a Coin Toss Genetics activity that helps students understand the probabilistic nature of Punnett square predictions, and an analysis of the inheritance of sickle cell anemia that reinforces the basic concepts and introduces some of the complexities of genetics. The Genetics Supplement includes two additional activities, an analysis of student data on the sex makeup of sibships and pedigree analyses of recessive and dominant alleles with challenge questions that introduce the role of mutations and an evaluation of Punnett squares and pedigrees as models of inheritance.

  9. Clinical Application of Antenatal Genetic Diagnosis of Osteogenesis Imperfecta Type IV

    PubMed Central

    Yuan, Jing; Li, Song; Xu, YeYe; Cong, Lin

    2015-01-01

    Background Clinical analysis and genetic testing of a family with osteogenesis imperfecta type IV were conducted, aiming to discuss antenatal genetic diagnosis of osteogenesis imperfecta type IV. Material/Methods Preliminary genotyping was performed based on clinical characteristics of the family members and then high-throughput sequencing was applied to rapidly and accurately detect the changes in candidate genes. Results Genetic testing of the III5 fetus and other family members revealed missense mutation in c.2746G>A, pGly916Arg in COL1A2 gene coding region and missense and synonymous mutation in COL1A1 gene coding region. Conclusions Application of antenatal genetic diagnosis provides fast and accurate genetic counseling and eugenics suggestions for patients with osteogenesis imperfecta type IV and their families. PMID:25835785

  10. Application of genetics knowledge to the solution of pedigree problems

    Microsoft Academic Search

    Mark W. Hackling

    1994-01-01

    This paper reports on a study of undergraduate genetics students' conceptual and procedural knowledge and how that knowledge influences students' success in pedigree problem solving. Findings indicate that many students lack the knowledge needed to test hypotheses relating to X-linked modes of inheritance using either patterns of inheritance or genotypes. Case study data illustrate how these knowledge deficiencies acted as

  11. An application of genetic algorithm for university course timetabling problem

    Microsoft Academic Search

    Xinyang Deng; Yajuan Zhang; Bingyi Kang; Jiyi Wu; Xiaohong Sun; Yong Deng

    2011-01-01

    Timetabling problems are a process of assigning a given set of events and resources to the limited space and time under hard constraints which are rigidly enforced and soft constraints which are satisfied as nearly as possible. As a kind of timetabling problems, university course timetabling is a very important administrative activity for a wide variety of schools. Genetic algorithm

  12. ORIGINAL ARTICLE A new scoring system in cancer genetics: application

    E-print Network

    Paris-Sud XI, Université de

    of cancer due to mutations of genes such as BRCA1 and BRCA2, methods have been proposed to predict rare mutations of genes, such as BRCA1 and BRCA2 for breast­ovarian cancer and the mismatch repair for recommendation of genetic testing to affected individuals have been defined.7 For BRCA1 and BRCA2 mutations, some

  13. Genetic transformation of conifers and its application in forest biotechnology

    Microsoft Academic Search

    W. Tang; R. J. Newton

    2003-01-01

    Genetic modification of conifers through gene transfer technology is now an important field in forest biotechnology. Two basic methodologies, particle bombardment and Agrobacterium-mediated transformation, have been used on conifers. The use of particle bombardment has produced stable transgenic plants in Picea abies, P. glauca, P. mariana, and Pinus radiata. Transgenic plants have been produced from Larix decidua, Picea abies, P.

  14. Fourth derivative UV-spectroscopy of proteins under high pressure II. Application to reversible structural changes

    Microsoft Academic Search

    R. Lange; N. Bec; V. V. Mozhaev; J. Frank

    1996-01-01

    The structural basis and the thermodynamics of pressure induced reversible spectral transitions in the fourth derivative ultraviolet absorbance spectra of proteins were analysed as described in the preceding paper. Three proteins were studied: adrenodoxin (a small iron-sulphur protein that serves as an electron donor for cytochrome P450scc), ribonuclease A, and methanol dehydrogenase (a tetrameric protein). Fourth derivative spectroscopy is used

  15. Some moment properties and limit theorems of the reversed generalized logistic distribution with applications

    Microsoft Academic Search

    Mohammed A. El-Saidi; Boyan Dimitrov; Stefanka Chukova

    1996-01-01

    In this paper we discuss an extended form of the logistic distribution and refer to it as the reversed generalized logistic distribution. We study some moment properties, and derive exact and explicit formulas for the mean, median, mode, variance, coefficients of skewness and kurtosis, and percentage points of this distribution. In addition, we study its limiting distributions as the shape

  16. APPLICATION OF A SPRAY DEPOSITION METHOD FOR REVERSED PHASE LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY

    EPA Science Inventory

    Four coal gasification wastewater samples were analyzed for nonvolatile and polar organics by liquid chromatography-mass spectrometry (LC/MS). Samples were separated on a reverse phase liquid chromatographic column using an aqueous solvent as the eluant. A special spray depositio...

  17. Application of reverse Monte Carlo simulations to diatomic molecules. Part 1. Noncomplete radial distribution functions

    Microsoft Academic Search

    Léo Degrève; Fernando L. B. da Silva; Clovis Quintale; Aguinaldo R. de Souza

    1995-01-01

    The reverse Monte Carlo (RMC) method generates sets of points in space which yield radial distribution functions (RDFS) that approximate those of the system of interest. Such sets of configurations should, in principle, be sufficient to determine the structural properties of the system. In this work we apply the RMC technique to fluids of hard diatomic molecules. The “experimental” RDFs

  18. Fouling Characteristic of Reverse Osmosis Membrane and Its Application to Landfill Leachate Treatment

    Microsoft Academic Search

    W. Ruakapana; C. Chiemchaisri; J. Takemura; T. Urase

    In this study, fouling characteristics of reverse osmosis (RO) membrane applied to leachate treatment at Nonthaburi solid waste disposal site, Thailand was investigated. The stabilized leachate accumulated at the site was primarily treated by chemical coagulation followed by sand and microfiltration filtration prior to RO membrane unit. Laboratory study using cross flow filtration unit revealed that the fouling potential of

  19. Application of the combined ultrafiltration and reverse osmosis for refinery wastewater reuse in Sinopec Yanshan Plant

    Microsoft Academic Search

    Daxin Wang; Flora Tong; Peter Aerts

    2011-01-01

    The refinery wastewater reuse system of Sinopec Yanshan Plant in Beijing (China) has been in operation for more than four years. The water reuse system combines biological treatment, media filtration with a combination of ultrafiltration (UF) and reverse osmosis (RO). After more than 30?times of chemical cleaning, the current RO system salt rejection is still above 97% at 80% system

  20. Far field model for time reversal and application to selective focusing on small dielectric inhomogeneities

    E-print Network

    Paris-Sud XI, Université de

    to the electric contrast and three to the magnetic one) while each corresponding eigenfunction generates an in] in the time-harmonic case and Chen et al. [9] in the time domain. For the case of small but not necessarily by the transducer i of the TRM when transducer j emits an impulse wave. The time reversal matrix T is then defined

  1. Scattering resonances, filtering with reversible SAS processing, and applications of quantitative ray theory

    Microsoft Academic Search

    Timothy M. Marston; Philip L. Marston; Kevin L. Williams

    2010-01-01

    Features present in synthetic aperture sonar (SAS) images associated with elasticity and the structural resonances of viewed objects are sometimes neglected when using SAS data for classification purposes. Other ways of processing sonar data sometimes emphasize the frequency response of the viewed object. The research described here concerns a hybrid approach based on a reversible SAS algorithm in which the

  2. H 2-reversal trajectory: A new mission application for high-performance solar sails

    Microsoft Academic Search

    Giovanni Mengali; Alessandro A. Quarta; Daniele Romagnoli; Christian Circi

    2011-01-01

    The aim of this paper is to quantify the performance of a flat solar sail to perform a double angular momentum reversal maneuver and produce a new class of two-dimensional, non-Keplerian orbits in the ecliptic plane. For a given pair of orbital parameters, the orbital period and the perihelion distance, it is possible to find the minimum solar sail characteristic

  3. Genetic algorithms and genetic programming for multiscale modeling: Applications in materials science and chemistry and advances in scalability

    NASA Astrophysics Data System (ADS)

    Sastry, Kumara Narasimha

    2007-03-01

    Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common building blocks in organic chemistry---indicate that MOGAs produce High-quality semiempirical methods that (1) are stable to small perturbations, (2) yield accurate configuration energies on untested and critical excited states, and (3) yield ab initio quality excited-state dynamics. The proposed method enables simulations of more complex systems to realistic, multi-picosecond timescales, well beyond previous attempts or expectation of human experts, and 2--3 orders-of-magnitude reduction in computational cost. While the two applications use simple evolutionary operators, in order to tackle more complex systems, their scalability and limitations have to be investigated. The second part of the thesis addresses some of the challenges involved with a successful design of genetic algorithms and genetic programming for multiscale modeling. The first issue addressed is the scalability of genetic programming, where facetwise models are built to assess the population size required by GP to ensure adequate supply of raw building blocks and also to ensure accurate decision-making between competing building blocks. This study also presents a design of competent genetic programming, where traditional fixed recombination operators are replaced by building and sampling probabilistic models of promising candidate programs. The proposed scalable GP, called extended compact GP (eCGP), combines the ideas from extended compact genetic algorithm (eCGA) and probabilistic incremental program evolution (PIPE) and adaptively identifies, propagates and exchanges important subsolutions of a search problem. Results show that eCGP scales cubically with problem size on both GP-easy and GP-hard problems. Finally, facetwise models are developed to explore limitations of scalability of MOGAs, where the scalability of multiobjective algorithms in reliably maintaining Pareto-optimal solutions is addressed. The results show that even when the building blocks are accurately identified, massive multimodality of the search problems can easily overwhelm the nicher (diversity preserving operator) and l

  4. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    PubMed

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

  5. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    PubMed Central

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. PMID:22253801

  6. Genetics

    NSDL National Science Digital Library

    National Science Teachers Association (NSTA)

    2005-04-01

    What affects how physical characteristics are transmitted from parent to offspring? This is a question that can be answered at many levels. Molecular biologists examine the pattern of nucleotides in deoxyribonucleic acid (DNA) and the effect of mutations on the proteins produced. Classical geneticists explore the patterns by which traits are transmitted through families. Medical geneticists attempt to describe and develop treatments for diseases that have a genetic component. Genetic engineers analyze how traits can be altered in organisms through modern technology. These are only a few of the strategies that scientists employ to explain the nature of heredity. Explore historical perspectives on the study of genetics and investigate how cutting-edge technology is being used to expand our understanding of heredity.

  7. Genetic Algorithms And Its Application To Economic Load Dispatch

    NASA Astrophysics Data System (ADS)

    Borana, Kavita

    2010-11-01

    Genetic Algorithm (GA) is a search method that simulates the process of natural selection and it attempts to find a good solution to some problem by randomly generating a collection of potential solutions to the problem and then manipulating those solutions using genetic operators. Through selection, mutation and re-combination (crossover) operations, better solutions are hopefully generated out of the current set of potential solutions. This process continues until an acceptable solution is found. GA is becoming popular to solve the optimization problems mainly because of its robustness in finding optimal solution and ability to provide near optimal solution close to global optimum. The ELD approach is tested on sample 3-generator system with the load of 24 hours.

  8. Polygenic risk scores in imaging genetics: Usefulness and applications.

    PubMed

    Dima, Danai; Breen, Gerome

    2015-08-01

    Genetic factors account for up to 80% of the liability for schizophrenia and bipolar disorder. Genome-wide association studies (GWAS) have successfully identified several single nucleotide polymorphisms (SNPs) and genes associated with increased risk for both disorders. Single SNP analyses alone do not address the overall genomic or polygenic architecture of psychiatric disorders as the amount of phenotypic variation explained by each GWAS-supported SNP is small whereas the number of SNPs/regions underlying risk for illness is thought to be very large. The polygenic risk score models the aggregate effect of alleles associated with disease status present in each individual and allows us to utilise the power of large GWAS to be applied robustly in small samples. Here we make the case that risk prediction, intervention and personalised medicine can only benefit with the inclusion of polygenic risk scores in imaging genetics research. PMID:25944849

  9. Version 3 June 25, 1996 for Handbook of Evolutionary Computation. Future Work and Practical Applications of Genetic Programming

    E-print Network

    Fernandez, Thomas

    Applications of Genetic Programming John R. Koza Computer Science Department Stanford University 258 Gates@CS.Stanford.Edu WWW ADDRESS: http://www-cs-faculty.stanford.edu/~koza/ ABSTRACT Genetic programming is a relatively avenues for possible future research on genetic programming, opportunities to extend the technique

  10. A Research and Knowledge Network on Genetic Health Services and is launching a call for applications for

    E-print Network

    Shoubridge, Eric

    1/3 A Research and Knowledge Network on Genetic Health Services and Policy is launching a call Institutes for Health Research Emerging Team Grant (CIHR, Institute of Genetics and Institute of Health health applications of genetic research. However, the lack of planning and the absence of a structured

  11. Application of genetics knowledge to the solution of pedigree problems

    Microsoft Academic Search

    Mark W Hackling

    1994-01-01

    This paper reports on a study of undergraduate genetics students' conceptual and procedural knowledge and how that knowledge\\u000a influences students' success in pedigree problem solving. Findings indicate that many students lack the knowledge needed to\\u000a test hypotheses relating to X-linked modes of inheritance using either patterns of inheritance or genotypes. Case study data\\u000a illustrate how these knowledge deficiencies acted as

  12. Barriers to application of genetically modified lactic acid bacteria.

    PubMed

    Verrips, C T; van den Berg, D J

    1996-10-01

    To increase the acceptability of food products containing genetically modified microorganisms it is necessary to provide in an early stage to the consumers that the product is safe and that the product provide a clear benefit to the consumer. To comply with the first requirement a systematic approach to analyze the probability that genetically modified lactic acid bacteria will transform other inhabitants of the gastro- intestinal (G/I) tract or that these lactic acid bacteria will pick up genetic information of these inhabitants has been proposed and worked out to some degree. From this analysis it is clear that reliable data are still missing to carry out complete risk assessment. However, on the basis of present knowledge, lactic acid bacteria containing conjugative plasmids should be avoided. Various studies show that consumers in developed countries will accept these products when they offer to them health or taste benefits or a better keepability. For the developing countries the biggest challenge for scientists is most likely to make indigenous fermented food products with strongly improved microbiological stability due to broad spectra bacteriocins produced by lactic acid bacteria. Moreover, these lactic acid bacteria may contribute to health. PMID:8879412

  13. Genetic algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  14. Sequential application of major habit-reversal components to treat motor tics in children.

    PubMed Central

    Woods, D W; Miltenberger, R G; Lumley, V A

    1996-01-01

    In this study, we sequentially administered up to four components of the habit-reversal treatment to 4 children with motor tics within a multiple baseline design. The habit-reversal components included (a) awareness training; (b) awareness training and self-monitoring; (c) awareness training, self-monitoring, and social support; and (d) awareness training, social support, and the use of a competing response. Results demonstrated that the combined use of awareness training, social support, and competing response training was effective in eliminating motor tics in 2 of 4 children, that awareness training alone was effective for 1 child, and that a combination of awareness training and self-monitoring was effective for the 4th child. The treatment and ensuing improvement were found to be socially valid. We discuss possible explanations for these results and recommend directions for future research. PMID:8995831

  15. A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity

    USGS Publications Warehouse

    Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M.; Vakharia, Vikram N.

    2011-01-01

    Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-?NV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-?NV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-?NV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines.

  16. A reverse genetics system for the Great Lakes strain of viral hemorrhagic septicemia virus: the NV gene is required for pathogenicity.

    PubMed

    Ammayappan, Arun; Kurath, Gael; Thompson, Tarin M; Vakharia, Vikram N

    2011-08-01

    Viral hemorrhagic septicemia virus (VHSV), belonging to the genus Novirhabdovirus in the family of Rhabdoviridae, causes a highly contagious disease of fresh and saltwater fish worldwide. Recently, a novel genotype of VHSV, designated IVb, has invaded the Great Lakes in North America, causing large-scale epidemics in wild fish. An efficient reverse genetics system was developed to generate a recombinant VHSV of genotype IVb from cloned cDNA. The recombinant VHSV (rVHSV) was comparable to the parental wild-type strain both in vitro and in vivo, causing high mortality in yellow perch (Perca flavescens). A modified recombinant VHSV was generated in which the NV gene was substituted with an enhanced green fluorescent protein gene (rVHSV-?NV-EGFP), and another recombinant was made by inserting the EGFP gene into the full-length viral clone between the P and M genes (rVHSV-EGFP). The in vitro replication kinetics of rVHSV-EGFP was similar to rVHSV; however, the rVHSV-?NV-EGFP grew 2 logs lower. In yellow perch challenges, wtVHSV and rVHSV induced 82-100% cumulative per cent mortality (CPM), respectively, whereas rVHSV-EGFP produced 62% CPM and rVHSV-?NV-EGFP caused only 15% CPM. No reversion of mutation was detected in the recovered viruses and the recombinant viruses stably maintained the foreign gene after several passages. These results indicate that the NV gene of VHSV is not essential for viral replication in vitro and in vivo, but it plays an important role in viral replication efficiency and pathogenicity. This system will facilitate studies of VHSV replication, virulence, and production of viral vectored vaccines. PMID:20936318

  17. Low-loss microelectrodes fabricated using reverse-side exposure for a tunable ferroelectric capacitor application

    Microsoft Academic Search

    Yong-Kyu Yoon; J Stevenson Kenney; Andrew T Hunt; Mark G Allen

    2006-01-01

    Narrowly spaced thick microelectrodes are fabricated using a self-aligned multiple reverse-side exposure scheme for an improved quality-factor tunable ferroelectric capacitor. The microelectrodes are fabricated on a functional substrate—a thin film ferroelectric (barium strontium titanate, BST; BaxSr1?xTiO3) coated sapphire substrate, which has an electric-field-dependent dielectric property providing tuning functionality, as well as UV transparency permitting an additional degree of freedom in

  18. Particulate and organic matter fouling of seawater reverse osmosis systems: Characterization, modelling and applications

    Microsoft Academic Search

    S. G. Salinas Rodriguez

    2011-01-01

    Particulate\\/colloidal and organic fouling in seawater reverse osmosis (SWRO) systems results in flux decline, higher energy costs, increased salt passage, increased cleaning frequency, and use of chemicals. In practice, indices like SDI and MFI are used to assess particulate fouling, but they are performed at very high initial flux (> 1500 L\\/m2-h) and do not take into account the deposition

  19. Performance and cost of energy transport and storage systems for dish applications using reversible chemical reactions

    Microsoft Academic Search

    J. M. Schredder; T. Fujita

    1984-01-01

    The use of reversible chemical reactions for energy transport and storage for parabolic dish networks is considered. Performance and cost characteristics are estimated for systems using three reactions (sulfur-trioxide decomposition, steam reforming of methane, and carbon-dioxide reforming of methane). Systems are considered with and without storage, and in several energy-delivery configurations that give different profiles of energy delivered versus temperature.

  20. Reverse line blot hybridization with species-specific oligonucleotide probes: application to piroplasm detection.

    PubMed

    Hurtado, Ana

    2015-01-01

    Reverse line blot (RLB) hybridization has become a well-established and widely used method for the multiplex identification of several Babesia and Theileria species in hosts and tick vectors. The procedure is based on the simultaneous PCR amplification of a polymorphic region of the 18S rRNA gene from different piroplasms followed by identification of the individual species by hybridization to species-specific oligonucleotide probes covalently linked to a nylon membrane in a macroarray format. PMID:25399097

  1. Applicability of the Reverse-Flow Filter Technique to Marine Microbial Studies1

    PubMed Central

    Griffiths, Robert P.; Hanus, F. J.; Morita, Richard Y.

    1973-01-01

    The use of the reverse-flow filtration technique to quantitatively concentrate marine bacteria was evaluated using both a pure culture and seawater samples. Our data indicate that the cells are altered during the filtration procedure and that a significant and inconsistent number of cells are lost on the membrane filter. The results obtained indicate that data on marine bacteria concentrated in this manner should be interpreted with caution. PMID:4586929

  2. H2-reversal trajectory: A new mission application for high-performance solar sails

    NASA Astrophysics Data System (ADS)

    Mengali, Giovanni; Quarta, Alessandro A.; Romagnoli, Daniele; Circi, Christian

    2011-12-01

    The aim of this paper is to quantify the performance of a flat solar sail to perform a double angular momentum reversal maneuver and produce a new class of two-dimensional, non-Keplerian orbits in the ecliptic plane. For a given pair of orbital parameters, the orbital period and the perihelion distance, it is possible to find the minimum solar sail characteristic acceleration required to fulfil a double angular momentum reversal trajectory. This problem is addressed using an optimal formulation and is solved through an indirect approach. The new trajectories are symmetrical with respect to the sun-perihelion line and exhibit a bean-like shape. Two main difficulties must be properly taken into account. On one side the sail is required to perform a rapid reorientation maneuver when it approaches the perihelion. Suitable simulations have shown that such a maneuver is feasible. In the second place the new trajectories require the use of high performance solar sails. For example, assuming an orbital period equal to 5 years, the required solar sail characteristic acceleration is greater than 3.4 mm/s2. Such a value, although beyond the currently available sail performance, is comparable to what is required by the original concept of H-reversal maneuvers introduced by Vulpetti in 1996.

  3. Reverse engineering biological networks :applications in immune responses to bio-toxins.

    SciTech Connect

    Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-12-01

    Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

  4. Noninvasive Genetic Techniques and itsNoninvasive Genetic Techniques and its Application in Wildlife ConservationApplication in Wildlife Conservation

    E-print Network

    Gray, Matthew

    Regurgitates Found at roosting sitesFound at roosting sites of owlsof owls UrineUrine Wolf and wolverine studiesWolf and wolverine studies ApplicationsApplications #12;9 Abundance EstimationAbundance Estimation Obtaining reliable

  5. Application of Carbonate Reservoir using waveform inversion and reverse-time migration methods

    NASA Astrophysics Data System (ADS)

    Kim, W.; Kim, H.; Min, D.; Keehm, Y.

    2011-12-01

    Recent exploration targets of oil and gas resources are deeper and more complicated subsurface structures, and carbonate reservoirs have become one of the attractive and challenging targets in seismic exploration. To increase the rate of success in oil and gas exploration, it is required to delineate detailed subsurface structures. Accordingly, migration method is more important factor in seismic data processing for the delineation. Seismic migration method has a long history, and there have been developed lots of migration techniques. Among them, reverse-time migration is promising, because it can provide reliable images for the complicated model even in the case of significant velocity contrasts in the model. The reliability of seismic migration images is dependent on the subsurface velocity models, which can be extracted in several ways. These days, geophysicists try to obtain velocity models through seismic full waveform inversion. Since Lailly (1983) and Tarantola (1984) proposed that the adjoint state of wave equations can be used in waveform inversion, the back-propagation techniques used in reverse-time migration have been used in waveform inversion, which accelerated the development of waveform inversion. In this study, we applied acoustic waveform inversion and reverse-time migration methods to carbonate reservoir models with various reservoir thicknesses to examine the feasibility of the methods in delineating carbonate reservoir models. We first extracted subsurface material properties from acoustic waveform inversion, and then applied reverse-time migration using the inverted velocities as a background model. The waveform inversion in this study used back-propagation technique, and conjugate gradient method was used in optimization. The inversion was performed using the frequency-selection strategy. Finally waveform inversion results showed that carbonate reservoir models are clearly inverted by waveform inversion and migration images based on the inversion results are quite reliable. Different thicknesses of reservoir models were also described and the results revealed that the lower boundary of the reservoir was not delineated because of energy loss. From these results, it was noted that carbonate reservoirs can be properly imaged and interpreted by waveform inversion and reverse-time migration methods. This work was supported by the Energy Resources R&D program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government Ministry of Knowledge Economy (No. 2009201030001A, No. 2010T100200133) and the Brain Korea 21 project of Energy System Engineering.

  6. Identification of Encephalomyocarditis Virus in Clinical Samples by Reverse Transcription-PCR Followed by Genetic Typing Using Sequence Analysis

    PubMed Central

    Vanderhallen, H.; Koenen, F.

    1998-01-01

    The objective of the present study was to gain a better understanding of the epidemiology of encephalomyocarditis virus (EMCV) infections in pigs by applying molecular techniques. The diagnostic potential of a reverse transcription-PCR (RT-PCR) targeting 286 nucleotides at the 3? end of the gene which encodes the viral polymerase was assessed with experimental and field samples. In addition, the use of the amplified sequences for an epidemiological study was evaluated. The heart was clearly shown to be the most suitable organ. The detection limit was determined to be 1 viral particle in 100 mg of heart tissue. The sensitivity and specificity of the assay on the basis of the results obtained in this study were 94 and 100%, respectively. Phylogenetic analysis of the amplified sequences classified EMCVs in two distinct lineages. Group A consists of the reference strain ATCC 129B, all isolates collected between 1991 and 1994 in Belgium in association with reproductive failure, and all Greek isolates. All Belgian isolates collected since the first isolation of EMCV in relation to myocardial failure in fatteners in Belgium group together with the isolates from Cyprus (1996 and 1997), Italy (1986 to 1996), and France (1995) in group B irrespective of their pathogenicity. The analyzed part of the 3D gene differed by 13.0% between Groups A and B. In contrast to the sequence homogeneity of the Belgian isolates collected between 1991 and 1994, molecular diversity, which ranged between 0 and 2%, was observed among the Belgian isolates collected in 1995 and 1996. Among all Greek isolates the diversity ranged between 1 and 8%. However, this diversity does not seem to reflect geographical links between the outbreaks. A RT-PCR for the rapid and specific diagnosis of EMCV in a variety of clinical samples followed by nucleotide sequence analysis proved to be valuable for molecular epidemiological studies. PMID:9817855

  7. Application of coevolutionary genetic algorithms for multiobjective optimization

    NASA Astrophysics Data System (ADS)

    Liu, Jian-guo; Li, Zu-shu; Wu, Wei-ping

    2007-12-01

    Multiobjective optimization is clearly one of the most important classes of problems in science and engineering. The solution of real problem involved in multiobjective optimization must satisfy all optimization objectives simultaneously, and in general the solution is a set of indeterminacy points. The task of multiobjective optimization is to estimate the distribution of this solution set, then to find the satisfying solution in it. Many methods solving multiobjective optimization using genetic algorithm have been proposed in recent twenty years. But these approaches tend to work negatively, causing that the population converges to small number of solutions due to the random genetic drift. To avoid this phenomenon, a multiobjective coevolutionary genetic algorithm (MoCGA) for multiobjective optimization is proposed. The primary design goal of the proposed approach is to produce a reasonably good approximation of the true Pareto front of a problem. In the algorithms, each objective corresponds to a population. At each generation, these populations compete among themselves. An ecological population density competition equation is used for reference to describe the relation between multiple objectives and to direct the adjustment over the relation at individual and population levels. The proposed approach store the Pareto optimal point obtained along the evolutionary process into external set. The proposed approach is validated using Schaffer's test function f II and it is compared with the Niched Pareto GA (nPGA). Simulation experiments prove that the algorithm has a better performance in finding the Pareto solutions, and the MoCGA can have advantages over the other algorithms under consideration in convergence to the Pareto-optimal front.

  8. Application of Genetic Algorithms in Nonlinear Heat Conduction Problems

    PubMed Central

    Khan, Waqar A.

    2014-01-01

    Genetic algorithms are employed to optimize dimensionless temperature in nonlinear heat conduction problems. Three common geometries are selected for the analysis and the concept of minimum entropy generation is used to determine the optimum temperatures under the same constraints. The thermal conductivity is assumed to vary linearly with temperature while internal heat generation is assumed to be uniform. The dimensionless governing equations are obtained for each selected geometry and the dimensionless temperature distributions are obtained using MATLAB. It is observed that GA gives the minimum dimensionless temperature in each selected geometry. PMID:24695517

  9. Application of genetic algorithms in nonlinear heat conduction problems.

    PubMed

    Kadri, Muhammad Bilal; Khan, Waqar A

    2014-01-01

    Genetic algorithms are employed to optimize dimensionless temperature in nonlinear heat conduction problems. Three common geometries are selected for the analysis and the concept of minimum entropy generation is used to determine the optimum temperatures under the same constraints. The thermal conductivity is assumed to vary linearly with temperature while internal heat generation is assumed to be uniform. The dimensionless governing equations are obtained for each selected geometry and the dimensionless temperature distributions are obtained using MATLAB. It is observed that GA gives the minimum dimensionless temperature in each selected geometry. PMID:24695517

  10. Feature generation using genetic programming with application to fault classification.

    PubMed

    Guo, Hong; Jack, Lindsay B; Nandi, Asoke K

    2005-02-01

    One of the major challenges in pattern recognition problems is the feature extraction process which derives new features from existing features, or directly from raw data in order to reduce the cost of computation during the classification process, while improving classifier efficiency. Most current feature extraction techniques transform the original pattern vector into a new vector with increased discrimination capability but lower dimensionality. This is conducted within a predefined feature space, and thus, has limited searching power. Genetic programming (GP) can generate new features from the original dataset without prior knowledge of the probabilistic distribution. In this paper, a GP-based approach is developed for feature extraction from raw vibration data recorded from a rotating machine with six different conditions. The created features are then used as the inputs to a neural classifier for the identification of six bearing conditions. Experimental results demonstrate the ability of GP to discover autimatically the different bearing conditions using features expressed in the form of nonlinear functions. Furthermore, four sets of results--using GP extracted features with artificial neural networks (ANN) and support vector machines (SVM), as well as traditional features with ANN and SVM--have been obtained. This GP-based approach is used for bearing fault classification for the first time and exhibits superior searching power over other techniques. Additionaly, it significantly reduces the time for computation compared with genetic algorithm (GA), therefore, makes a more practical realization of the solution. PMID:15719936

  11. The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry

    ERIC Educational Resources Information Center

    Gary, Ronald K.

    2004-01-01

    The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to…

  12. Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus

    PubMed Central

    Scobey, Trevor; Yount, Boyd L.; Sims, Amy C.; Donaldson, Eric F.; Agnihothram, Sudhakar S.; Menachery, Vineet D.; Graham, Rachel L.; Swanstrom, Jesica; Bove, Peter F.; Kim, Jeeho D.; Grego, Sonia; Randell, Scott H.; Baric, Ralph S.

    2013-01-01

    Severe acute respiratory syndrome with high mortality rates (?50%) is associated with a novel group 2c betacoronavirus designated Middle East respiratory syndrome coronavirus (MERS-CoV). We synthesized a panel of contiguous cDNAs that spanned the entire genome. Following contig assembly into genome-length cDNA, transfected full-length transcripts recovered several recombinant viruses (rMERS-CoV) that contained the expected marker mutations inserted into the component clones. Because the wild-type MERS-CoV contains a tissue culture-adapted T1015N mutation in the S glycoprotein, rMERS-CoV replicated ?0.5 log less efficiently than wild-type virus. In addition, we ablated expression of the accessory protein ORF5 (rMERS•ORF5) and replaced it with tomato red fluorescent protein (rMERS-RFP) or deleted the entire ORF3, 4, and 5 accessory cluster (rMERS-?ORF3–5). Recombinant rMERS-CoV, rMERS-CoV•ORF5, and MERS-CoV-RFP replicated to high titers, whereas MERS-?ORF3–5 showed 1–1.5 logs reduced titer compared with rMERS-CoV. Northern blot analyses confirmed the associated molecular changes in the recombinant viruses, and sequence analysis demonstrated that RFP was expressed from the appropriate consensus sequence AACGAA. We further show dipeptidyl peptidase 4 expression, MERS-CoV replication, and RNA and protein synthesis in human airway epithelial cell cultures, primary lung fibroblasts, primary lung microvascular endothelial cells, and primary alveolar type II pneumocytes, demonstrating a much broader tissue tropism than severe acute respiratory syndrome coronavirus. The availability of a MERS-CoV molecular clone, as well as recombinant viruses expressing indicator proteins, will allow for high-throughput testing of therapeutic compounds and provide a genetic platform for studying gene function and the rational design of live virus vaccines. PMID:24043791

  13. A General Reversible Hereditary Constitutive Model. Part 2; Application to a Titanium Alloy

    NASA Technical Reports Server (NTRS)

    Arnold, S. M.; Saleeb, A. F.; Castelli, M. G.

    1997-01-01

    Given the mathematical framework and specific viscoelastic model in Part 1 our primary goal in this second part is focused on model characterization and assessment for the specific titanium alloy, TIMETAL 21S. The model is motivated by experimental evidence suggesting the presence of significant rate/time effects in the so-called quasilinear, reversible, material response range. An explanation of the various experiments performed and their corresponding results are also included. Finally, model correlations and predictions are presented for a wide temperature range.

  14. Development of a reverse-genetics system for Avian pneumovirus demonstrates that the small hydrophobic (SH) and attachment (G) genes are not essential for virus viability.

    PubMed

    Naylor, Clive J; Brown, Paul A; Edworthy, Nicole; Ling, Roger; Jones, Richard C; Savage, Carol E; Easton, Andrew J

    2004-11-01

    Avian pneumovirus (APV) is a member of the genus Metapneumovirus of the subfamily Pneumovirinae. This study describes the development of a reverse-genetics system for APV. A minigenome system was used to optimize the expression of the nucleoprotein, phosphoprotein, M2 and large polymerase proteins when transfected into Vero cells under the control of the bacteriophage T7 promoter. Subsequently, cDNA was transcribed from the virion RNA to make a full-length antigenome, which was also cloned under the control of the T7 promoter. Transfection of the full-length genome plasmid, together with the plasmids expressing the functional proteins in the transcription and replication complex, generated APV in the transfected cells. The recombinant virus was passaged and was identified by cytopathic effect (CPE) that was typical of APV, the presence of a unique restriction-endonuclease site in the cDNA copy of the genome and immunofluorescence staining with anti-APV antibodies. Replacement of the full-length wild-type antigenome with one lacking the small hydrophobic (SH) protein and the attachment (G) genes generated a virus that grew more slowly and produced atypical CPE with syncytia much larger than those seen with wild-type virus. PMID:15483235

  15. Generation by reverse genetics of an effective, stable, live-attenuated newcastle disease virus vaccine based on a currently circulating, highly virulent Indonesian strain.

    PubMed

    Xiao, Sa; Nayak, Baibaswata; Samuel, Arthur; Paldurai, Anandan; Kanabagattebasavarajappa, Mallikarjuna; Prajitno, Teguh Y; Bharoto, Eny E; Collins, Peter L; Samal, Siba K

    2012-01-01

    Newcastle disease virus (NDV) can cause severe disease in chickens. Although NDV vaccines exist, there are frequent reports of outbreaks in vaccinated chickens. During 2009-2010, despite intense vaccination, NDV caused major outbreaks among commercial poultry farms in Indonesia. These outbreaks raised concern regarding the protective immunity of current vaccines against circulating virulent strains in Indonesia. In this study, we investigated whether a recombinant attenuated Indonesian NDV strain could provide better protection against prevalent Indonesian viruses. A reverse genetics system for the highly virulent NDV strain Banjarmasin/010/10 (Ban/010) isolated in Indonesia in 2010 was constructed. The Ban/010 virus is classified in genotype VII of class II NDV, which is genetically distinct from the commercial vaccine strains B1 and LaSota, which belong to genotype II, and shares only 89 and 87% amino acid identity for the protective antigens F and HN, respectively. A mutant virus, named Ban/AF, was developed in which the virulent F protein cleavage site motif "RRQKR?F" was modified to an avirulent motif "GRQGR?L" by three amino acid substitutions (underlined). The Ban/AF vaccine virus did not produce syncytia or plaques in cell culture, even in the presence of added protease. Pathogenicity tests showed that Ban/AF was completely avirulent. Ban/AF replicated efficiently during 10 consecutive passages in chickens and remained genetically stable. Serological analysis showed that Ban/AF induced higher neutralization and hemagglutination inhibition antibody titers against the prevalent viruses than the commercial vaccines B1 or LaSota. Both Ban/AF and commercial vaccines provided protection against clinical disease and mortality after challenge with virulent NDV strain Ban/010 (genotype VII) or GB Texas (genotype II). However, Ban/AF significantly reduced challenge virus shedding from the vaccinated birds compared to B1 vaccine. These results suggest that Ban/AF can provide better protection than commercial vaccines and is a promising vaccine candidate against NDV strains circulating in Indonesia. PMID:23285174

  16. Time reversal of scattering wavefield with applications for imaging fault damaged zones close to bimaterial interfaces

    NASA Astrophysics Data System (ADS)

    Benites, R. A.; Ben-Zion, Y.

    2010-12-01

    We demonstrate that a time-reverse mirror (TRM) of data recorded by an array of broadband surface seismometers distributed across a bimaterial fault interface separating two quarter spaces, one of which includes a damaged zone with high crack density, can be used to image the spatial distribution of the damage. The generic cases presented in this study consider the damaged zone to be a region containing many thin, elliptical cracks randomly distributed laterally next to the fault and extending vertically down, in the medium with slower average S-wave velocity. The incident seismic wave is produced by a strike-slip line source corresponding to slip right on the fault plane at some prescribed depth. We first solve the forward problem, i.e. compute the full waveform synthetic seismogram at each element of the array using a boundary integral numerical scheme. Then we subtract the incident wave from each seismogram and time-reverse only the scattered wavefield, last phase first, back to their origin. The results show that the computed image can be obtained with high resolution for an array aperture size comparable to four times the largest length scale (width or depth) of the damage zone, and a seismometer interval distance comparable to one quarter of the smallest wavelength considered in the calculations. We present results of such images for several random realizations of crack distribution.

  17. The Application of Genetic Fuzzy Neural Network in Project Cost Estimate

    Microsoft Academic Search

    Wen-Juan Zhu; Wen-Feng Feng; Yu-Guang Zhou

    2010-01-01

    Applications of neural network were widely used in construct project cost estimate. Aim at handling weakness of poor convergence and insufficient forecast, an improved fuzzy neural network method based on SOFM (self-organizing feature map) and GA (genetic algorithm) was proposed to replace the fashionable T-S fuzzy neural network. The method illustrated how to apply SOFM and GA to improve the

  18. Application of Pareto ranked genetic algorithm to a wearable ball spiral antenna

    Microsoft Academic Search

    R. M. Edwards; J. A. Brister; M. I. Khattak

    2010-01-01

    This paper is concerned with the application of a Pareto ranked genetic algorithm to a new type of wearable antenna. To illustrate the method the technique was first applied as a multiobjective method search with a curl antenna. This antenna was an equivalent printed spiral which was a probe fed single arm Archimedean spiral. The same technique will then be

  19. A low sidelobe level nonequispaced microstrip array antenna design for BTS application using genetic algorithm

    Microsoft Academic Search

    S. Ebadi; N. Amiri; K. Forooraghi

    2005-01-01

    Achieving low side lobe level array antennas without implementation of phase shifters or amplitude tapering is a valuable solution in cases, which the simplicity of the structure is of high importance. In this paper a low sidelobe level microstrip array antenna is designed for GSM base-station antenna application using genetic algorithm by variation of the distances between elements around their

  20. THE HUMAN GENOME & GENETIC DISEASES MED263: Bioinformatic Applications to Human Disease

    E-print Network

    Gleeson, Joseph G.

    you will learn. History of the human genome project Structure and content of the human genome HapTHE HUMAN GENOME & GENETIC DISEASES MED263: Bioinformatic Applications to Human Disease #12;WhatMap project Categories of Human Disease: Monogenic (Single gene disorders) Multigenic (Complex disorders

  1. Parallelized genetic optimization of spatial light modulator addressing for diffractive applications.

    PubMed

    Haist, Tobias; Lingel, Christian; Adler, Rodolfo; Osten, Wolfgang

    2014-03-01

    We describe a new technique for optimizing the addressing of spatial light modulators in dynamic holographic applications. The method utilizes 200 times parallelization using imaging of subholograms in combination with genetic optimization. Compared to a fixed linear addressing curve for all different gratings, the diffraction efficiency can be improved by up to 25% for a Holoeye Pluto LCoS modulator. PMID:24663371

  2. A self-tuning genetic algorithm with applications in biomarker discovery

    E-print Network

    A self-tuning genetic algorithm with applications in biomarker discovery Dusan Popovic, Charalampos, feature selection, biomarker discovery I. INTRODUCTION The rapid development of high of the biomarker discovery process. Typical high-throughput experiment results in several thousands measures per

  3. Application of the polymerase chain reaction to the diagnosis of human genetic disease

    Microsoft Academic Search

    Jochen Reiss; David N. Cooper

    1990-01-01

    In vitro DNA amplification by means of the polymerase chain reaction is currently revolutionizing human molecular genetics. Since its inception in 1985, a wide variety of different methods and their applications in the diagnosis of disease have been described. This review is intended to serve as a brief guide to current and emerging possibilities in this rapidly expanding field.

  4. Computing genetic evaluations through application of generalized least squares to an animal model

    E-print Network

    Paris-Sud XI, Université de

    Computing genetic evaluations through application of generalized least squares to an animal model G.F.S. HUDSON Department of Animal Sciences, University of Maryland, College Park, Maryland 20742, U.S.A. Summary The animal model for performance data is rewritten in the form of a fixed model with uncorrelated

  5. Genetics

    NSDL National Science Digital Library

    The Tech Museum of Innovation

    2004-01-01

    This online tutorial from the TheTech Museum of Innovation focuses on genetics. The interactive topics will initially introduce the user to the DNA, chromosomes, and the make up of human genes. Further topics will examine forensic science, the history of forensics, fingerprinting, and cloning background research and community response to cloning. Finally, the resource provides connections to gallery exhibits, science labs, and a design challenge that engages the learner to write a persuasive letter to a group or organization responsible for cloning or DNA decision making. Copyright 2005 International Technology Education Association

  6. Application of Genetic Algorithm to Optimal Design of Central Air-Conditioning Water System

    E-print Network

    Feng, X.; Zou, Y.; Long, W.

    2006-01-01

    Efficiency and Comfort, Vol. VI-2-1 inherited[1,2,3]. Genetic algorithms applicated in pipe optimal design have the advantages as follows. (1)Genetic algorithms only need fitness value and don?t depend on the question. It can adapt to the requirement... is high. (3) When objective function change with system running cases ,some optimal algorithms lying upon objective function can not fit to the change. However, GA don?t depend on objective functions, It can adapt to new conditions when some small...

  7. Efficient Reverse Genetics Reveals Genetic Determinants of Budding and Fusogenic Differences between Nipah and Hendra Viruses and Enables Real-Time Monitoring of Viral Spread in Small Animal Models of Henipavirus Infection

    PubMed Central

    Yun, Tatyana; Park, Arnold; Hill, Terence E.; Pernet, Olivier; Beaty, Shannon M.; Juelich, Terry L.; Smith, Jennifer K.; Zhang, Lihong; Wang, Yao E.; Vigant, Frederic; Gao, Junling; Wu, Ping

    2014-01-01

    ABSTRACT Nipah virus (NiV) and Hendra virus (HeV) are closely related henipaviruses of the Paramyxovirinae. Spillover from their fruit bat reservoirs can cause severe disease in humans and livestock. Despite their high sequence similarity, NiV and HeV exhibit apparent differences in receptor and tissue tropism, envelope-mediated fusogenicity, replicative fitness, and other pathophysiologic manifestations. To investigate the molecular basis for these differences, we first established a highly efficient reverse genetics system that increased rescue titers by ?3 log units, which offset the difficulty of generating multiple recombinants under constraining biosafety level 4 (BSL-4) conditions. We then replaced, singly and in combination, the matrix (M), fusion (F), and attachment glycoprotein (G) genes in mCherry-expressing recombinant NiV (rNiV) with their HeV counterparts. These chimeric but isogenic rNiVs replicated well in primary human endothelial and neuronal cells, indicating efficient heterotypic complementation. The determinants of budding efficiency, fusogenicity, and replicative fitness were dissociable: HeV-M budded more efficiently than NiV-M, accounting for the higher replicative titers of HeV-M-bearing chimeras at early times, while the enhanced fusogenicity of NiV-G-bearing chimeras did not correlate with increased replicative fitness. Furthermore, to facilitate spatiotemporal studies on henipavirus pathogenesis, we generated a firefly luciferase-expressing NiV and monitored virus replication and spread in infected interferon alpha/beta receptor knockout mice via bioluminescence imaging. While intraperitoneal inoculation resulted in neuroinvasion following systemic spread and replication in the respiratory tract, intranasal inoculation resulted in confined spread to regions corresponding to olfactory bulbs and salivary glands before subsequent neuroinvasion. This optimized henipavirus reverse genetics system will facilitate future investigations into the growing numbers of novel henipavirus-like viruses. IMPORTANCE Nipah virus (NiV) and Hendra virus (HeV) are recently emergent zoonotic and highly lethal pathogens with pandemic potential. Although differences have been observed between NiV and HeV replication and pathogenesis, the molecular basis for these differences has not been examined. In this study, we established a highly efficient system to reverse engineer changes into replication-competent NiV and HeV, which facilitated the generation of reporter-expressing viruses and recombinant NiV-HeV chimeras with substitutions in the genes responsible for viral exit (the M gene, critical for assembly and budding) and viral entry (the G [attachment] and F [fusion] genes). These chimeras revealed differences in the budding and fusogenic properties of the M and G proteins, respectively, which help explain previously observed differences between NiV and HeV. Finally, to facilitate future in vivo studies, we monitored the replication and spread of a bioluminescent reporter-expressing NiV in susceptible mice; this is the first time such in vivo imaging has been performed under BSL-4 conditions. PMID:25392218

  8. The effect of ultrafiltration as pretreatment to reverse osmosis in wastewater reuse and seawater desalination applications

    Microsoft Academic Search

    S. C. J. M. van Hoof; A. Hashim; A. J. Kordes

    1999-01-01

    With an ever-growing world-wide demand for water and decreasing availability, emerging technologies such as ultrafiltration (UF) hold the key to future water treatment. Two applications to use unconventional sources for water production are described. The reuse of effluent of wastewater treatment plants (WWTP) for high-quality water production will certainly be an interesting application of UF in the years to come.

  9. The reversibility of ionic transport in PEDOT with application to a complementary electrochromic device

    NASA Astrophysics Data System (ADS)

    Chiang, Tun-Yuan; Huang, Ming-Chao; Tsai, Chien-Huang

    2014-07-01

    The electrochemistry and ion transport properties of PEDOT in different solvents have been investigated. Conductivity enhancement has been observed in dimethyl sulfoxide (DMSO) and ethylene glycol (EG). This is attributed to the transformation of polymer chains from compact to linear structure induced by such high dipole moment solvent treatment (DMSO or EG). The results of electrochemical quartz crystal microbalance (EQCM) indicate that the solvent plays an important role in redox process. The poly(3,4-ethylenedioxythiophene) (PEDOT) reveals a better reversibility of ionic transfer in DMSO compared with that measured in acetonitrile (ACN). A solution and thin film system electrochromic device (ECD) based on 4-phenothiazin-10-yl-anisole (APS) solution and a PEDOT thin film was assembled and studied. The device demonstrates the color change from colorless (0 V) to deep blue violet (1.6 V). A maximum transmittance window 65% was obtained at 520 nm with the operating potentials between 0 and 1.6 V in DMSO electrolytes. Coloration efficiency of the ECD has been found to be 410 cm2/C. No pre-darkening or pre-bleaching of the electrodes is required for assembly of such ECD.

  10. Ultrasonic Time Reversal Mirrors

    NASA Astrophysics Data System (ADS)

    Fink, Mathias; Montaldo, Gabriel; Tanter, Mickael

    2004-11-01

    For more than ten years, time reversal techniques have been developed in many different fields of applications including detection of defects in solids, underwater acoustics, room acoustics and also ultrasound medical imaging and therapy. The essential property that makes time reversed acoustics possible is that the underlying physical process of wave propagation would be unchanged if time were reversed. In a non dissipative medium, the equations governing the waves guarantee that for every burst of sound that diverges from a source there exists in theory a set of waves that would precisely retrace the path of the sound back to the source. If the source is pointlike, this allows focusing back on the source whatever the medium complexity. For this reason, time reversal represents a very powerful adaptive focusing technique for complex media. The generation of this reconverging wave can be achieved by using Time Reversal Mirrors (TRM). It is made of arrays of ultrasonic reversible piezoelectric transducers that can record the wavefield coming from the sources and send back its time-reversed version in the medium. It relies on the use of fully programmable multi-channel electronics. In this paper we present some applications of iterative time reversal mirrors to target detection in medical applications.

  11. Solid-Phase Extraction and Reverse-Phase HPLC: Application to Study the Urinary Excretion Pattern of Benzophenone-3 and its Metabolite 2,4-Dihydroxybenzophenone in Human Urine

    PubMed Central

    Gonzalez, Helena; Jacobson, Carl-Eric; Wennberg, Ann-Marie; Larkö, Olle; Farbrot, Anne

    2008-01-01

    Background: Benzophenone-3 (BZ-3) is a common ultraviolet (UV) absorbing compound in sunscreens. It is the most bioavailable species of all UV-absorbing compounds after topical application and can be found in plasma and urine. Objectives: The aim of this study was to develop a reverse-phase high performance liquid chromatography (HPLC) method for determining the amounts BZ-3 and its metabolite 2,4-dihydroxybenzophenone (DHB) in human urine. The method had to be suitable for handling a large number of samples. It also had to be rapid and simple, but still sensitive, accurate and reproducible. The assay was applied to study the urinary excretion pattern after repeated whole-body applications of a commercial sunscreen, containing 4% BZ-3, to 25 healthy volunteers. Methods: Each sample was analyzed with regard to both conjugated/non-conjugated BZ-3 and conjugated/non-conjugated DHB, since both BZ-3 and DHB are extensively conjugated in the body. Solid-phase extraction (SPE) with C8 columns was followed by reverse-phase HPLC. For separation a Genesis C18 column was used with an acethonitrile-water mobile phase and the UV-detector was set at 287 nm. Results: The assay was linear r2 > 0.99, with detection limits for BZ-3 and DHB of 0.01 ?mol L?1 and 0.16 ?mol L?1 respectively. Relative standard deviation (RSD) was less than 10% for BZ-3 and less than 13% for DHB. The excretion pattern varied among the human volunteers; we discerned different patterns among the individuals. Conclusions: The reverse-phase HPLC assay and extraction procedures developed are suitable for use when a large number of samples need to be analyzed and the method fulfilled our objectives. The differences in excretion pattern may be due to differences in enzyme activity but further studies, especially about genetic polymorphism, need to be performed to verify this finding. PMID:19609385

  12. Implementation of time reversal method (TRM) and its application to magnetoacoustic tomography (MAT)

    Microsoft Academic Search

    Xun Li; Sanqing Hu

    2010-01-01

    We introduce the logic process of the TRM derivation, and propose the assumptions for the implementation of the TRM. The numerical simulations are conducted with four sound sources models including one point source, two adjacent point sources, sources on a circle and sources on two closed curves, to evaluate the performance of TRM and its application to MAT. The results

  13. Automated Reverse Engineering of Legacy 4GL Information System Applications Using the ITOC Workbench

    Microsoft Academic Search

    John V. Harrison; Wie Ming Lim

    1998-01-01

    . Most contemporary fourth-generation languages (4GLs) are tightly coupled withthe relational database and other subsystems provided by the vendor. As a result, organisationswishing to change database vendors are typically forced to rewrite their applications using thenew vendor's 4GL. The anticipated cost of this redevelopment can deter an organisation fromchanging vendors, hence denying it the benefits that would otherwise result, for

  14. Bis sigma-bond dihydrogen and borane ruthenium complexes: bonding nature, catalytic applications, and reversible hydrogen release.

    PubMed

    Alcaraz, Gilles; Grellier, Mary; Sabo-Etienne, Sylviane

    2009-10-20

    Hydrogen, the simplest element in the periodic table, plays a tremendous role in organic and inorganic chemistry. For years, it was inconceivable that dihydrogen could be bound to a metal center without breaking the H-H bond. Thus, oxidative addition of H(2) was universally recognized as a key elementary step in hydrogenation processes. In 1984, Kubas and co-workers reported the first example of a complex in which dihydrogen was coordinated to a metal center without breaking of the H-H bond. This opened a new area in coordination chemistry: sigma-complexes were born, complementing the well-known Werner-type family of complexes. Since then, hundreds of stable dihydrogen complexes have been isolated, and their properties have been investigated in detail. By comparison, very little information is available for the analogous class of sigma-borane complexes, in which sigma-H-B bonds are complexed to a metal (in the manner of H-H bonds in sigma-dihydrogen complexes). Since the first example published in 1996 by Hartwig and co-workers, very few sigma-borane complexes have been isolated. Scientists have maintained a continuous interest in catalytic hydrogenation reactions. Almost a century ago, in 1912, Paul Sabatier, the father of the hydrogenation process, received the Nobel prize, and the selection of Noyori and Knowles in 2001 for their studies on enantioselective catalyzed hydrogenations amply demonstrates the ongoing importance of the field. Moreover, during the past decade, dihydrogen has attracted considerable attention as a possible "fuel of the future". This endeavor has furthered interest in sigma-borane complexes, as more and more evidence links their chemistry to that of amine-borane derivatives. Indeed, ammonia-borane (NH(3)BH(3)) is attracting significant interest for hydrogen storage applications. One of the main limitations is the lack of reversibility associated with the production of dehydrogenated (BNH)(x) materials. Of major importance will be a better understanding of the coordination of H(2) to a metal center, and more generally of the coordination of H-E bonds (E = B, C), which are likely to play a critical role in the reversible dehydrogenation process. In this Account, we review our recent results in the field of dihydrogen and borane activation, with a specific focus on the problem of reversible dehydrogenation pathways. We concentrate on the chemistry of ruthenium complexes incorporating two sigma-ligands: either two dihydrogen or two sigma-B-H bonds. We describe our synthetic strategies to prepare such unusual structures. Their characterization is discussed in detail, highlighting the importance of an experimental and theoretical approach (NMR, structural, and theoretical studies). Some catalytic applications are discussed and put into context, and their reactivity toward reversible hydrogen release is detailed. PMID:19586012

  15. Application of a reversible chemical reaction system to solar thermal power plants

    Microsoft Academic Search

    E. J. Hanseth; Y. S. Won; L. P. Seibowitz

    1980-01-01

    Three distributed dish solar thermal power systems using various applications of SO2\\/SO3 chemical energy storage and transport technology were comparatively assessed. Each system features various roles for the chemical system: (1) energy storage only, (2) energy transport, or (3) energy transport and storage. These three systems were also compared with the dish-Stirling, using electrical transport and battery storage, and the

  16. Detection of Colorado tick fever virus by using reverse transcriptase PCR and application of the technique in laboratory diagnosis.

    PubMed Central

    Johnson, A J; Karabatsos, N; Lanciotti, R S

    1997-01-01

    Colorado tick fever (CTF) virus elicits an acute illness in humans, producing nonspecific flu-like symptoms and a biphasic fever in approximately 50% of patients. The disease is transmitted by the adult Rocky Mountain wood tick (Dermacentor andersoni), and therefore incidence is limited by the habitat and life cycle of that vector. The early symptoms of infection are difficult to distinguish from those of several other agents, especially Rickettsia rickettsii. Serologic testing is usually unable to provide evidence of CTF viral infection during the acute phase because of the late appearance of the various antibodies. Here we report the development and clinical application of a test to diagnose this disease during the acute stages. Oligonucleotide primers to the S2 segment of CTF (Florio) virus were made, and these were used in the amplification of a 528-bp fragment of DNA, transcribed from the double-stranded CTF virus RNA template by reverse transcriptase PCR. RNAs processed from 16 CTF virus isolates yielded similar results when analyzed on agarose gels. These were distinguishable from their antigenic relatives Eyach, S6-14-03, and T5-2092 and from other coltiviruses and an orbivirus but not from the antigenically distinct CTF virus-related isolate 720896. A mouse model demonstrated the utility of this method with whole-blood specimens, and CTF virus was successfully detected in human sera from the initial day of the onset of symptoms to 8 days later. The reverse transcriptase PCR method is a promising tool for the early diagnosis of CTF viral infection, or for ruling out CTF virus as the etiologic agent, in order to facilitate appropriate medical support. PMID:9114408

  17. An Advanced Reverse Osmosis Technology For Application in Nuclear Desalination Facilities

    SciTech Connect

    Humphries, J.R.; Davies, K.; Ackert, J.A. [CANDESAL Technologies Limited, Ottawa (Canada)

    2002-07-01

    The lack of adequate supplies of clean, safe water is a growing global problem that has reached crisis proportions in many parts of the world. It is estimated that 1.5 billion people do not have access to adequate supplies of safe water, and that as a result nearly 10,000 people die every day and thousands more suffer from a range of debilitating illnesses due to water related diseases. Included in this total is an estimated 2.2 million child deaths annually. As the world's need for additional sources of fresh water continues to grow, seawater and brackish water desalination are providing an increasingly important contribution to the solution of this problem. Because desalination is an energy intensive process, nuclear desalination provides an economically attractive and environmentally sound alternative to the burning of fossil fuels for desalination. Nevertheless, the enormity of the problem dictates that additional steps must be taken to improve the efficiency of energy utilization and reduce the cost of water production in order to reduce the financial and environmental burden to communities in need. An advanced reverse osmosis (RO) desalination technology has been developed that emphasizes a nontraditional approach to system design and operation, and makes use of a sophisticated design optimization process that can lead to highly optimized design configurations and operating regimes. The technology can be coupled with a nuclear generating station (NGS) to provide an integrated facility for the co-generation of both water and electricity. Waste heat from the NGS allows the use of 'preheated' feedwater into the RO system, improving the efficiency of the RO process and reducing the cost of water production. Because waste heat, rather than process heat, is used the desalination system can be readily coupled to any existing or advanced reactor technology with little or no impact on reactor design and operation and without introducing additional reactor safety considerations. Analyses of nuclear desalination systems employing this advanced RO technology under a variety of seawater feed conditions have consistently shown that the cost of potable water production can be reduced by as much as 15-20% relative to systems designed in a more traditional manner. Demonstration testing has been carried out using a trailer mounted system producing up to 150 m{sup 3}/d of potable water. Experimental results from the demonstration testing are behaving as expected based on the analytical performance models, validating the advanced design concept and confirming that the performance improvements indicated by the analyses can be achieved in operating systems. Further demonstration testing is planned using a 1000 m{sup 3}/d containerized system, currently under design, coupled to an existing nuclear power reactor. (authors)

  18. Reverse Osmosis

    NSDL National Science Digital Library

    Reverse Osmosis: In reverse osmosis, the idea is to use the membrane to act like an extremely fine filter to create drinkable water from salty (or otherwise contaminated) water. A complete explanation is here along with helpful diagrams.

  19. Should There Be An Obligation of Disclosure of Origin of Genetic Resources in Patent Applications? Learning Lessons from Developing Countries 

    E-print Network

    Laurie, Graeme

    2005-01-01

    The article discusses whether there should be an obligation of disclosure of origin of genetic resources in patent applications. In particular, Laurie comments on the evolving relations of the intellectual property world ...

  20. Contribution of genetics to ecological restoration.

    PubMed

    Mijangos, Jose Luis; Pacioni, Carlo; Spencer, Peter B S; Craig, Michael D

    2015-01-01

    Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration. PMID:25377524

  1. Application of a reversible chemical reaction system to solar thermal power plants

    NASA Technical Reports Server (NTRS)

    Hanseth, E. J.; Won, Y. S.; Seibowitz, L. P.

    1980-01-01

    Three distributed dish solar thermal power systems using various applications of SO2/SO3 chemical energy storage and transport technology were comparatively assessed. Each system features various roles for the chemical system: (1) energy storage only, (2) energy transport, or (3) energy transport and storage. These three systems were also compared with the dish-Stirling, using electrical transport and battery storage, and the central receiver Rankine system, with thermal storage, to determine the relative merit of plants employing a thermochemical system. As an assessment criterion, the busbar energy costs were compared. Separate but comparable solar energy cost computer codes were used for distributed receiver and central receiver systems. Calculations were performed for capacity factors ranging from 0.4 to 0.8. The results indicate that SO2/SO3 technology has the potential to be more cost effective in transporting the collected energy than in storing the energy for the storage capacity range studied (2-15 hours)

  2. Application of a reversible chemical reaction system to solar thermal power plants

    NASA Astrophysics Data System (ADS)

    Hanseth, E. J.; Won, Y. S.; Seibowitz, L. P.

    1980-08-01

    Three distributed dish solar thermal power systems using various applications of SO2/SO3 chemical energy storage and transport technology were comparatively assessed. Each system features various roles for the chemical system: (1) energy storage only, (2) energy transport, or (3) energy transport and storage. These three systems were also compared with the dish-Stirling, using electrical transport and battery storage, and the central receiver Rankine system, with thermal storage, to determine the relative merit of plants employing a thermochemical system. As an assessment criterion, the busbar energy costs were compared. Separate but comparable solar energy cost computer codes were used for distributed receiver and central receiver systems. Calculations were performed for capacity factors ranging from 0.4 to 0.8. The results indicate that SO2/SO3 technology has the potential to be more cost effective in transporting the collected energy than in storing the energy for the storage capacity range studied (2-15 hours)

  3. Application of real-time reverse transcription polymerase chain reaction for the detection of SVDV.

    PubMed

    Niedbalski, W

    2009-01-01

    Application of real-time RT-PCR (rRT-PCR) for detection of swine vesicular disease virus (SVDV) in samples of archival SVDV isolates and clinical samples collected from SVDV infected pigs was described. A primer set that targets the IRES region of the SVDV genome and TaqMan probe specific for a highly conserved region in SVDV RNA IRES region were used. The assay detected viral RNA in all tested archival strains of SVDV isolated in Europe during years 1972-73 and 1992 as well as in clinical samples collected from experimentally infected pigs. The rRT-PCR can provide quantitative and qualitative information and is more sensitive and faster to perform than the conventional RT-PCR. PMID:19459449

  4. Nested Quantization Index Modulation for Reversible Watermarking and Its Application to Healthcare Information Management Systems

    PubMed Central

    Ko, Lu-Ting; Chen, Jwu-E.; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

    2012-01-01

    Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented. PMID:22194776

  5. Nested quantization index modulation for reversible watermarking and its application to healthcare information management systems.

    PubMed

    Ko, Lu-Ting; Chen, Jwu-E; Shieh, Yaw-Shih; Hsin, Hsi-Chin; Sung, Tze-Yun

    2012-01-01

    Digital watermarking has attracted lots of researches to healthcare information management systems for access control, patients' data protection, and information retrieval. The well-known quantization index modulation-(QIM-) based watermarking has its limitations as the host image will be destroyed; however, the recovery of medical images is essential to avoid misdiagnosis. In this paper, we propose the nested QIM-based watermarking, which is preferable to the QIM-based watermarking for the medical image applications. As the host image can be exactly reconstructed by the nested QIM-based watermarking. The capacity of the embedded watermark can be increased by taking advantage of the proposed nest structure. The algorithm and mathematical model of the nested QIM-based watermarking including forward and inverse model is presented. Due to algorithms and architectures of forward and inverse nested QIM, the concurrent programs and special processors for the nested QIM-based watermarking are easily implemented. PMID:22194776

  6. Reversal of Acute Complex Regional Pain Syndrome Using the Practical Application of Neurodiagnostic Evaluation Process: A Case Study

    PubMed Central

    Anderson, Karen E

    2013-01-01

    In 2005, a patient in my practice developed complex regional pain syndrome type 1 (CRPS 1) after bunion surgery. The condition was properly diagnosed within 4 weeks with a diagnostic technique that I routinely use to diagnose chronic musculoskeletal pain, and it was successfully treated. The tests, which are based on primitive and postural reflexes in infants, were adapted to reflect normal and abnormal motor behaviors in adults after provocation of reflexes of the autonomic nervous system (afferent C fibers in peripheral nerves). Approximately 60 days after my patient’s operation, the tests indicated a positive reflex at the posterior tibial nerve in the operated foot. Surgery to remove an accessory ossicle from the talus adjacent to this nerve resolved the CRPS 1 within 2 weeks. Since CRPS 1 is a dysfunctional state of the autonomic regulatory control of pain, it was postulated that a test based on autonomic nerve function could isolate the source of CRPS 1. The Practical Application of Neurodiagnostic Evaluation process was shown to be diagnostic for the cause of acute CRPS 1 and to allow its reversal. Further evaluation of the test for diagnosis and treatment of CRPS is needed. PMID:24355904

  7. Global intellectual deterioration in Alzheimer's disease and a reverse model of intellectual development: an applicability of the Binet scale.

    PubMed

    Shimada, M; Meguro, K; Inagaki, H; Ishizaki, J; Yamadori, A

    2001-12-01

    Since intellectual deterioration in Alzheimer's disease (AD) might be considered to demonstrate a reverse of the intellectual development of children, we herein investigated the applicability of the Tanaka-Binet Intelligence scale (TB scale). This scale can assess the mental age (MA) and the lower-limit age (LLAge) values, and was reported to be correlated with the tasks determining Piaget's developmental stages of intelligence. Thirty AD patients and 30 age-matched normal control subjects were examined with the scale. We found that the mean MA values of the AD patients and controls were 97.4 and 150.3 months, respectively. In the control group, there were significant correlations between the MA and chronological age, and between the MA and years of education. In the AD patients, there was a significant correlation between the MA and the MMSE score. Regarding the LLAge for the AD patients, similar to the theory of Piaget, there was a tendency that they could be classified into three LLAge groups. We consider that the TB scale is useful in assessing the intellectual function in AD patients. PMID:11737787

  8. Application of genetic algorithms to processing of reflectance spectra of semiconductor compounds

    NASA Astrophysics Data System (ADS)

    Zaharov, Ivan S.; Kochura, Alexey V.; Kurkin, Alexandr Y.; Belogorohov, Alexandr I.

    2004-11-01

    The basic task of mathematical processing of reflectance spectra - restoration from them of a view of dependence of inductivity, which is responsible for the response of a crystal to an external electromagnetic field from frequency of incident radia-tion. The most modern and perspective way of the solution of this task is the dis-persion analysis (DA). However DA requires large volume of computing works on selection of optimum parameters of phonons. The rapid development of computer facilities recently promotes overcoming of this difficulty. However without appli-cation of effective methods of optimization practically it is impossible to execute DA for composite reflectance spectra. In this paper the questions of application of Genetic algorithms (GA) to processing reflectance spectra of crystal materials are considered. GA is a rather new class of methods of optimization belonging to family of evolutionary algorithms. The basic features distinguishing GA from algorithms of other classes: - GA is an iterative algorithm of generations, in which the search of an extreme is made not in initial space of search, but in the conjugate set of chromosomes. The set of chromosomes on each step of iterations of algorithm is termed as a popula-tion; - The generation of the new trial solutions in this set is carried out by a set of the special genetic operators. The genetic operators are probabilistic, i.e. the result of their application to the concrete chromosome is not unequivocal; - The creation of a new population from the solutions of the current population and solutions generated by the genetic operators is carried out by special algorithms of selection. The efficiency GA strongly depends on such details, as a method of coding of the solutions, embodying of the genetic operators, mechanisms of selection, adjust-ment of other parameters of algorithm, criterion of success. The theoretical work reflected in the literature devoted to these algorithms does not give the bases to speak about existence of any strict mechanisms for precise predictions of function-ing GA. For the effective solution of a concrete task it is necessary in appropriate way to modify or to develop all components GA. In this paper we offer modification GA for the solution of the reflectance spectra processing problem and results of the obtained algorithm work.

  9. Warfarin reversal

    PubMed Central

    Hanley, J P

    2004-01-01

    Warfarin is the most commonly used oral anticoagulant in the UK. It is associated with few side effects apart from haemorrhage. The most appropriate way to reverse the anticoagulant effect of warfarin depends on the clinical circumstances. In serious bleeding, rapid reversal is required, whereas in minor bleeding or asymptomatic over anticoagulation, a more leisurely approach is usually appropriate. This review discusses the current approaches to warfarin reversal in clinical practice. The development of a uniform approach to warfarin reversal in the Northern Region is described. PMID:15509671

  10. Using Reverse Genetics to Manipulate the NSs Gene of the Rift Valley Fever Virus MP-12 Strain to Improve Vaccine Safety and Efficacy

    PubMed Central

    Kalveram, Birte; Lihoradova, Olga; Indran, Sabarish V.; Ikegami, Tetsuro

    2011-01-01

    Rift Valley fever virus (RVFV), which causes hemorrhagic fever, neurological disorders or blindness in humans, and a high rate abortion and fetal malformation in ruminants1, has been classified as a HHS/USDA overlap select agent and a risk group 3 pathogen. It belongs to the genus Phlebovirus in the family Bunyaviridae and is one of the most virulent members of this family. Several reverse genetics systems for the RVFV MP-12 vaccine strain2,3 as well as wild-type RVFV strains 4-6, including ZH548 and ZH501, have been developed since 2006. The MP-12 strain (which is a risk group 2 pathogen and a non-select agent) is highly attenuated by several mutations in its M- and L-segments, but still carries virulent S-segment RNA3, which encodes a functional virulence factor, NSs. The rMP12-C13type (C13type) carrying 69% in-frame deletion of NSs ORF lacks all the known NSs functions, while it replicates as efficient as does MP-12 in VeroE6 cells lacking type-I IFN. NSs induces a shut-off of host transcription including interferon (IFN)-beta mRNA7,8 and promotes degradation of double-stranded RNA-dependent protein kinase (PKR) at the post-translational level.9,10 IFN-beta is transcriptionally upregulated by interferon regulatory factor 3 (IRF-3), NF-kB and activator protein-1 (AP-1), and the binding of IFN-beta to IFN-alpha/beta receptor (IFNAR) stimulates the transcription of IFN-alpha genes or other interferon stimulated genes (ISGs)11, which induces host antiviral activities, whereas host transcription suppression including IFN-beta gene by NSs prevents the gene upregulations of those ISGs in response to viral replication although IRF-3, NF-kB and activator protein-1 (AP-1) can be activated by RVFV7. . Thus, NSs is an excellent target to further attenuate MP-12, and to enhance host innate immune responses by abolishing the IFN-beta suppression function. Here, we describe a protocol for generating a recombinant MP-12 encoding mutated NSs, and provide an example of a screening method to identify NSs mutants lacking the function to suppress IFN-beta mRNA synthesis. In addition to its essential role in innate immunity, type-I IFN is important for the maturation of dendritic cells and the induction of an adaptive immune response12-14. Thus, NSs mutants inducing type-I IFN are further attenuated, but at the same time are more efficient at stimulating host immune responses than wild-type MP-12, which makes them ideal candidates for vaccination approaches. PMID:22083261

  11. Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications.

    PubMed

    Wong, A; Forbes, M R; Smith, M L

    2001-08-01

    Amplified fragment length polymorphism (AFLP) analysis is becoming increasingly popular as a method for generating molecular markers for population genetic applications. For practical considerations, it is generally assumed in population studies that AFLPs segregate as dominant markers, i.e., that present and absent are the only possible states of a given locus. We tested the assumption of dominance in natural populations of the damselfly Nehalennia irene (Hagen) (Odonata: Coenagrionidae). Electro-blotted AFLP products from 21 samples were probed with individual markers. Eleven markers were analyzed, of which two were monomorphic and nine were polymorphic. Only two of the polymorphic markers behaved in a strictly dominant manner. The remaining seven polymorphic markers displayed various degrees of codominance, with 2-10 visible alleles in the sample. Of the three markers displaying the highest degree of variability, two contained microsatellite repeat tracts. Our results suggest that the assumption of dominance is unfounded. As a result, AFLP analysis may be unsuitable for estimating several important population genetic parameters, including genetic diversity. PMID:11550904

  12. First successful application of preimplantation genetic diagnosis and haplotyping for congenital hyperinsulinism.

    PubMed

    Qubbaj, Wafa; Al-Swaid, Abdulrahman; Al-Hassan, Saad; Awartani, Khalid; Deek, Hesham; Coskun, Serdar

    2011-01-01

    Congenital hyperinsulinism is the most common cause of persistent hypoglycaemia in infancy. Early surgical intervention is usually required to prevent brain damage. The prevention of the transmission to the offspring is important in families carrying the mutated gene. Preimplantation genetic diagnosis (PGD) is an early genetic testing procedure for couples at risk of transmitting inherited diseases. A 36-year-old Saudi woman married to her first cousin with four affected children was referred for PGD. The hyperinsulinism disease was caused by a novel homozygous mutation in the KCNJ11 gene, an arginine 301 to proline (R301P) substitution.PGD was achieved by whole genome amplification followed by mutation detection combined with short tandem repeat identifier analysis in the first cycle and with haplotyping in the second cycle. The first and second cycles resulted in the births of healthy twin girls and a boy, respectively. As far as is known, this is the first application of PGD to hyperinsulinism. A feasible strategy including whole genome amplification followed by direct mutation detection combined with haplotyping is described.Utilizing haplotyping increases the efficiency of PGD diagnosis as well as confirming the genetic diagnosis. It reveals the parental origin of each inherited chromosome. PMID:21115269

  13. Neuro-Genetic Optimization of the Diffuser Elements for Applications in a Valveless Diaphragm Micropumps System

    PubMed Central

    Lee, Hing Wah; Azid, Ishak Hj Abdul

    2009-01-01

    In this study, a hybridized neuro-genetic optimization methodology realized by embedding numerical simulations trained artificial neural networks (ANN) into a genetic algorithm (GA) is used to optimize the flow rectification efficiency of the diffuser element for a valveless diaphragm micropump application. A higher efficiency ratio of the diffuser element consequently yields a higher flow rate for the micropump. For that purpose, optimization of the diffuser element is essential to determine the maximum pumping rate that the micropump is able to generate. Numerical simulations are initially carried out using CoventorWare® to analyze the effects of varying parameters such as diffuser angle, Reynolds number and aspect ratio on the volumetric flow rate of the micropump. A limited range of simulation results will then be used to train the neural network via back-propagation algorithm and optimization process commence subsequently by embedding the trained ANN results as a fitness function into GA. The objective of the optimization is to maximize the efficiency ratio of the diffuser element for the range of parameters investigated. The optimized efficiency ratio obtained from the neuro-genetic optimization is 1.38, which is higher than any of the maximum efficiency ratio attained from the overall parametric studies, establishing the superiority of the optimization method. PMID:22400004

  14. Insights into the biology of Borrelia burgdorferi gained through the application of molecular genetics.

    PubMed

    Groshong, Ashley M; Blevins, Jon S

    2014-01-01

    Borrelia burgdorferi, the vector-borne bacterium that causes Lyme disease, was first identified in 1982. It is known that much of the pathology associated with Lyme borreliosis is due to the spirochete's ability to infect, colonize, disseminate, and survive within the vertebrate host. Early studies aimed at defining the biological contributions of individual genes during infection and transmission were hindered by the lack of adequate tools and techniques for molecular genetic analysis of the spirochete. The development of genetic manipulation techniques, paired with elucidation and annotation of the B. burgdorferi genome sequence, has led to major advancements in our understanding of the virulence factors and the molecular events associated with Lyme disease. Since the dawn of this genetic era of Lyme research, genes required for vector or host adaptation have garnered significant attention and highlighted the central role that these components play in the enzootic cycle of this pathogen. This chapter covers the progress made in the Borrelia field since the application of mutagenesis techniques and how they have allowed researchers to begin ascribing roles to individual genes. Understanding the complex process of adaptation and survival as the spirochete cycles between the tick vector and vertebrate host will lead to the development of more effective diagnostic tools as well as identification of novel therapeutic and vaccine targets. In this chapter, the Borrelia genes are presented in the context of their general biological roles in global gene regulation, motility, cell processes, immune evasion, and colonization/dissemination. PMID:24377854

  15. Interactive genetic algorithms with multi-population adaptive hierarchy and their application in fashion design

    Microsoft Academic Search

    Dun-wei Gong; Guo-sheng Hao; Yong Zhou; Xiao-yan Sun

    2007-01-01

    Limitations of existing interactive genetic algorithms are analyzed and interactive genetic algorithms with multi-population adaptive hierarchy proposed. A model for interactive genetic algorithms with multi-population is established and a strategy for individuals’ migration is designed. Adaptive genetic operators are applied to interactive genetic algorithms with a single population, and when a condition for hierarchy is met, the algorithms will evolve

  16. Hybrid Algorithms for Fuzzy Reverse Supply Chain Network Design

    PubMed Central

    Che, Z. H.; Chiang, Tzu-An; Kuo, Y. C.

    2014-01-01

    In consideration of capacity constraints, fuzzy defect ratio, and fuzzy transport loss ratio, this paper attempted to establish an optimized decision model for production planning and distribution of a multiphase, multiproduct reverse supply chain, which addresses defects returned to original manufacturers, and in addition, develops hybrid algorithms such as Particle Swarm Optimization-Genetic Algorithm (PSO-GA), Genetic Algorithm-Simulated Annealing (GA-SA), and Particle Swarm Optimization-Simulated Annealing (PSO-SA) for solving the optimized model. During a case study of a multi-phase, multi-product reverse supply chain network, this paper explained the suitability of the optimized decision model and the applicability of the algorithms. Finally, the hybrid algorithms showed excellent solving capability when compared with original GA and PSO methods. PMID:24892057

  17. Reverse Logistics

    Microsoft Academic Search

    Chaihou Zhao; Weiming Liu; Bei Wang

    2008-01-01

    Environmental concerns and rapid development of e-commerce bring a new focused field in reverse logistics. In order to avoid return losses and add customerspsila value, there is a need for companies to find proper ways to reduce wastes and recover the value from used products for further utilities. All these challenges make reverse logistics a contemporary area of interest among

  18. Enhanced conjugation of Candida rugosa lipase onto multiwalled carbon nanotubes using reverse micelles as attachment medium and application in nonaqueous biocatalysis.

    PubMed

    Raghavendra, Tripti; Vahora, Uzma; Shah, Amita R; Madamwar, Datta

    2014-01-01

    Three liquid phases (viz. aqueous, nonaqueous, and reverse micelles) were scrutinized as medium for attachment of the enzyme Candida rugosa lipase (CRL) onto multiwalled carbon nanotubes (CNTs). The nanotubes were functionalized to attain carboxyl and amino groups on their surfaces before enzyme conjugation. Transmission electron microscopy and Fourier transformation infrared spectroscopic studies were used for characterization of the nanotubes during the course of functionalization. High enzyme loadings associated with the functionalized CNTs were observed when reverse micelles were used as the attachment medium. In addition, high activity in terms of ester synthesis in organic solvents was also observed while using those preparations. The nanobioconjugates prepared using reverse micelles were found to be highly sturdy and exhibited appreciable operational stability of around 95 ± 3% at 20th cycle (in case of carboxylated nanotubes) and 90 ± 5% at 10th cycle (in case of aminated nanotubes) for esterification. This shows the potential application of reverse micelles as the attachment medium for surface active enzymes such as CRL onto CNTs. PMID:24828252

  19. Reversible shape memory

    NASA Astrophysics Data System (ADS)

    Sheiko, Sergei; Zhou, Jing; White, Sarah; Ashby, Valerie

    2012-02-01

    An ``Achilles' heel'' of shape memory materials is that shape transformations triggered by an external stimulus are usually irreversible. Here we present a new concept of reversible transitions between two well-defined shapes by controlling hierarchic crystallization of a dual-network elastomer. The reversibility was demonstrated for different types of shape transformations including rod bending, winding of a helical coil, and widening an aperture. The distinct feature of the reversible shape alterations is that both counter-shapes are infinitely stable at a temperature of exploitation. Shape reversibility is highly desirable property in many practical applications such as non-surgical removal of a previously inserted catheter and handfree wrapping up of an earlier unraveled solar sail on a space shuttle.

  20. Analysis of tactile perceptions of textile materials using artificial intelligence techniques : Part 2: reverse engineering using genetic algorithm coupled neural network

    Microsoft Academic Search

    B. Karthikeyan; Les M. Sztandera

    2010-01-01

    Purpose – The second of a two-part series, this paper aims to explain the design and development of a hybrid system for reverse engineering. Design\\/methodology\\/approach – A prediction engine to map the perception of tactile sensations using a neural network engine was developed. Since seventeen mechanical properties form the input - and tactile compfort score is used as the output

  1. Genetics and Evolution: An iOS Application to Supplement Introductory Courses in Transmission and Evolutionary Genetics

    PubMed Central

    Myers, Russell B.; Millman, Brandon; Noor, Mohamed A. F.

    2014-01-01

    Students in college courses struggle to understand many concepts fundamental to transmission and evolutionary genetics, including multilocus inheritance, recombination, Hardy-Weinberg, and genetic drift. These students consistently ask for more demonstrations and more practice problems. With this demand in mind, the “Genetics and Evolution” app was designed to help students (and their instructors) by providing a suite of tools granting them the ability to: (1) simulate genetic crosses with varying numbers of genes and patterns of inheritance, (2) simulate allele frequency changes under natural selection and/ or genetic drift, (3) quiz themselves to reinforce terminology (customizable by any instructor for their whole classroom), *4) solve various problems (recombination fractions, Hardy-Weinberg, heritability, population growth), and (5) generate literally an infinite number of practice problems in all of these areas to try on their own. Although some of these functions are available elsewhere, the alternatives do not have the ability to instantly generate new practice problems or achieve these diverse functions in devices that students carry in their pockets every day. PMID:24727286

  2. Reversible Sterilization

    ERIC Educational Resources Information Center

    Largey, Gale

    1977-01-01

    Notes that difficult questions arise concerning the use of sterilization for alleged eugenic and euthenic purposes. Thus, how reversible sterilization will be used with relation to the poor, mentally ill, mentally retarded, criminals, and minors, is questioned. (Author/AM)

  3. Reversible Cardiomyopathies

    PubMed Central

    Patel, Harsh; Madanieh, Raef; Kosmas, Constantine E; Vatti, Satya K; Vittorio, Timothy J

    2015-01-01

    Cardiomyopathies (CMs) have many etiological factors that can result in severe structural and functional dysregulation. Fortunately, there are several potentially reversible CMs that are known to improve when the root etiological factor is addressed. In this article, we discuss several of these reversible CMs, including tachycardia-induced, peripartum, inflammatory, hyperthyroidism, Takotsubo, and chronic illness–induced CMs. Our discussion also includes a review on their respective pathophysiology, as well as possible management solutions. PMID:26052233

  4. PT-Flax (phenotyping and TILLinG of flax): development of a flax (Linum usitatissimum L.) mutant population and TILLinG platform for forward and reverse genetics

    PubMed Central

    2013-01-01

    Background Flax (Linum usitatissimum L.) is an economically important fiber and oil crop that has been grown for thousands of years. The genome has been recently sequenced and transcriptomics are providing information on candidate genes potentially related to agronomically-important traits. In order to accelerate functional characterization of these genes we have generated a flax EMS mutant population that can be used as a TILLinG (Targeting Induced Local Lesions in Genomes) platform for forward and reverse genetics. Results A population of 4,894 M2 mutant seed families was generated using 3 different EMS concentrations (0.3%, 0.6% and 0.75%) and used to produce M2 plants for subsequent phenotyping and DNA extraction. 10,839 viable M2 plants (4,033 families) were obtained and 1,552 families (38.5%) showed a visual developmental phenotype (stem size and diameter, plant architecture, flower-related). The majority of these families showed more than one phenotype. Mutant phenotype data are organised in a database and can be accessed and searched at UTILLdb (http://urgv.evry.inra.fr/UTILLdb). Preliminary screens were also performed for atypical fiber and seed phenotypes. Genomic DNA was extracted from 3,515 M2 families and eight-fold pooled for subsequent mutant detection by ENDO1 nuclease mis-match cleavage. In order to validate the collection for reverse genetics, DNA pools were screened for two genes coding enzymes of the lignin biosynthesis pathway: Coumarate-3-Hydroxylase (C3H) and Cinnamyl Alcohol Dehydrogenase (CAD). We identified 79 and 76 mutations in the C3H and CAD genes, respectively. The average mutation rate was calculated as 1/41?Kb giving rise to approximately 9,000 mutations per genome. Thirty-five out of the 52 flax cad mutant families containing missense or codon stop mutations showed the typical orange-brown xylem phenotype observed in CAD down-regulated/mutant plants in other species. Conclusions We have developed a flax mutant population that can be used as an efficient forward and reverse genetics tool. The collection has an extremely high mutation rate that enables the detection of large numbers of independant mutant families by screening a comparatively low number of M2 families. The population will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in flax. PMID:24128060

  5. Application of Genetic Algorithms To Identify Optimal Groundwater Monitoring Well Locations in 3D

    NASA Astrophysics Data System (ADS)

    Abdeh-Kolahchi, A.; Satish, M.; Datta, B.

    2004-12-01

    Monitoring groundwater aquifers for possible sources of contamination is an important aspect of water resources management. The design of monitoring networks has been one of the key concerns of researchers who deal with the management of groundwater quality. Optimal monitoring network design can be beneficial to both groundwater simulation as well as optimization modeling. This paper discusses the applications of various optimization techniques from traditional to global methods for the solution of groundwater monitoring network and groundwater quality management problems. In order to solve optimization-based groundwater management models, various mathematical programming techniques such as linear/nonlinear programming, mixed-integer programming, differential dynamic programming, stochastic programming, as well as global optimization methods such as Genetic Algorithms are used by researchers to obtain optimal solutions for groundwater management. The resent study will also discuss a state of the art method, which combines simulation of groundwater flow and transport with genetic algorithm optimization. In order to ensure that the optimal management strategy is physically acceptable, a simulation model is necessary to simulate the system behavior. The simulation model basically provides solutions that satisfy the equations governing the relevant processes in the system. Thus the simulation models can be used for checking the feasibility of a management strategy. Once the optimization model is formulated, a suitable mathematical programming technique such as genetic algorithm is applied to obtain the optimal solution. This approach not only accounts for the complex and non-linear behavior of the groundwater system, but also identifies the best monitoring strategy under a specific objective function with several constraints. The solution identifies the best location of monitoring wells.

  6. The evolution of colorectal cancer genetics-Part 2: clinical implications and applications.

    PubMed

    Schlussel, Andrew T; Gagliano, Ronald A; Seto-Donlon, Susan; Eggerding, Faye; Donlon, Timothy; Berenberg, Jeffrey; Lynch, Henry T

    2014-10-01

    The genetic understanding of colorectal cancer (CRC) continues to grow, and it is now estimated that 10% of the population has a known hereditary CRC syndrome. This article will examine the evolving surgical and medical management of hereditary CRC syndromes, and the impact of tumor genetics on therapy. This review will focus on the most common hereditary CRC-prone diseases seen in clinical practice, which include Lynch syndrome (LS), familial adenomatous polyposis (FAP) & attenuated FAP (AFAP), MutYH-associated polyposis (MAP), and serrated polyposis syndrome (SPS). Each section will review the current recommendations in the evaluation and treatment of these syndromes, as well as review surgical management and operative planning. A highly detailed multigeneration cancer family history with verified genealogy and pathology documentation whenever possible, coupled with germline mutation testing when indicated, is critically important to management decisions. Although caring for patients with these syndromes remains complex, the application of this knowledge facilitates better treatment of both individuals and their affected family members for generations to come. PMID:25276406

  7. The evolution of colorectal cancer genetics—Part 2: clinical implications and applications

    PubMed Central

    Schlussel, Andrew T.; Gagliano, Ronald A.; Eggerding, Faye; Donlon, Timothy; Berenberg, Jeffrey; Lynch, Henry T.

    2014-01-01

    The genetic understanding of colorectal cancer (CRC) continues to grow, and it is now estimated that 10% of the population has a known hereditary CRC syndrome. This article will examine the evolving surgical and medical management of hereditary CRC syndromes, and the impact of tumor genetics on therapy. This review will focus on the most common hereditary CRC-prone diseases seen in clinical practice, which include Lynch syndrome (LS), familial adenomatous polyposis (FAP) & attenuated FAP (AFAP), MutYH-associated polyposis (MAP), and serrated polyposis syndrome (SPS). Each section will review the current recommendations in the evaluation and treatment of these syndromes, as well as review surgical management and operative planning. A highly detailed multigeneration cancer family history with verified genealogy and pathology documentation whenever possible, coupled with germline mutation testing when indicated, is critically important to management decisions. Although caring for patients with these syndromes remains complex, the application of this knowledge facilitates better treatment of both individuals and their affected family members for generations to come. PMID:25276406

  8. Reversible Thermoelectric Nanomaterials

    Microsoft Academic Search

    T. E. Humphrey; H. Linke

    2005-01-01

    Irreversible effects in thermoelectric materials limit their efficiency and economy for applications in power generation and refrigeration. While electron transport is unavoidably irreversible in bulk materials, here we derive conditions under which reversible diffusive electron transport can be achieved in nanostructured thermoelectric materials. We provide a fundamental thermodynamic explanation for why the optimum density of states in a thermoelectric material

  9. A School-Based Application of Modified Habit Reversal for Tourette Syndrome via a Translator: A Case Study

    ERIC Educational Resources Information Center

    Gilman, Rich; Connor, Nancy; Haney, Michelle

    2005-01-01

    A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline…

  10. A novel application of time-reversed acoustics: Salt-dome flank imaging using walkaway VSP surveys

    Microsoft Academic Search

    Mark E. Willis; Rongrong Lu; Xander Campman; M. Nafi Toksöz; Yang Zhang; Maarten V. de Hoop

    2006-01-01

    In this paper we present initial results of applying Time-Reversed Acoustics (TRA) technology to salt- dome flank, seismic imaging. We created a set of syn- thetic traces representing a multilevel, walkaway VSP for a model composed of a simplified Gulf of Mexico vertical-velocity gradient and an embedded salt dome. We first applied the concepts of TRA to the synthetic traces

  11. An Application of Reverse Engineering to Automatic Item Generation: A Proof of Concept Using Automatically Generated Figures

    ERIC Educational Resources Information Center

    Lorié, William A.

    2013-01-01

    A reverse engineering approach to automatic item generation (AIG) was applied to a figure-based publicly released test item from the Organisation for Economic Cooperation and Development (OECD) Programme for International Student Assessment (PISA) mathematical literacy cognitive instrument as part of a proof of concept. The author created an item…

  12. MONITORING MYCOTOXIN PRODUCTION AT THE GENETIC LEVEL ON VARIOUS GROWTH SUBSTRATES USING QUANTITATIVE REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION?EXPERIMENT DESIGN

    EPA Science Inventory

    The paper describes a method of analyzing the production of mycotoxins at the genetic level by monitoring the intracellular levels of messenger RNA (mRNA). Initial work will focus on threshing out the mycotoxin gene clusters in Stachybotrys chartarum followed by analysis of toxin...

  13. Application of Genetic Algorithm to the Design Optimization of Complex Energy Saving Glass Coating Structure

    NASA Astrophysics Data System (ADS)

    Johar, F. M.; Azmin, F. A.; Shibghatullah, A. S.; Suaidi, M. K.; Ahmad, B. H.; Abd Aziz, M. Z. A.; Salleh, S. N.; Shukor, M. Md

    2014-04-01

    Attenuation of GSM, GPS and personal communication signal leads to poor communication inside the building using regular shapes of energy saving glass coating. Thus, the transmission is very low. A brand new type of band pass frequency selective surface (FSS) for energy saving glass application is presented in this paper for one unit cell. Numerical Periodic Method of Moment approach according to a previous study has been applied to determine the new optimum design of one unit cell energy saving glass coating structure. Optimization technique based on the Genetic Algorithm (GA) is used to obtain an improved in return loss and transmission signal. The unit cell of FSS is designed and simulated using the CST Microwave Studio software at based on industrial, scientific and medical bands (ISM). A unique and irregular shape of an energy saving glass coating structure is obtained with lower return loss and improved transmission coefficient.

  14. Route to genetically targeted optical electrophysiology: development and applications of voltage-sensitive fluorescent proteins

    PubMed Central

    Akemann, Walther; Song, Chenchen; Mutoh, Hiroki; Knöpfel, Thomas

    2015-01-01

    The invention of membrane voltage protein indicators widens the reach of optical voltage imaging in cell physiology, most notably neurophysiology, by enabling membrane voltage recordings from genetically defined cell types in chronic and life-long preparations. While the last years have seen a dramatic improvement in the technical performance of these indicators, concomitant innovations in optogenetics, optical axon tracing, and high-speed digital microscopy are beginning to fulfill the age-old vision of an all-optical analysis of neuronal circuits, reaching beyond the limits of traditional electrode-based recordings. We will present our personal account of the development of protein voltage indicators from the pioneering days to the present state, including their applications in neurophysiology that has inspired our own work for more than a decade.

  15. Application of genetic algorithms to the optimization design of electron optical system

    NASA Astrophysics Data System (ADS)

    Gu, Changxin; Wu, M. Q.; Shan, Liying; Lin, G.

    2001-12-01

    The application of Genetic Algorithms (GAs) to the optimization design method, such as Simplex method and Powell method etc, can determine the final optimum structure and electric parameters of an electron optical system from given electron optical properties, but it may be landed in the localization of optimum search process. The GAs is a novel direct search optimization method based on principles of natural selection and survival of the fittest from natural evolution. Through the reproduction, crossover, and mutation iterative process, GAs can search the global optimum result. We applied the GAs to optimize an electron emission system and an extended field lens (EFL) respectively. The optimal structure and corresponding electrical parameters with a criterion of minimum objective function value, crossover radius for electron emission system and spherical aberration coefficient for EFL, have been searched and presented in this paper. The GAs, as a direct search method and an adaptive search technique, has significant advantage in the optimization design of electron optical systems.

  16. Emerging applications of sperm, embryo and somatic cell cryopreservation in maintenance, relocation and rederivation of swine genetics

    PubMed Central

    Men, H.; Walters, EM.; Nagashima, H.; Prather, RS.

    2012-01-01

    Advances in porcine assisted reproductive technology (ART) make it possible to use cryopreserved sperm, embryos and somatic cells in the maintenance, relocation and regeneration of swine genetics. In this review, development of key application-limiting technology is discussed in each cell type, focusing on the efficiencies, ease of storage and transportation, and minimization of pathogen transmission. Methods to regenerate swine genetics and/or models using frozen sperm, embryos and somatic cells in combination with other porcine ARTs, such as in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and somatic cell nuclear transplantation (SCNT), are also discussed. The applications of these ARTs utilizing cryopreserved cells will greatly increase the efficiency as well as biosecurity for maintenance, relocation and rederivation of swine genetics/models. PMID:22898022

  17. Post-Doctoral Fellowships The Department of Biostatistics and Center for Statistical Genetics invite applications for post-

    E-print Network

    Queitsch, Christine

    Post-Doctoral Fellowships The Department of Biostatistics and Center for Statistical Genetics invite applications for post- doctoral fellowships emphasizing the statistical methods development, and in the development of key genomic resources and analysis methods and software. Post-doctoral positions may emphasize

  18. The partially reversible formation of Li-metal particles on a solid Li electrolyte: applications toward nanobatteries

    SciTech Connect

    Arruda, Thomas M [ORNL; Kumar, Amit [ORNL; Kalinin, Sergei V [ORNL; Jesse, Stephen [ORNL

    2012-01-01

    The feasibility of large-scale implementation of Li-air batteries (LABs) hinges on understanding the thermodynamic and kinetic factors that control charge-discharge rates, efficiency and life times. Here, the kinetics of bias-induced reactions is explored locally on the surface of Li-ion conductive glass ceramics, a preferred electrolyte for LABs, using direct current-voltage and strain spectroscopies. Above a critical bias, particle growth kinetics were found to be linear in both the bias and time domains. Partial reversibility was observed for Li particles as evidenced by the presence of anodic peaks following the Li{sup +} reduction, as well an associated reduction in particle height. The degree of reversibility was highest for the smallest particles formed. These observations thus suggest the possibility of producing nanobatteries with an active anode volume of the order of 0.1 al.

  19. Colored reverse-banding of human chromosomes with acridine orange following alkaline\\/formalin treatment: Densitometric validation and applications

    Microsoft Academic Search

    Herman E. Wyandt; Robert F. Vlietinck; R. Ellen Magenis; Frederick Hecht

    1974-01-01

    A technique is described in detail for 1. differentially denaturing DNA along chromosome arms with sodium hydroxide containing formalin (NaOH-F) and 2. staining with acridine orange (AO). The NaOH-F\\/AO technique results in chromosomes with red, yellow, brown and green colored bands which, when photographed in black and white, appear to be the reverse of Q bands. Densitometry tracings of these

  20. Determination of Cinnarizine in Whole Blood and Plasma by Reversed Phase HFLC and its Application to a Pharmacokinetic Study

    Microsoft Academic Search

    M. Puttemans; M. Bogaert; G. Hoogewijs; L. Dryon; D. L. Massart; L. Vanhaelst

    1984-01-01

    Cinnarizine is determined in whole blood and plasma by reversed phase HPLC on a RP-18 stationary phase. The one-step extraction is performed with a chloroform\\/hexane (2\\/3) mixture. A high recovery of 91% and a detection limit of 2 ng\\/ml are obtained as well as a good precision. The internal standard is meclozine. Pharmacokinetic parameters found are in accordance with data

  1. Reversible concentric ring microfluidic interconnects

    E-print Network

    Thompson, Mary Kathryn, 1980-

    2004-01-01

    A reversible, Chip-to-Chip microfluidic interconnect was designed for use in high temperature, high pressure applications such as chemical microreactor systems. The interconnect uses two sets of concentric, interlocking ...

  2. Application of Microsatellite Markers in Conservation Genetics and Fisheries Management: Recent Advances in Population Structure Analysis and Conservation Strategies

    PubMed Central

    Abdul-Muneer, P. M.

    2014-01-01

    Microsatellites are the most popular and versatile genetic marker with myriads of applications in population genetics, conservation biology, and evolutionary biology. These are the arrays of DNA sequences, consisting of tandemly repeating mono-, di-, tri-, and tetranucleotide units, which are distributed throughout the genomes of most eukaryotic species. Microsatellites are codominant in nature, highly polymorphic, easily typed, and Mendelian inherited, all properties which make them very suitable for the study of population structure and pedigree analysis and capable of detecting differences among closely related species. PCR for microsatellites can be automated for identifying simple sequence repeat polymorphism. Small amount of blood samples or alcohol preserved tissue is adequate for analyzing them. Most of the microsatellites are noncoding, and therefore variations are independent of natural selection. These properties make microsatellites ideal genetic markers for conservation genetics and fisheries management. This review addresses the applications of microsatellite markers in conservation genetics and recent advances in population structure analysis in the context of fisheries management. PMID:24808959

  3. Reverse osmosis reverses conventional wisdom with Superfund cleanup success

    SciTech Connect

    Collins, M. (French Ltd. Task Group, Crosby, TX (United States)); Miller, K. (Rochem Environmental Inc., Houston, TX (United States))

    1994-09-01

    Although widely recognized as the most efficient means of water purification, reverse osmosis has not been considered effective for remediating hazardous wastewater. Scaling and fouling, which can cause overruns and downtime, and require membrane replacement, have inhibited success in high-volume wastewater applications. Despite this background, a reverse osmosis technology developed in Europe recently was used successfully to treat large volumes of contaminated water at a major Superfund site in Texas. The technology's success there may increase the chances for reverse osmosis to find wider use in future cleanups and other waste treatment applications.

  4. Rapid on-chip genetic detection microfluidic platform for real world applications.

    PubMed

    Senapati, Satyajyoti; Mahon, Andrew R; Gordon, Jason; Nowak, Carsten; Sengupta, Shramik; Powell, Thomas H Q; Feder, Jeffrey; Lodge, David M; Chang, Hsueh-Chia

    2009-01-01

    The development of genetic detection protocols for field applications is an important aspect of modern medical diagnostic technology and environmental monitoring. In this paper, we report a rapid, portable, and inexpensive DNA hybridization technique using a bead-based microfluidic platform that functions by passing fluorescently labeled target DNA through a chamber packed with functionalized beads within a microfluidic channel. DNA hybridization is then assessed using a digital camera attached to a Clare Chemical DR-45M dark reader non-UV transilluminator that uses visible light as an excitation source and a blue and amber filter to reveal fluorescence. This microfluidic approach significantly enhances hybridization by reducing the diffusion time between target DNA and the silica surface. The use of probe-functionalized beads as solid support also enhances the sensitivity and limit of detection due to a larger surface area per unit volume. This platform could be adapted for use in medical applications and environmental monitoring, including the detection of harmful organisms in the ballast water of ships. PMID:19693342

  5. Back analysis of thermal field of concrete and its application based on niche genetic algorithms

    Microsoft Academic Search

    Chen Shou-kai; Zhu Yue-ming; Shuai Wei

    2010-01-01

    An improved form of basic genetic algorithm: Niche genetic algorithm which is based on sharing function is designed. It is aiming at the premature problem of basic genetic algorithm that existed in the back analysis of parameters of concrete thermal field. According to the measured temperature of concrete of rock anchor beam during construction period, its program composition is used

  6. Reverse mortgages.

    PubMed

    Farnesi, D

    1995-09-01

    Elders and their families are often caught in a financial bind when it comes to paying for much-needed home care services. Reverse mortgages may offer a solution to elderly home care clients who own their homes but have a limited income with which to maintain their independence. PMID:10151233

  7. A school-based application of modified habit reversal for Tourette syndrome via a translator: a case study.

    PubMed

    Gilman, Rich; Connor, Nancy; Haney, Michelle

    2005-11-01

    A school-based modified habit reversal intervention was utilized with an adolescent diagnosed with Tourette syndrome who recently immigrated from Mexico. Because the student possessed little proficiency of the English language, an interpreter was needed to help implement the procedure. The frequency of motor tics markedly decreased from baseline to intervention across classroom settings. Results of two follow-up phases revealed that motor tic levels remained below those observed in the baseline phase. Implications and limitations of these findings are noted. PMID:16204418

  8. Genetic algorithm based input selection for a neural network function approximator with applications to SSME health monitoring

    NASA Technical Reports Server (NTRS)

    Peck, Charles C.; Dhawan, Atam P.; Meyer, Claudia M.

    1991-01-01

    A genetic algorithm is used to select the inputs to a neural network function approximator. In the application considered, modeling critical parameters of the space shuttle main engine (SSME), the functional relationship between measured parameters is unknown and complex. Furthermore, the number of possible input parameters is quite large. Many approaches have been used for input selection, but they are either subjective or do not consider the complex multivariate relationships between parameters. Due to the optimization and space searching capabilities of genetic algorithms they were employed to systematize the input selection process. The results suggest that the genetic algorithm can generate parameter lists of high quality without the explicit use of problem domain knowledge. Suggestions for improving the performance of the input selection process are also provided.

  9. Reverse Osmosis

    NSDL National Science Digital Library

    North Dakota State University presents the theories behind reverse osmosis and how it affects household water supplies. The site addresses the impurities which are removed by this process. It also speaks of testing, the process itself and even the disadvantages of this process. A fairly encompassing site is what amounts from the work done by the University, it gives a clear and concise viewpoint of this process.

  10. Reversible Circuit Realizations of Boolean Functions

    Microsoft Academic Search

    Alex Brodsky

    2004-01-01

    Reversible circuits are a concrete model of reversible computation with applications in areas such as quantum computing and\\u000a analysis of cryptographic block cyphers. In 1980, Toffoli showed how to realize a Boolean function by a reversible circuit,\\u000a however the resulting complexity of such circuits has remained an open problem. We investigate the reversible circuit complexity\\u000a of families of Boolean functions

  11. Functional, fractal nonlinear response with application to rate processes with memory, allometry, and population genetics

    PubMed Central

    Vlad, Marcel O.; Morán, Federico; Popa, Vlad T.; Szedlacsek, Stefan E.; Ross, John

    2007-01-01

    We give a functional generalization of fractal scaling laws applied to response problems as well as to probability distributions. We consider excitations and responses, which are functions of a given state vector. Based on scaling arguments, we derive a general nonlinear response functional scaling law, which expresses the logarithm of a response at a given state as a superposition of the values of the logarithms of the excitations at different states. Such a functional response law may result from the balance of different growth processes, characterized by variable growth rates, and it is the first order approximation of a perturbation expansion similar to the phase expansion. Our response law is a generalization of the static fractal scaling law and can be applied to the study of various problems from physics, chemistry, and biology. We consider some applications to heterogeneous and disordered kinetics, organ growth (allometry), and population genetics. Kinetics on inhomogeneous reconstructing surfaces leads to rate equations described by our nonlinear scaling law. For systems with dynamic disorder with random energy barriers, the probability density functional of the rate coefficient is also given by our scaling law. The relative growth rates of different biological organs (allometry) can be described by a similar approach. Our scaling law also emerges by studying the variation of macroscopic phenotypic variables in terms of genotypic growth rates. We study the implications of the causality principle for our theory and derive a set of generalized Kramers–Kronig relationships for the fractal scaling exponents. PMID:17360340

  12. Construction and application of a protein and genetic interaction network (yeast interactome)

    PubMed Central

    Stuart, Gregory R.; Copeland, William C.; Strand, Micheline K.

    2009-01-01

    Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome. PMID:19273534

  13. Genetic characterization of caffeine degradation by bacteria and its potential applications.

    PubMed

    Summers, Ryan M; Mohanty, Sujit K; Gopishetty, Sridhar; Subramanian, Mani

    2015-05-01

    The ability of bacteria to grow on caffeine as sole carbon and nitrogen source has been known for over 40 years. Extensive research into this subject has revealed two distinct pathways, N-demethylation and C-8 oxidation, for bacterial caffeine degradation. However, the enzymological and genetic basis for bacterial caffeine degradation has only recently been discovered. This review article discusses the recent discoveries of the genes responsible for both N-demethylation and C-8 oxidation. All of the genes for the N-demethylation pathway, encoding enzymes in the Rieske oxygenase family, reside on 13.2-kb genomic DNA fragment found in Pseudomonas putida?CBB5. A nearly identical DNA fragment, with homologous genes in similar orientation, is found in Pseudomonas sp. CES. Similarly, genes for C-8 oxidation of caffeine have been located on a 25.2-kb genomic DNA fragment of Pseudomonas sp. CBB1. The C-8 oxidation genes encode enzymes similar to those found in the uric acid metabolic pathway of Klebsiella pneumoniae. Various biotechnological applications of these genes responsible for bacterial caffeine degradation, including bio-decaffeination, remediation of caffeine-contaminated environments, production of chemical and fuels and development of diagnostic tests have also been demonstrated. PMID:25678373

  14. Genetic evidence for the offsite transport of E. coli associated with land application of Class B biosolids on agricultural fields.

    PubMed

    Esseili, Malak A; Kassem, Issmat I; Sigler, Von; Czajkowski, Kevin; Ames, April

    2012-09-01

    The land-application of Class B biosolids is tightly regulated to allow for natural attenuation of co-applied pathogens. Since many agricultural fields that receive biosolids are artificially drained through subsurface tiles, it is possible that under scenarios of excessive drainage associated with heavy rainfall events, co-applied pathogens might be carried offsite to contaminate nearby surface waters. To address this concern, we used genetic as well as traditional methods to investigate the impact of rainfall on the offsite drainage of Escherichia coli from agricultural fields during biosolids application. Water samples from field drain tiles and a reference field (no biosolids applied) were collected pre-, during and post-biosolids application, while samples of applied biosolids were collected on site during application. The samples were analyzed for E. coli-density and community- and isolate-fingerprinting to assess the genetic link between E. coli in drainage water and those co-applied with biosolids. In contrast to E. coli densities present in the reference field drainage, our results revealed that post-application drainage water collected from biosolids treated fields contained significantly higher E. coli densities following heavy rainfall events, as compared to light rainfall events. Also, in contrast to the reference field, heavy rainfall correlated significantly with increased similarity of E. coli community fingerprints occurring in biosolids to those draining from treated field. Fingerprinting of individual E. coli revealed a high similarity (>94%) between some isolates collected from biosolids and post-application drainage water. Using a combination of enumeration and genetic typing methods, we show that heavy rainfall following biosolids application to agricultural fields induced the offsite transport of biosolids-associated E. coli, potentially compromising the quality of water draining through the watershed. PMID:22796725

  15. Research of Quantum Genetic Algorith and its application in blind source separation

    Microsoft Academic Search

    Junan Yang; Bin Li; Zhenquan Zhuang

    2003-01-01

    This letter proposes two algorithms: a novel Quantum Genetic Algorithm (QGA) based on the improvement of Han’s Genetic Quantum\\u000a Algorithm (GQA) and a new Blind Source Separation (BSS) method based on QGA and Independent Component Analysis (ICA). The\\u000a simulation result shows that the efficiency of the new BSS method is obviously higher than that of the Conventional Genetic\\u000a Algorithm (CGA).

  16. Reversible thermoelectric nanomaterials.

    PubMed

    Humphrey, T E; Linke, H

    2005-03-11

    Irreversible effects in thermoelectric materials limit their efficiency and economy for applications in power generation and refrigeration. While electron transport is unavoidably irreversible in bulk materials, here we derive conditions under which reversible diffusive electron transport can be achieved in nanostructured thermoelectric materials. We provide a fundamental thermodynamic explanation for why the optimum density of states in a thermoelectric material is a delta function and for why inhomogeneous doping and segmentation improve the thermoelectric figure of merit. PMID:15783983

  17. Application of the genetic algorithm for global scheduling and a single machine scheduling problem with periodic maintenance and semiresumable jobs

    E-print Network

    Graves, Gregory Howard

    1998-01-01

    APPLICATION OF THE GENETIC ALGORITHM FOR GLOBAL SCHEDULING AND A SINGLE MACHINE SCHEDULING PROBLEM WITH PERIODIC MAINTENANCE AND SEMIRESUMABLE JOBS A Thesis by GREGORY HOWARD GRAVES Submitted to the Office of Graduate Studies of Texas A... MAINTENANCE AND SEMIRESUMABLE JOBS A Thesis by GREGORY HOWARD GRAVES Submitted to Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved as to style and content by: Chung- Yee Lee (Chair...

  18. Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development

    SciTech Connect

    Jin, Huanan; Song, Zhihong; Nikolau, Basil J.

    2012-03-31

    Acetoacetyl CoA thiolase (AACT, EC 2.3.1.9) catalyzes the condensation of two acetyl?CoA molecules to form acetoacetyl?CoA. Two AACT?encoding genes, At5g47720 (AACT1) and At5g48230 (AACT2), were functionally identified in the Arabidopsis genome by direct enzymological assays and functional expression in yeast. Promoter::GUS fusion experiments indicated that AACT1 is primarily expressed in the vascular system and AACT2 is highly expressed in root tips, young leaves, top stems and anthers. Characterization of T?DNA insertion mutant alleles at each AACT locus established that AACT2 function is required for embryogenesis and for normal male gamete transmission. In contrast, plants lacking AACT1 function are completely viable and show no apparent growth phenotypes, indicating that AACT1 is functionally redundant with respect to AACT2 function. RNAi lines that express reduced levels of AACT2 show pleiotropic phenotypes, including reduced apical dominance, elongated life span and flowering duration, sterility, dwarfing, reduced seed yield and shorter root length. Microscopic analysis reveals that the reduced stature is caused by a reduction in cell size and fewer cells, and male sterility is caused by loss of the pollen coat and premature degeneration of the tapetal cells. Biochemical analyses established that the roots of AACT2 RNAi plants show quantitative and qualitative alterations in phytosterol profiles. These phenotypes and biochemical alterations are reversed when AACT2 RNAi plants are grown in the presence of mevalonate, which is consistent with the role of AACT2 in generating the bulk of the acetoacetyl?CoA precursor required for the cytosol?localized, mevalonate?derived isoprenoid biosynthetic pathway.

  19. Genetic analysis without replications: Model evaluation and application in spring wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic data collected from plant breeding and genetic studies may not be replicated in field designs even though field variation is present. In this study, we addressed this problem using spring wheat (Triticum eastivum L.) trial data collected from two locations. There were no intra-location repl...

  20. GENETIC NEURAL NETWORK BASED DATA MINING AND APPLICATION IN CASE ANALYSIS OF POLICE OFFICE

    Microsoft Academic Search

    LIU Han-li; LI Lin; ZHU Hai-hong

    This paper puts forward a method that combines the learning algorithm of BP neural network with genetic algorithm to train BP network and optimize the weight values of the network in a global scale. This method is featured as global optimization, high accuracy and fast convergence. The data-mining model based on genetic neural network has been widely applied to the

  1. Applications and Implications of Advances in Human Genetics: Perspectives from a Group of Black Americans

    Microsoft Academic Search

    Jane P. Sheldon; Toby Epstein Jayaratne; Merle B. Feldbaum; Courtney D. DiNardo; Elizabeth M. Petty

    2007-01-01

    Objectives: We explored the opinions of 40 Black Americans regarding: (1) what they thought most Blacks and Whites believe about genetic causes for perceived race differences in human traits, and (2) the impact of genetic science on them, their families, and Black people. Methods: We conducted in-depth telephone interviews with 40 self-identified Black men and women. Transcripts of the interviews

  2. Independent component analysis based on improved quantum genetic algorithm: application in hyperspectral images

    Microsoft Academic Search

    Na Li; Peng Du; Huijie Zhao

    2005-01-01

    To avoid the restriction of neuron activation functions of neural learning algorithm and the disadvantage of getting into local optimum solution with general numerical computation method, a novel independent component analysis (ICA) based on improved quantum genetic algorithm (IQGA) is proposed in our paper. Moreover, Han's quantum genetic algorithm (QGA) is improved by adopting the quantum crossover and quantum mutation

  3. Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins

    Microsoft Academic Search

    Aaron L Kurtzman; Sridhar Govindarajan; Katherine Vahle; Jennifer T Jones; Volker Heinrichs; Phillip A Patten

    2001-01-01

    Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic

  4. Application of Genetic Algorithm in the Optimization of Water Pollution Control Scheme

    Microsoft Academic Search

    Rui-Ming Zhao; Dong-Ping Qian

    2007-01-01

    Genetic Algorithm (Genetic Algorithm Chine write for the GA) is a kind of hunting Algorithm bionic global optimization imitating the Darwinian biological evolution theories, is advancing front of complex nonlinear science and artificial intelligence science. In the basic of introducing the GA basic principle and optimization Algorithm, this text leads the GA into the domain of the water pollution control

  5. On the application of parallel genetic algorithms in X-ray crystallography

    Microsoft Academic Search

    C.-S. Chang; G. DeTitta; R. Miller

    1994-01-01

    Discusses the design and implementations of a parallel genetic algorithm (PGA) for function optimization. The proposed PGA employs a coarse-grained approach in which a physical processor (a CPU) maintains several semi-isolated subpopulations (in the nodes), each of which operates an independent genetic plan. With this design, the entire population can preserve diversity by allowing each subpopulation to evolve relatively independently.

  6. The Science of Breeding and Its Application to the Breeder Genetic Algorithm (BGA)

    Microsoft Academic Search

    Heinz Mühlenbein; Dirk Schlierkamp-voosen

    1993-01-01

    The breeder genetic algorithm (BGA) models artificial selection as performed by human breeders. The science of breeding is based on advanced statistical methods. In this paper a connection between genetic algorithm theory and the science of breeding is made. We show how the response to selection equation and the concept of heritability can be applied to predict the behavior of

  7. Inference of genetic networks using linear programming machines: Application of a priori knowledge

    Microsoft Academic Search

    Shuhei Kimura; Yuichi Shiraishi; Mariko Hatakeyama

    2009-01-01

    Recently, the inference of genetic networks was defined as a series of discrimination tasks. The inference method based on this problem definition infers genetic networks by obtaining predictors that can predict the signs of the differential coefficients of the gene expression levels. As these predictors are obtained by solving linear programming problems, the computational time of the method is very

  8. K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.

    PubMed

    Wen, Jia; Chan, Raymond H F; Yau, Shek-Chung; He, Rong L; Yau, Stephen S T

    2014-08-01

    Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency. PMID:24858075

  9. Reversible Computation and Reversible Programming Languages

    Microsoft Academic Search

    Tetsuo Yokoyama

    2010-01-01

    A reversible programming language supports deterministic forward and backward computation. This tutorial focuses on a high-level reversible programming language Janus. In common with other programming paradigms, reversible programming has its own programming methodology. Janus is simple, yet powerful, and its constructs can serve as a model for designing reversible languages in general.

  10. An application of LOH analysis for detecting the genetic influences of space environmental radiation

    NASA Astrophysics Data System (ADS)

    Yatagai, F.; Umebayashi, Y.; Honma, M.; Abe, T.; Suzuki, H.; Shimazu, T.; Ishioka, N.; Iwaki, M.

    To detect the genetic influence of space environmental radiation at the chromosome level we proposed an application of loss of heterozygosity LOH analysis system for the mutations induced in human lymphoblastoid TK6 cells Surprisingly we succeeded the mutation detection in the frozen dells which were exposed to a low-dose 10 cGy of carbon-ion beam irradiation Mutation assays were performed within a few days or after about one month preservation at --80 r C following irradiation The results showed an increase in mutation frequency at the thymidine kinase TK gene locus 1 6-fold 2 5 X 10 -6 to 3 9 X 10 -6 and 2 1-fold 2 5 X 10 -6 to 5 3 X 10 -6 respectively Although the relative distributions of mutation classes were not changed by the radiation exposure in either assay an interesting characteristic was detected using this LOH analysis system two TK locus markers and eleven microsatellite loci spanning chromosome 17 The radiation-specific patterns of interstitial deletions were observed in the hemizygous LOH mutants which were considered as a result of end-joining repair of carbon ion-induced DNA double-strand breaks These results clearly demonstrate that this analysis can be used for the detection of low-dose ionizing radiation effects in the frozen cells In addition we performed so called adaptive response experiments in which TK6 cells were pre-irradiated with low-dose 2 5 sim 10 cGy of X-ray and then exposed to challenging dose 2Gy of X-rays Interestingly the

  11. Visual & reversible sensing of cyanide in real samples by an effective ratiometric colorimetric probe & logic gate application.

    PubMed

    Bhardwaj, Shubhrajyotsna; Singh, Ashok Kumar

    2015-10-15

    A novel anion probe 3 (2,4-di-tert-butyl-6-((2(2,4-dinitrophenyl) hydrazono) methyl) phenol) has been unveiled as an effective ratiometric and colorimetric sensor for selective and rapid detection of cyanide. The sensing behavior was demonstrated by UV-vis experiments and NMR studies. This sensory system exhibited prominent visual color change toward cyanide ion over other testing anions in DMSO (90%) solvent, with a 1:1 binding stoichiometry and a detection limit down to 3.6×10(-8)molL(-1). Sensor reveals specific anti-jamming activity and reversible in the presence of Cu(2+) ions. This concept has been applied to design a logic gate circuit at the molecular level. Further we developed coated graphite electrode using probe 3 as ionophore and studied the performance characteristics of electrode. The sensitivity of ratiometric-based colorimetric assay is below the 1.9?M, accepted by the World Health Organization as the highest permissible cyanide concentration in drinking water. So it can be applied for both quantitative determination and qualitative supervising of cyanide concentrations in real samples. PMID:25913671

  12. A Reversible Crystallinity-Preserving Phase Transition in Metal-Organic Frameworks: Discovery, Mechanistic Studies, and Potential Applications.

    PubMed

    Liu, Dahuan; Liu, Tian-Fu; Chen, Ying-Pin; Zou, Lanfang; Feng, Dawei; Wang, Kecheng; Zhang, Qiang; Yuan, Shuai; Zhong, Chongli; Zhou, Hong-Cai

    2015-06-24

    A quenching-triggered reversible single-crystal-to-single-crystal (SC-SC) phase transition was discovered in a metal-organic framework (MOF) PCN-526. During the phase transition, the one-dimensional channel of PCN-526 distorts from square to rectangular in shape while maintaining single crystallinity. Although SC-SC transformations have been frequently observed in MOFs, most reports have focused on describing the resulting structural alterations without shedding light on the mechanism for the transformation. Interestingly, modifying the occupancy or species of metal ions in the extra-framework sites, which provides mechanistic insight into the causes for the transformation, can forbid this phase transition. Moreover, as a host scaffold, PCN-526 presents a platform for modulation of the photoluminescence properties by encapsulation of luminescent guest molecules. Through judicious choice of these guest molecules, responsive luminescence caused by SC-SC transformations can be detected, introducing a new strategy for the design of novel luminescent MOF materials. PMID:26011818

  13. Genetic Counseling Program Information

    E-print Network

    Berdichevsky, Victor

    Genetic Counseling Program Information for Potential Applicants #12;Wayne State Genetic Counseling Program Overview "Genetic counseling is the process of helping people understand and adapt to the medical of Medicine at Wayne State University offers a fully accredited Master's level graduate program in genetic

  14. Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV).

    PubMed

    Yanez Barrientos, Eunice; Wrobel, Kazimierz; Lopez Torres, Adolfo; Gutiérrez Corona, Felix; Wrobel, Katarzyna

    2013-03-01

    In the present work, application of the previously established reversed-phase liquid chromatography procedure based on fluorescent labeling of cytosine and methylcytosine moieties with 2-bromoacetophenone (HPLC-FLD) is presented for simultaneous evaluation of global DNA and total RNA methylation at cytosine carbon 5. The need for such analysis was comprehended from the recent advances in the field of epigenetics that highlight the importance of non-coding RNAs in DNA methylation and suggest that RNA methylation might play a similar role in the modulation of genetic information, as previously demonstrated for DNA. In order to adopt HPLC-FLD procedure for DNA and RNA methylation analysis in a single biomass extract, two extraction procedures with different selectivity toward nucleic acids were examined, and a simplified calibration was designed allowing for evaluation of methylation percentage based on the ratio of chromatographic peak areas: cytidine/5-methylcytidine for RNA and 2'-deoxycytidine/5-methyl-2'-deoxycytidine for DNA. As a proof of concept, global DNA and total RNA methylation were determined in Lepidium sativum hydroponically grown in the presence of different Cd(II) or Se(IV) concentrations, expecting that plant exposure to abiotic stress might affect not only global DNA but also total RNA methylation. The results obtained showed the increase of DNA methylation in the treated plants up to concentration levels 2 mg L(-1) Cd and 1 mg L(-1) Se in the growth medium. For higher stressors' concentration, global DNA methylation tended to decrease. Most importantly, an inverse correlation was found between DNA and RNA methylation levels (r = -0.6788, p = 0.031), calling for further studies of this particular modification of nucleic acids in epigenetic context. PMID:23322354

  15. Critical overview of applications of genetic testing in sport talent identification.

    PubMed

    Roth, Stephen M

    2012-12-01

    Talent identification for future sport performance is of paramount interest for many groups given the challenges of finding and costs of training potential elite athletes. Because genetic factors have been implicated in many performance- related traits (strength, endurance, etc.), a natural inclination is to consider the addition of genetic testing to talent identification programs. While the importance of genetic factors to sport performance is generally not disputed, whether genetic testing can positively inform talent identification is less certain. The present paper addresses the science behind the genetic tests that are now commercially available (some under patent protection) and aimed at predicting future sport performance potential. Also discussed are the challenging ethical issues that emerge from the availability of these tests. The potential negative consequences associated with genetic testing of young athletes will very likely outweigh any positive benefit for sport performance prediction at least for the next several years. The paper ends by exploring the future possibilities for genetic testing as the science of genomics in sport matures over the coming decade(s). PMID:22789017

  16. Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)

    PubMed Central

    Holtgräwe, Daniela; Sörensen, Thomas Rosleff; Viehöver, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

    2014-01-01

    Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers. PMID:25302600

  17. Proc. of Formal Methods in Prog. & their Applications, Lect. Notes in Comp. Sci., pp. 335348, July 1993 A TwoPhase Approach to Reverse Engineering

    E-print Network

    Cheng, Betty H.C.

    1993 A Two­Phase Approach to Reverse Engineering Using Formal Methods Gerald C. Gannod and Betty H. C. Reverse engineering of program code is the process of construct­ ing a higher level abstraction in software development and object­oriented program­ ming, have prompted a need to reverse engineer and re­engineer

  18. Applications of Improved Multi-Agent Genetic Algorithm to Water Pollution Control System Planning

    NASA Astrophysics Data System (ADS)

    Dong, Qianjin; Lu, Fan; Gao, Shichun

    2010-05-01

    Combining the ability of apperception and counteractive to environment of agent with search method of genetic algorithm, an improved multi-agent genetic algorithm (MAGA) is advanced. It ensures diversity of population and improves local search ability of genetic algorithm by simulating competition, cooperate and self-study of different agents using neighboring cross operator, aberrance operator and self-learning operator of agent. The algorithm is applied to the optimal planning for the waste treatment system of Urumqi, Xinjiang. Results demonstrate an improved performance in finding the global minimum when water quality requirements have been fulfilled. The result demonstrates nicer performance and factual value of MAGA.

  19. Design and analysis of genetical genomics studies and their potential applications in livestock research 

    E-print Network

    Lam, Alex C.

    2009-01-01

    Quantitative Trait Loci (QTL) mapping has been widely used to identify genetic loci attributable to the variation observed in complex traits. In recent years, gene expression phenotypes have emerged as a new type of ...

  20. Genetics of Type 2 Diabetes: Insights into the Pathogenesis and Its Clinical Application

    PubMed Central

    Sun, Xue; Yu, Weihui; Hu, Cheng

    2014-01-01

    With rapidly increasing prevalence, diabetes has become one of the major causes of mortality worldwide. According to the latest studies, genetic information makes substantial contributions towards the prediction of diabetes risk and individualized antidiabetic treatment. To date, approximately 70 susceptibility genes have been identified as being associated with type 2 diabetes (T2D) at a genome-wide significant level (P < 5 × 10?8). However, all the genetic loci identified so far account for only about 10% of the overall heritability of T2D. In addition, how these novel susceptibility loci correlate with the pathophysiology of the disease remains largely unknown. This review covers the major genetic studies on the risk of T2D based on ethnicity and briefly discusses the potential mechanisms and clinical utility of the genetic information underlying T2D. PMID:24864266

  1. Cancer risk assessment using genetic panel testing: considerations for clinical application.

    PubMed

    Hiraki, Susan; Rinella, Erica S; Schnabel, Freya; Oratz, Ruth; Ostrer, Harry

    2014-08-01

    With the completion of the Human Genome Project and the development of high throughput technologies, such as next-generation sequencing, the use of multiplex genetic testing, in which multiple genes are sequenced simultaneously to test for one or more conditions, is growing rapidly. Reflecting underlying heterogeneity where a broad range of genes confer risks for one or more cancers, the development of genetic cancer panels to assess these risks represents just one example of how multiplex testing is being applied clinically. There are a number of issues and challenges to consider when conducting genetic testing for cancer risk assessment, and these issues become exceedingly more complex when moving from the traditional single-gene approach to panel testing. Here, we address the practical considerations for clinical use of panel testing for breast, ovarian, and colon cancers, including the benefits, limitations and challenges, genetic counseling issues, and management guidelines. PMID:24599651

  2. Application of Genetic Algorithms and Thermogravimetry to Determine the Kinetics of Polyurethane Foam in Smoldering Combustion 

    E-print Network

    Rein, Guillermo; Lautenberger, Chris; Fernandez-Pello, Carlos; Torero, Jose L; Urban, David

    In this work, the kinetic parameters governing the thermal and oxidative degradation of flexible polyurethane foam are determined using thermogravimetric data and a genetic algorithm. These kinetic parameters are needed ...

  3. Application of Genetic Algorithm to Optimal Design of Central Air-Conditioning Water System 

    E-print Network

    Feng, X.; Zou, Y.; Long, W.

    2006-01-01

    algorithm (GA ) has special advantages in tackling this problem based on its inherent characteristics.Genetic algorithm (GA) is adopted and applied in the optimal design of air-conditioning water system in this study. A mathematical model and constrained...

  4. The application of genetic algorithms to the design of reconfigurable reasoning VLSI chips

    Microsoft Academic Search

    Moritoshi Yasunaga; Jung Hwan Kim; Ikuo Yoshihara

    2000-01-01

    In this paper, we present a new genetic-algorithm-based design methodology for reasoning VLSI chips, called as LoDETT (logic design with the evolved truth table). In LoDETT, each task's case database is transformed into truth tables, which are evolved to obtain generalization capability (i.e. rules behind the past cases) through genetic algorithms. Digital circuits are synthesized from the evolved truth-tables. Parallelism

  5. Applications of the Saccharomyces cerevisiae Flp-FRT System in Bacterial Genetics

    Microsoft Academic Search

    Herbert P. Schweizer

    2003-01-01

    The Flp-FRT site-specific recombinationsystem from Saccharomyces cerevisiae is a powerful and efficient tool for high-throughput genetic analysis of bacteria in the postgenomic era. This review highlights the features of the Flp-FRT system, describes current bacterial genetic methods incorporating this technology and, finally, suggests potential future uses of this system. In combination with improved allele replacement methods, recyclable FRT mutagenesis cassettes,

  6. Data Mining with Constrained-Syntax Genetic Programming: Applications in Medical Data Set

    Microsoft Academic Search

    Celia C. Bojarczuk; Heitor S. Lopes; Alex A. Freitas

    2001-01-01

    This work is intended to discover classification rules fordiagnosing certain pathologies. In order to discover theserules we have developed a new constrained-syntax geneticprogramming algorithm based on some concepts of datamining, particularly with emphasis on the discovery ofcomprehensible knowledge. We compare the performanceof the proposed GP algorithm with a genetic algorithmand with the very well-known decision-tree algorithmC4.5.Keywords:Genetic Programming, Data Mining,...

  7. Analysis of genetic variation and potential applications in genome-scale metabolic modeling.

    PubMed

    Cardoso, João G R; Andersen, Mikael Rørdam; Herrgård, Markus J; Sonnenschein, Nikolaus

    2015-01-01

    Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic variation during a long term production process may lead to significant economic losses and it is important to understand how to control this type of variation. With the emergence of next-generation sequencing technologies, genetic variation in microbial strains can now be determined on an unprecedented scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular phenotypes. PMID:25763369

  8. A Novel Genetic Score Approach Using Instruments to Investigate Interactions between Pathways and Environment: Application to Air Pollution

    PubMed Central

    Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

    2014-01-01

    Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999–2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (pinteraction?=?0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (pinteraction?=?0.12), CRP (pinteraction?=?0.02), and ICAM-1 (pinteraction?=?0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications. PMID:24755831

  9. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities

    PubMed Central

    Lin, Xi; Tang, Wenxue; Ahmad, Shoeb; Lu, Jingqiao; Colby, Candice C.; Zhu, Jason; Yu, Qing

    2013-01-01

    The goal of sequencing the entire human genome for $1,000 is almost in sight. However, the total costs including DNA sequencing, data management, and analysis to yield a clear data interpretation are unlikely to be lowered significantly any time soon to make studies on a population scale and daily clinical uses feasible. Alternatively, the targeted enrichment of specific groups of disease and biological pathway-focused genes and the capture of up to an entire human exome (~1% of the genome) allowing an unbiased investigation of the complete protein-coding regions in the genome are now routine. Targeted gene capture followed by sequencing with massively parallel next-generation sequencing (NGS) has the advantages of 1) significant cost saving, 2) higher sequencing accuracy because of deeper achievable coverage, 3) a significantly shorter turnaround time, and 4) a more feasible data set for a bioinformatic analysis outcome that is functionally interpretable. Gene capture combined with NGS has allowed a much greater number of samples to be examined than is currently practical with whole-genome sequencing. Such an approach promises to bring a paradigm shift to biomedical research of Mendelian disorders and their clinical diagnoses, ultimately enabling personalized medicine based on one’s genetic profile. In this review, we describe major methodologies currently used for gene capture and detection of genetic variations by NGS. We will highlight applications of this technology in studies of genetic disorders and discuss issues pertaining to applications of this powerful technology in genetic screening and the discovery of genes implicated in syndromic and non-syndromic hearing loss. PMID:22269275

  10. Isolobal analogies in intermetallics: the reversed approximation MO approach and applications to CrGa4- and Ir3Ge7-type phases.

    PubMed

    Yannello, Vincent J; Kilduff, Brandon J; Fredrickson, Daniel C

    2014-03-01

    Intermetallic phases offer a wealth of unique and unexplained structural features, which pose exciting challenges for the development of new bonding concepts. In this article, we present a straightforward approach to rapidly building bonding descriptions of such compounds: the reversed approximation Molecular Orbital (raMO) method. In this approach, we reverse the usual technique of using linear combinations of simple functions to approximate true wave functions and employ the fully occupied crystal orbitals of a compound as a basis set for the determination of the eigenfunctions of a simple, chemically transparent model Hamiltonian. The solutions fall into two sets: (1) a series of functions representing the best-possible approximations to the model system's eigenstates constructible from the occupied crystal orbitals and (2) a second series of functions that are orthogonal to the bonding picture represented by the model Hamiltonian. The electronic structure of a compound is thus quickly resolved into a series of orthogonal bonding subsystems. We first demonstrate the raMO analysis on a familiar molecule, 1,3-butadiene, and then move to illustrating its use in discovering new bonding phenomena through applications to three intermetallic phases: the PtHg4-type CrGa4 and the Ir3Ge7-type compounds Os3Sn7 and Ir3Sn7. For CrGa4, a density of states (DOS) minimum coinciding with its Fermi energy is traced to 18-electron configurations on the Cr atoms. For Os3Sn7 and Ir3Sn7, 18-electron configurations also underlie DOS pseudogaps. This time, however, the 18-electron counts involve multicenter interactions isolobal with classical Ir-Ir or Os-Os covalent bonds, as well as Sn-Sn single bonds serving as electron reservoirs. Our results are based on DFT-calibrated Hückel calculations, but in principle the raMO analysis can be implemented in any method employing one-electron wave functions. PMID:24555770

  11. Application of long-range and binding reverse transcription-quantitative PCR to indicate the viral integrities of noroviruses.

    PubMed

    Li, Dan; De Keuckelaere, Ann; Uyttendaele, Mieke

    2014-10-01

    This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60°C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60°C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm(2), no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles. PMID:25107982

  12. Application of Long-Range and Binding Reverse Transcription-Quantitative PCR To Indicate the Viral Integrities of Noroviruses

    PubMed Central

    De Keuckelaere, Ann; Uyttendaele, Mieke

    2014-01-01

    This study intends to establish and apply methods evaluating both viral capsid and genome integrities of human noroviruses (NoVs), which thus far remain nonculturable. Murine norovirus 1 (MNV-1) and human NoV GII.4 in phosphate-buffered saline suspensions were treated with heat, UV light, or ethanol and detected by reverse transcription-quantitative PCR (RT-qPCR), long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR. For MNV-1 heated at 60°C for 2 and 30 min, limited reductions of genomic copies (<0.3-log) were obtained by RT-qPCR and long-range RT-qPCR, while the cell-binding pretreatments obtained higher reductions (>1.89-log reduction after 60°C for 30 min by binding long-range RT-qPCR). The human NoV GII.4 was found to be more heat resistant than MNV-1. For both MNV-1 and human NoV GII.4 after UV treatments of 20 and 200 mJ/cm2, no significant difference (P > 0.05) was observed between the dose-dependent reductions obtained by the four detection methodologies. Treatment of 70% ethanol for 1 min was shown to be more effective for inactivation of both MNV-1 and human NoV GII.4 than the heat and UV treatments used in this study. Subsequently, eight raspberry and four shellfish samples previously shown to be naturally contaminated with human NoVs by RT-qPCR (GI and GII; thus, 24 RT-qPCR signals) were subjected to comparison by this method. RT-qPCR, long-range RT-qPCR, binding RT-qPCR, and binding long-range RT-qPCR detected 20/24, 14/24, 24/24, and 23/24 positive signals, respectively, indicating the abundant presence of intact NoV particles. PMID:25107982

  13. Genetic variation and its maintenance

    SciTech Connect

    Roberts, D.F.; De Stefano, G.F.

    1986-01-01

    This book contains several papers divided among three sections. The section titles are: Genetic Diversity--Its Dimensions; Genetic Diversity--Its Origin and Maintenance; and Genetic Diversity--Applications and Problems of Complex Characters.

  14. Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications

    NASA Astrophysics Data System (ADS)

    Aria, Adrianus Indrat

    In this thesis, dry chemical modification methods involving UV/ozone, oxygen plasma, and vacuum annealing treatments are explored to precisely control the wettability of CNT arrays. The effect of oxidation using UV/ozone and oxygen plasma treatments is highly reversible as long as the O/C ratio of the CNT arrays is kept below 18%. At O/C ratios higher than 18%, the effect of oxidation is no longer reversible. This irreversible oxidation is caused by irreversible changes to the CNT atomic structure during the oxidation process. During the oxidation process, CNT arrays undergo three different processes. For CNT arrays with O/C ratios lower than 40%, the oxidation process results in the functionalization of CNT outer walls by oxygenated groups. Although this functionalization process introduces defects, vacancies and micropores opening, the graphitic structure of the CNT is still largely intact. For CNT arrays with O/C ratios between 40% and 45%, the oxidation process results in the etching of CNT outer walls. This etching process introduces large scale defects and holes that can be obviously seen under TEM at high magnification. Most of these holes are found to be several layers deep and, in some cases, a large portion of the CNT side walls are cut open. For CNT arrays with O/C ratios higher than 45%, the oxidation process results in the exfoliation of the CNT walls and amorphization of the remaining CNT structure. This amorphization process can be implied from the disappearance of C-C sp2 peak in the XPS spectra associated with the pi-bond network. The impact behavior of water droplet impinging on superhydrophobic CNT arrays in a low viscosity regime is investigated for the first time. Here, the experimental data are presented in the form of several important impact behavior characteristics including critical Weber number, volume ratio, restitution coefficient, and maximum spreading diameter. As observed experimentally, three different impact regimes are identified while another impact regime is proposed. These regimes are partitioned by three critical Weber numbers, two of which are experimentally observed. The volume ratio between the primary and the secondary droplets is found to decrease with the increase of Weber number in all impact regimes other than the first one. In the first impact regime, this is found to be independent of Weber number since the droplet remains intact during and subsequent to the impingement. Experimental data show that the coefficient of restitution decreases with the increase of Weber number in all impact regimes. The rate of decrease of the coefficient of restitution in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Experimental data also show that the maximum spreading factor increases with the increase of Weber number in all impact regimes. The rate of increase of the maximum spreading factor in the high Weber number regime is found to be higher than that in the low and moderate Weber number. Phenomenological approximations and interpretations of the experimental data, as well as brief comparisons to the previously proposed scaling laws, are shown here. Dry oxidation methods are used for the first time to characterize the influence of oxidation on the capacitive behavior of CNT array EDLCs. The capacitive behavior of CNT array EDLCs can be tailored by varying their oxygen content, represented by their O/C ratio. The specific capacitance of these CNT arrays increases with the increase of their oxygen content in both KOH and Et4NBF4/PC electrolytes. As a result, their gravimetric energy density increases with the increase of their oxygen content. However, their gravimetric power density decreases with the increase of their oxygen content. The optimally oxidized CNT arrays are able to withstand more than 35,000 charge/discharge cycles in Et4NBF4/PC at a current density of 5 A/g while only losing 10% of their original capacitance. (Abstract shortened by UMI.)

  15. Multi-modal applicability of a reversed-phase\\/weak-anion exchange material in reversed-phase, anion-exchange, ion-exclusion, hydrophilic interaction and hydrophobic interaction chromatography modes

    Microsoft Academic Search

    Michael Lämmerhofer; Raquel Nogueira; Wolfgang Lindner

    2011-01-01

    We recently introduced a mixed-mode reversed-phase\\/weak anion-exchange type separation material based on silica particles\\u000a which consisted of a hydrophobic alkyl strand with polar embedded groups (thioether and amide functionalities) and a terminal\\u000a weak anion-exchange-type quinuclidine moiety. This stationary phase was designed to separate molecules by lipophilicity and\\u000a charge differences and was mainly devised for peptide separations with hydroorganic reversed-phase type

  16. Molecular Studies in Horses with SRY-Positive XY Sex Reversal 

    E-print Network

    Fang, Erica

    2012-02-14

    determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY...

  17. Molecular Studies in Horses with SRY-Positive XY Sex Reversal

    E-print Network

    Fang, Erica

    2012-02-14

    determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY...

  18. Molecular diagnosis of inheritable neuromuscular disorders. Part II: Application of genetic testing in neuromuscular disease.

    PubMed

    Greenberg, Steven A; Walsh, Ronan J

    2005-04-01

    Molecular genetic advances have led to refinements in the classification of inherited neuromuscular disease, and to methods of molecular testing useful for diagnosis and management of selected patients. Testing should be performed as targeted studies, sometimes sequentially, but not as wasteful panels of multiple genetic tests performed simultaneously. Accurate diagnosis through molecular testing is available for the vast majority of patients with inherited neuropathies, resulting from mutations in three genes (PMP22, MPZ, and GJB1); the most common types of muscular dystrophies (Duchenne and Becker, facioscapulohumeral, and myotonic dystrophies); the inherited motor neuron disorders (spinal muscular atrophy, Kennedy's disease, and SOD1 related amyotrophic lateral sclerosis); and many other neuromuscular disorders. The role of potential multiple genetic influences on the development of acquired neuromuscular diseases is an increasingly active area of research. PMID:15704143

  19. Ion-pair reversed-phase chromatography of short double-stranded deoxyribonucleic acid in silicon micro-pillar array columns: retention model and applications.

    PubMed

    Zhang, Lei; Majeed, Bivragh; Lagae, Liesbet; Peumans, Peter; Van Hoof, Chris; De Malsche, Wim

    2013-06-14

    Separation of double-stranded (ds) DNAs is important in numerous biochemical analyses relevant for clinical applications. A widely used separation technique is high performance liquid chromatography (HPLC), in the variant of ion-pair reversed-phase (IP-RP) chromatography. HPLC can be miniaturized by means of silicon micro-pillar array columns leading to on-chip fast and high resolution dsDNA separation with limited sample quantity. However, theoretical studies of retentive behavior of dsDNA in miniaturized chromatographic columns are hardly available, despite their enormous practical relevance. This paper established a new retention model to describe the size dependent separation of dsDNAs for any characteristic of the linear mobile phase gradient, in analogy to the model used to describe the retention of polymer chains with repeating units in RP HPLC. The model agrees with a large amount of dsDNA retention data, measured using DNA molecules in the size range of 10-400 base pairs in columns with different lengths (2 and 40cm) and different micro-pillar sizes (2 and 2.5?m in diameter), in various mobile phase gradients. The model is particularly useful in practice, since it requires no numerical solutions and the column-specific fitting parameters (4 or 5) can be determined in a limited number of separation runs. As examples of its applications, the model has been used for the optimization of dsDNA step-gradient separations (5 dsDNAs separated within 8min) and for the determination of the size of dsDNA fragment (with uncertainty of about 2%). These applications are especially relevant for on-chip DNA analysis devices. PMID:23647613

  20. Genetics of Primary Inherited Disorders of the Optic Nerve: Clinical Applications.

    PubMed

    Allen, Keri F; Gaier, Eric D; Wiggs, Janey L

    2015-01-01

    Inherited disorders of the optic nerve significantly impact vision in children and adults. The optic nerve disorders most commonly encountered clinically are glaucoma and primary optic neuropathy including Leber's hereditary optic neuropathy (LHON) and autosomal dominant or Kjer's optic atrophy. Current knowledge of the genetics of optic neuropathy and glaucoma makes it possible to test for mutations in disease-causing genes allowing for presymptomatic testing and risk assessment, and recent advances have revealed important disease mechanisms that may suggest potential therapeutic targets. In this perspective, we describe the current approaches and limitations to genetic testing for these disorders and provide an update on the development of gene-based therapies. PMID:26134840

  1. Adaptive Immune Genetic Algorithm and its application in PID parameter optimization for main steam temperature control system

    Microsoft Academic Search

    Guili Yuan; Yan-guang Xue; Jizhen Liu

    2010-01-01

    Aiming at prematureness, slow convergence rate and reduction in diversity which exist in Genetic Algorithm (GA), this paper presents Adaptive Immune Genetic Algorithm (AIGA) based on GA and immune system mechanism. Adaptive Immune Genetic Algorithm introduces antigens recognition function, immune memory function and antibodies self-adjusting function to Genetic Algorithm, and replaces the fixed probability crossover and mutation operator of Genetic

  2. GENETIC DETECTION OF EDWARDSIELLA ICTALURI: APPLICATION IN A CHANNEL CATFISH SELECTIVE BREEDING PROGRAM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sensitive detection of ESC (Enteric Septicemia of Catfish) is important to the successful development of a selective breeding program for ESC resistance in channel catfish. Therefore, a genetic assay using quantitative PCR (polymerase chain reaction) was developed for early detection of E. ictaluri...

  3. The Applications of Genetic Algorithms in Stock Market Data Mining Optimisation

    E-print Network

    Cao, Longbing

    : Technical trading rule; Genetic Algorithm; sub-domain; Parameter combination; 1 Introduction In stock market of trading rules from which the current GA may have been applied to. In stock market, when the brokers of trading (price changes, volume of transactions, etc.) in a certain stock or in "the Averages

  4. Neural Network Model Predictive Control with Genetic Algorithm Optimization and Its Application to Turbofan Engine Starting

    Microsoft Academic Search

    Yu Bo; Zhu Jihong

    2010-01-01

    Turbofan engine starting is one of the most important procedures during the whole process of job, but also very complicated due to its nonlinear dynamic working procedure. Recognizing the weaknesses of predict model and traditional algorithm for rolling optimization to deal with strong nonlinear systems, this paper presents neural network model predictive control method with genetic algorithm optimization, and uses

  5. Genetic algorithms and neuro-dynamic programming: application to water supply networks

    Microsoft Academic Search

    M. Damas; M. Salmeron; A. Diaz; J. Ortega; A. Prieto; G. Olivares

    2000-01-01

    Genetic algorithms, time series prediction, and Monte Carlo simulation are applied to dynamic programming in order to solve complex planning and control problems in which decisions are made in stages, and the states and control belong to a continuous space. Each decision has an immediate associated cost and also affects the cost of future stages. Therefore, a balance is required

  6. Comparison of a genetic algorithm and simulated annealing in an application to statistical image reconstruction

    Microsoft Academic Search

    LUISA FRANCONI; CHRISTOPHER JENNISON

    1997-01-01

    Genetic algorithms (GAs) are adaptive search techniques designed to find near-optimal solutions of large scale optimization problems with multiple local maxima. Standard versions of the GA are defined for objective functions which depend on a vector of binary variables. The problem of finding the maximum a posteriori (MAP) estimate of a binary image in Bayesian image analysis appears to be

  7. Application of genetic algorithms in sensorless speed vector-controlled AC speed adjusting system

    Microsoft Academic Search

    Liang Zhonghua; Hu Qing; Yu Haiyan; Ge Linjun; Yang Xia

    2001-01-01

    To solve the problems of the position estimation of an AC motor rotor depends upon the parameters of the motor. In this paper, a novel self-adaptive PI controller based on genetic algorithms is used in a sensorless speed vector control AC speed adjusting system. The robustness of the system is confirmed by simulation

  8. New microsatellite loci for the mandarin fish Siniperca chuatsi and their application in population genetic analysis.

    PubMed

    Tian, C X; Liang, X-F; Yang, M; Dou, Y Q; Zheng, H Z; Cao, L; Yuan, Y C; Zhao, C

    2014-01-01

    The mandarin fish is a popular fresh water food fish in China. Fifty-three polymorphic microsatellite markers were isolated through construction of an enriched library of genomic DNA of Siniperca chuatsi (Percichthyidae). We found 2 to 7 alleles per locus. The observed and expected heterozygosity values varied from 0.059 to 1.000 and from 0.305 to 0.818, respectively. The polymorphic information content value varied from 0.255 to 0.782. Twelve microsatellite loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction. These markers were evaluated in five species of sinipercine fish; 98% of the 265 locus/taxon combinations tested gave cross-amplification. Eight polymorphic microsatellite markers were randomly selected for genetic characterization of three S. chuatsi populations. The Ganjiang River and Yuanjiang River populations had moderate levels of genetic diversity, while the Mudanjiang River population had a relatively low level genetic diversity. Genetic distance-based cluster analysis showed clustering of the Ganjiang River and Yuanjiang River populations in a single group and the Mudanjiang River population in a separate group. Based on these results, we suggest that S. chuatsi from the Yangtze River watershed are distinct from the Mudanjiang River population. These SSR markers will be useful for diversity, mapping and marker assisted studies of S. chuatsi and other sinipercine fishes. PMID:24535883

  9. Application of multiple trait analysis in animal breeding research Department of Animal Breeding and Genetics

    E-print Network

    Paris-Sud XI, Université de

    The free fatty acid (FFA) content in milk from 60 cows were determined. Fresh and stored samples from both Breeding and Genetics Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden lifetime milk production, productive life, level of production and a lifetime profit function in cows A

  10. Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines

    Microsoft Academic Search

    W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

    1995-01-01

    Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of

  11. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  12. Application of genetic algorithm for modeling of dense packing of concrete aggregates

    Microsoft Academic Search

    Konstantin Sobolev; Adil Amirjanov

    2010-01-01

    Sequential Packing Algorithm (SPA) was developed to model the dense packing of large assemblies of particulate materials (in the order of millions). These assemblies represent the real aggregate systems of portland cement or asphalt concrete. To improve the SPA performance, the program engine was updated with a genetic algorithm (GA) search module. Multi-cell packing procedures, fine adjustment of the algorithm’s

  13. Genetic-based fuzzy image filter and its application to image processing.

    PubMed

    Lee, Chang-Shing; Guo, Shu-Mei; Hsu, Chin-Yuan

    2005-08-01

    In this paper, we propose a Genetic-based Fuzzy Image Filter (GFIF) to remove additive identical independent distribution (i.i.d.) impulse noise from highly corrupted images. The proposed filter consists of a fuzzy number construction process, a fuzz filtering process, a genetic learning process, and an image knowledge base. First, the fuzzy number construction process receives sample images or the noise-free image and then constructs an image knowledge base for the fuzzy filtering process. Second, the fuzzy filtering process contains a parallel fuzzy inference mechanism, a fuzzy mean process, and a fuzzy decision process to perform the task of noise removal. Finally, based on the genetic algorithm, the genetic learning process adjusts the parameters of the image knowledge base. By the experimental results, GFIF achieves a better performance than the state-of-the-art filters based on the criteria of Peak-Signal-to-Noise-Ratio (PSNR), Mean-Square-Error (MSE), and Mean-Absolute-Error (MAE). On the subjective evaluation of those filtered images, GFIF also results in a higher quality of global restoration. PMID:16128454

  14. Application of Genetic Algorithms and Possibility Theory in Rolling Bearing Compound Fault Diagnosis

    Microsoft Academic Search

    Luo Zhi-gao; Pang Chao-li; Chen Bao-lei; Chen Peng

    2010-01-01

    The characteristic parameters of mechanical fault are found, on the basis of characteristic component collection according to wavelet transform, through optimizing the commonly-used characteristic parameters reflecting rolling bearing fault by genetic algorithms theory. The relationship between the characteristic fault and the mode of fault is created based on the possibility theory. The article also studies the successive fault diagnosis method

  15. Genetic Operator PSO with Information Reused Scheme and its Application in VRP

    Microsoft Academic Search

    Huang Xiaoyan; Wen Zhan; Fu Kechang; Zhu Ming

    2009-01-01

    For the sake of characters of logistics, Improved genetic operator based particle swarm optimization (GOPSO) is proposed. An pseudo-continuous encoding algorithm are proposed to the GOPSO for the vehicle routing problem (VRP), then information of all the particles is reserved and stored. The reserved information can be utilized to reform and update the particles, by which the efficiency of GOPSO

  16. Genetic Algorithms, a Nature-Inspired Tool: Survey of Applications in Materials Science and Related Fields

    Microsoft Academic Search

    Wojciech Paszkowicz

    2009-01-01

    Genetic algorithms (GAs) are a tool used to solve high-complexity computational problems. Apart from modelling the phenomena occurring in Nature, they help in optimization, simulation, modelling, design and prediction purposes in science, medicine, technology, and everyday life. They can be adapted to the given task, be joined with other ones (this leads to combined or hybrid methods), and can work

  17. Application of a hybrid of particle swarm and genetic algorithm for structural damage detection

    Microsoft Academic Search

    S. Sandesh; K. Shankar

    2010-01-01

    This study presents a novel optimization algorithm which is a hybrid of particle swarm optimization (PSO) method and genetic algorithm (GA). Using the Ackley and Schwefel multimodal benchmark functions incorporating up to 25 variables, the performance of the hybrid is compared with pure PSO and GA and found to be far superior in convergence and accuracy. The hybrid algorithm is

  18. An application of genetic algorithms to lot-streaming flow shop scheduling

    Microsoft Academic Search

    Suk-Hun Yoon; Jose A. Ventura

    2002-01-01

    A Hybrid Genetic Algorithm (HGA) approach is proposed for a lot-streaming flow shop scheduling problem, in which a job (lot) is split into a number of smaller sublots so that successive operations can be overlapped. The objective is the minimization of the mean weighted absolute deviation of job completion times from due dates. This performance criterion has been shown to

  19. The Application of Immune Genetic Algorithm in PID Parameter Optimization for Level Control System

    Microsoft Academic Search

    Chengwei Li; Jiandong Lian

    2007-01-01

    This work discusses the use of an Evolvable Proportional-Integral-Derivative (PID) controller that consists of an evolvable PID controller hardware whose gains can be set by Evolutionary Computation techniques, such as Genetic Algorithms in water level control system. Due to PID controllers' widespread use in industry, tuning procedures for them are always a topic of interest. An evolutionary immune inspired algorithm,

  20. Synthesis of magnetic molecularly imprinted polymers by reversible addition fragmentation chain transfer strategy and its application in the Sudan dyes residue analysis.

    PubMed

    Xie, Xiaoyu; Chen, Liang; Pan, Xiaoyan; Wang, Sicen

    2015-07-31

    Magnetic molecularly imprinted polymers (MMIPs) have become a hotspot owing to the dual functions of target recognition and magnetic separation. In this study, the MMIPs were obtained by the surface-initiated reversible addition fragmentation chain transfer (RAFT) polymerization using Sudan I as the template. The resultant MMIPs were characterized by transmission electron microscope, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometer, and X-ray diffraction. Benefiting from the controlled/living property of the RAFT strategy, the uniform MIP layer was successfully grafted on the surface of RAFT agent-modified Fe3O4@SiO2 nanoparticles, favoring the fast mass transfer and rapid binding kinetics. The developed MMIPs were used as the solid-phase extraction sorbents to selectively extract four Sudan dyes (Sudan I, II, III, and IV) from chili powder samples. The recoveries of the spiked samples in chili powder samples ranged from 74.1 to 93.3% with RSD lower than 6.4% and the relative standard uncertainty lower than 0.029. This work provided a good platform for the extraction and removal of Sudan dyes in complicated matrixes and demonstrated a bright future for the application of the well-constructed MMIPs in the field of solid-phase extraction. PMID:26077971

  1. 3rd World Congress on Industrial Process Tomography, Banff, Canada Application of Simulated Annealing and Genetic Algorithms

    E-print Network

    Martin, Roland

    Annealing and Genetic Algorithms to the Reconstruction of Electrical Permittivity Images in Capacitance annealing (SA) and genetic algorithms (GA) inversion methods to the reconstruction of permittivity images reconstructions. Keywords Simulated annealing, Genetic algorithms, Capacitance tomography, Global optimisation

  2. Potential applications of cryogenic technologies to plant genetic improvement and pathogen eradication.

    PubMed

    Wang, Biao; Wang, Ren-Rui; Cui, Zhen-Hua; Bi, Wen-Lu; Li, Jing-Wei; Li, Bai-Quan; Ozudogru, Elif Aylin; Volk, Gayle M; Wang, Qiao-Chun

    2014-01-01

    Rapid increases in human populations provide a great challenge to ensure that adequate quantities of food are available. Sustainable development of agricultural production by breeding more productive cultivars and by increasing the productive potential of existing cultivars can help meet this demand. The present paper provides information on the potential uses of cryogenic techniques in ensuring food security, including: (1) long-term conservation of a diverse germplasm and successful establishment of cryo-banks; (2) maintenance of the regenerative ability of embryogenic tissues that are frequently the target for genetic transformation; (3) enhancement of genetic transformation and plant regeneration of transformed cells, and safe, long-term conservation for transgenic materials; (4) production and maintenance of viable protoplasts for transformation and somatic hybridization; and (5) efficient production of pathogen-free plants. These roles demonstrate that cryogenic technologies offer opportunities to ensure food security. PMID:24681087

  3. The Application of the Genetic Algorithm to the Numerical Simulation in Sheet Metal Forming

    Microsoft Academic Search

    Jingjing Xu; Changdong Li; Yimin Wu; Wei Huang

    2006-01-01

    This study presents a genetic algorithm GA adopted for recognizing the material parameters with the nonlinear relation in\\u000a the sheet metal forming. Firstly the nonlinear regression model is established for the parameters estimation. Then based on\\u000a the material tensile test the parameters estimation is finished by GA and the least square method LS. At last GA is applied\\u000a for recognizing

  4. Application of rapd in the determination of genetic fidelity in micropropagated Drosera plantlets

    Microsoft Academic Search

    Anna Kawiak; Ewa ?ojkowska

    2004-01-01

    Summary  Random amplified polymorphic DNA (RAPD) markers were used to verify the clonal fidelity of two micropropagated Drosera species, D. anglica and D. binata, which were regenerated by adventitious budding from leaf explants and shoot tips, respectively. Twenty arbitrary decamers\\u000a were used to screen 15 randomly selected plantlets of each species. No genetic variation was detected among D. binata regenerants, whereas

  5. An Exemplary Introduction to Structure and Application of Genetic Algorithms in Economic Research

    Microsoft Academic Search

    Thomas Riechmann

    \\u000a The goal of this chapter is to provide a simple introduction into the kind of genetic algorithms applied in economic theory.\\u000a The main focus will be on technical aspects, the economic example merely serves as an illustration. This means that in this\\u000a chapter new economic results will hardly be found. The model shown here is very simple and, more than

  6. Telegenetics: application of a tele-education program in genetic syndromes for Brazilian students.

    PubMed

    Maximino, Luciana Paula; Picolini-Pereira, Mirela Machado; Carvalho, José Luiz Brito

    2014-01-01

    With the high occurrence of genetic anomalies in Brazil and the manifestations of communication disorders associated with these conditions, the development of educative actions that comprise these illnesses can bring unique benefits in the identification and appropriate treatment of these clinical pictures. Objective The aim of this study was to develop and analyze an educational program in genetic syndromes for elementary students applied in two Brazilian states, using an Interactive Tele-education model. Material and Methods The study was carried out in 4 schools: two in the state of São Paulo, Southeast Region, Brazil, and two in the state of Amazonas, North Region, Brazil. Forty-five students, both genders, aged between 13 and 14 years, of the 9th grade of the basic education of both public and private system, were divided into two groups: 21 of São Paulo Group (SPG) and 24 of Amazonas Group (AMG). The educational program lasted about 3 months and was divided into two stages including both classroom and distance activities on genetic syndromes. The classroom activity was carried out separately in each school, with expository lessons, graphs and audiovisual contents. In the activity at a distance the educational content was presented to students by means of the Interactive Tele-education model. In this stage, the students had access a Cybertutor, using the Young Doctor Project methodology. In order to measure the effectiveness of the educational program, the Problem Situation Questionnaire (PSQ) and the Web Site Motivational Analysis Checklist adapted (FPM) were used. Results The program developed was effective for knowledge acquisition in 80% of the groups. FPM showed a high satisfaction index from the participants in relation to the Interactive Tele-education, evaluating the program as "awesome course". No statistically significant differences between the groups regarding type of school or state were observed. Conclusion Thus, the Tele-Education Program can be used as a tool for educational purposes in genetic syndromes of other populations, in several regions of Brazil. PMID:25591016

  7. Optimization of fuels from waste composition with application of genetic algorithm.

    PubMed

    Ma?gorzata, Wzorek

    2014-05-01

    The objective of this article is to elaborate a method to optimize the composition of the fuels from sewage sludge (PBS fuel - fuel based on sewage sludge and coal slime, PBM fuel - fuel based on sewage sludge and meat and bone meal, PBT fuel - fuel based on sewage sludge and sawdust). As a tool for an optimization procedure, the use of a genetic algorithm is proposed. The optimization task involves the maximization of mass fraction of sewage sludge in a fuel developed on the basis of quality-based criteria for the use as an alternative fuel used by the cement industry. The selection criteria of fuels composition concerned such parameters as: calorific value, content of chlorine, sulphur and heavy metals. Mathematical descriptions of fuel compositions and general forms of the genetic algorithm, as well as the obtained optimization results are presented. The results of this study indicate that the proposed genetic algorithm offers an optimization tool, which could be useful in the determination of the composition of fuels that are produced from waste. PMID:24718361

  8. Genetic Counseling Program Information

    E-print Network

    Finley Jr., Russell L.

    Genetic Counseling Program Information for Potential Applicants #12;Page 2 of 12 8.24.11 Program of Medicine at Wayne State University offers a Master's level graduate program in genetic counseling.24.11 Wayne State University School of Medicine Graduate Program in Genetic Counseling Curriculum Overview

  9. Changes in the level of endogenous gibberellins and auxins in apical buds of Chenopodium rubrum L. after application of growth substances reversing the effect of (2-chlorethyl)-trimethylammonium chloride (CCC) on flowering

    Microsoft Academic Search

    Lola Teltscherová

    1968-01-01

    The application of CCC at concentrations inhibiting flowering ofChenopodium rubrum reduces the level of endogenous gibberellins in the apical buds of the plants. The effect of CCC may be reversed by appropriate\\u000a concentrations of gibberellin (GA-), indole acetic acid (IAA) or kinetin. Kinetin applied to the apical bud during floral\\u000a induction reduced the level of endogenous gibberellins similarly as CCC

  10. Nonparametric methods for incorporating genomic information into genetic evaluations: an application to mortality in broilers.

    PubMed

    González-Recio, Oscar; Gianola, Daniel; Long, Nanye; Weigel, Kent A; Rosa, Guilherme J M; Avendaño, Santiago

    2008-04-01

    Four approaches using single-nucleotide polymorphism (SNP) information (F(infinity)-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14-42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods. PMID:18430951

  11. Application of Massively Parallel Sequencing to Genetic Diagnosis in Multiplex Families with Idiopathic Sensorineural Hearing Impairment

    PubMed Central

    Wu, Chen-Chi; Lin, Yin-Hung; Lu, Ying-Chang; Chen, Pei-Jer; Yang, Wei-Shiung; Hsu, Chuan-Jen; Chen, Pei-Lung

    2013-01-01

    Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes. PMID:23451214

  12. Nonparametric Methods for Incorporating Genomic Information Into Genetic Evaluations: An Application to Mortality in Broilers

    PubMed Central

    González-Recio, Oscar; Gianola, Daniel; Long, Nanye; Weigel, Kent A.; Rosa, Guilherme J. M.; Avendaño, Santiago

    2008-01-01

    Four approaches using single-nucleotide polymorphism (SNP) information (F?-metric model, kernel regression, reproducing kernel Hilbert spaces (RKHS) regression, and a Bayesian regression) were compared with a standard procedure of genetic evaluation (E-BLUP) of sires using mortality rates in broilers as a response variable, working in a Bayesian framework. Late mortality (14–42 days of age) records on 12,167 progeny of 200 sires were precorrected for fixed and random (nongenetic) effects used in the model for genetic evaluation and for the mate effect. The average of the corrected records was computed for each sire. Twenty-four SNPs seemingly associated with late mortality were included in three methods used for genomic assisted evaluations. One thousand SNPs were included in the Bayesian regression, to account for markers along the whole genome. The posterior mean of heritability of mortality was 0.02 in the E-BLUP approach, suggesting that genetic evaluation could be improved if suitable molecular markers were available. Estimates of posterior means and standard deviations of the residual variance were 24.38 (3.88), 29.97 (3.22), 17.07 (3.02), and 20.74 (2.87) for E-BLUP, the linear model on SNPs, RKHS regression, and the Bayesian regression, respectively, suggesting that RKHS accounted for more variance in the data. The two nonparametric methods (kernel and RKHS regression) fitted the data better, having a lower residual sum of squares. Predictive ability, assessed by cross-validation, indicated advantages of the RKHS approach, where accuracy was increased from 25 to 150%, relative to other methods. PMID:18430951

  13. Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.

    PubMed

    Davis, Nicholas A; Lareau, Caleb A; White, Bill C; Pandey, Ahwan; Wiley, Graham; Montgomery, Courtney G; Gaffney, Patrick M; McKinney, B A

    2013-09-01

    Open source tools are needed to facilitate the construction, analysis, and visualization of gene-gene interaction networks for sequencing data. To address this need, we present Encore, an open source network analysis pipeline for genome-wide association studies and rare variant data. Encore constructs Genetic Association Interaction Networks or epistasis networks using two optional approaches: our previous information-theory method or a generalized linear model approach. Additionally, Encore includes multiple data filtering options, including Random Forest/Random Jungle for main effect enrichment and Evaporative Cooling and Relief-F filters for enrichment of interaction effects. Encore implements SNPrank network centrality for identifying susceptibility hubs (nodes containing a large amount of disease susceptibility information through the combination of multivariate main effects and multiple gene-gene interactions in the network), and it provides appropriate files for interactive visualization of a network using tools from our online Galaxy instance. We implemented these algorithms in C++ using OpenMP for shared-memory parallel analysis on a server or desktop. To demonstrate Encore's utility in analysis of genetic sequencing data, we present an analysis of exome resequencing data from healthy individuals and those with Systemic Lupus Erythematous (SLE). Our results verify the importance of the previously associated SLE genes HLA-DRB and NCF2, and these two genes had the highest gene-gene interaction degrees among the susceptibility hubs. An additional 14 genes previously associated with SLE emerged in our epistasis network model of the exome data, and three novel candidate genes, ST8SIA4, CMTM4, and C2CD4B, were implicated in the model. In summary, we present a comprehensive tool for epistasis network analysis and the first such analysis of exome data from a genetic study of SLE. PMID:23740754

  14. [Genetics and endocrinology of male sex differentiation: application to molecular study of male pseudohermaphroditism].

    PubMed

    Sultan, C; Lumbroso, S; Poujol, N; Boudon, C; Georget, V; Térouanne, B; Belon, C; Lobaccaro, J M

    1995-01-01

    The various processes involved in sexual differentiation have been considerably clarified over the last few years through advances in biochemistry and molecular genetics. The cloning of the gene responsible for testicular determination SRY, of the anti-Müllerian hormone and anti-Müllerian hormone receptor genes, of the several steroidogenic enzymes genes, of the 5 alpha-reductase type 2 gene and of the androgen receptor gene has permitted to elucidate the molecular defects causing abnormal sexual differentiation. These data have brought a substantial impact on the understanding of human male sexual differentiation and its main disorders. PMID:8673622

  15. Reverse Engineering Adverse Outcome Pathways in Ecotoxicology

    EPA Science Inventory

    The toxicological effects of many stressors are mediated through unknown, or incompletely characterized, mechanisms of action. We describe the application of reverse engineering complex interaction networks from high dimensional omics data (gene, protein, meabolic, signaling) t...

  16. Development and application of one-step multiplex reverse transcription PCR for simultaneous detection of five diarrheal viruses in adult cattle.

    PubMed

    Fukuda, Masaharu; Kuga, Kazufumi; Miyazaki, Ayako; Suzuki, Tohru; Tasei, Keito; Aita, Tsunehiko; Mase, Masaji; Sugiyama, Makoto; Tsunemitsu, Hiroshi

    2012-06-01

    A one-step multiplex reverse transcription (RT)-PCR method was developed for the simultaneous detection of five viruses causing diarrhea in adult cattle: bovine group A rotavirus (GAR), bovine group B rotavirus (GBR), bovine group C rotavirus (GCR), bovine coronavirus (BCV), and bovine torovirus (BToV). The detection limit of the one-step multiplex RT-PCR for GAR, GCR, BCV, and BToV was 10(2), 10(0), 10(1), and 10(2) TCID(50)/ml, respectively, and that for GBR was 10(6) copies/ml. The one-step multiplex RT-PCR with newly designed primers to detect GAR had higher sensitivity than a single RT-PCR with conventional primers, with no false-positive reactions observed for ten other kinds of bovine RNA viruses To assess its field applicability, 59 of 60 fecal samples containing one of these five viruses from all 25 epidemic diarrhea outbreaks in adult cattle were positive in the one-step multiplex RT-PCR assay. Furthermore, using four additional fecal samples containing two viruses (GBR and BCV or BToV), two amplified products of the expected sizes were obtained simultaneously. In contrast, all 80 fecal samples lacking the five target viruses from normal adult cattle were negative in the multiplex assay. Taken together, our results indicate that the one-step multiplex RT-PCR developed here for the detection of GAR, GBR, GCR, BCV, and BToV can be expected to be a useful tool for the rapid and cost-effective diagnosis and surveillance of viral diarrhea in adult cattle. PMID:22407445

  17. On Derivations Of Genetic Algebras

    NASA Astrophysics Data System (ADS)

    Mukhamedov, Farrukh; Qaralleh, Izzat

    2014-11-01

    A genetic algebra is a (possibly non-associative) algebra used to model inheritance in genetics. In application of genetics this algebra often has a basis corresponding to genetically different gametes, and the structure constant of the algebra encode the probabilities of producing offspring of various types. In this paper, we find the connection between the genetic algebras and evolution algebras. Moreover, we prove the existence of nontrivial derivations of genetic algebras in dimension two.

  18. The Genetic Basis of Complex Human Behaviors

    Microsoft Academic Search

    Robert Plomin; Michael J. Owen; Peter McGuffin

    1994-01-01

    Quantitative genetic research has built a strong case for the importance of genetic factors in many complex behavioral disorders and dimensions in the domains of psychopathology, personality, and cognitive abilities. Quantitative genetics can also provide an empirical guide and a conceptual framework for the application of molecular genetics. The success of molecular genetics in elucidating the genetic basis of behavioral

  19. Curve-based multivariate distance matrix regression analysis: application to genetic association analyses involving repeated measures

    PubMed Central

    Salem, Rany M.; O'Connor, Daniel T.

    2010-01-01

    Most, if not all, human phenotypes exhibit a temporal, dosage-dependent, or age effect. Despite this fact, it is rare that data are collected over time or in sequence in relevant studies of the determinants of these phenotypes. The costs and organizational sophistication necessary to collect repeated measurements or longitudinal data for a given phenotype are clearly impediments to this, but greater efforts in this area are needed if insights into human phenotypic expression are to be obtained. Appropriate data analysis methods for genetic association studies involving repeated or longitudinal measures are also needed. We consider the use of longitudinal profiles obtained from fitted functions on repeated data collections from a set of individuals whose similarities are contrasted between sets of individuals with different genotypes to test hypotheses about genetic influences on time-dependent phenotype expression. The proposed approach can accommodate uncertainty of the fitted functions, as well as weighting factors across the time points, and is easily extended to a wide variety of complex analysis settings. We showcase the proposed approach with data from a clinical study investigating human blood vessel response to tyramine. We also compare the proposed approach with standard analytic procedures and investigate its robustness and power via simulation studies. The proposed approach is found to be quite flexible and performs either as well or better than traditional statistical methods. PMID:20423962

  20. [Application of molecular genetic methods during Legionnaires' disease outbreak in town Verkhnyaya Pyshma].

    PubMed

    Iatsyshina, S B; Astakhova, T S; Romanenko, V V; Platonov, A E; Zhukova, Iu V; Braslavskaia, S I; Tartakovski?, I S; Shipulin, G A

    2008-01-01

    The aim of the study was to perform molecular genetic analysis based on multi-locus sequence typing in order to identify source of Legionnaires' disease outbreak in town Verkhnyaya Pyshma in July 2007 and genetic profile of the causative agent. Sequence-based typing protocol recommended by European Working Group on Legionella infection (EWGLI) was used. It was not possible to obtain satisfactory results of Fla gene sequencing for all samples. Obtained allelic profiles of other genes were typical for L. pneumophila. Allelic profiles of L. pneumophila isolated from patients were identical and matched with L. pneumophila DNA detected in water from hot water supply of domestic building, but differed from cooling tower's isolates and isolates from showerhead in apartment of one patient. Identity of 5 genes of L. pneumophila isolated from autopsy samples and from hot water of central hot water supply of domestic building confirms aspiration route of infection through hot water contaminated by the microorganism. L. pneumophila detected in water from cooling tower, showerhead in apartment of one patient, and from drainage canal of hot water supply station belonged to other allelic variants and, therefore, are not related with the outbreak. PMID:18464536

  1. Representation of DNA sequences in genetic codon context with applications in exon and intron prediction.

    PubMed

    Yin, Changchuan

    2015-04-01

    To apply digital signal processing (DSP) methods to analyze DNA sequences, the sequences first must be specially mapped into numerical sequences. Thus, effective numerical mappings of DNA sequences play key roles in the effectiveness of DSP-based methods such as exon prediction. Despite numerous mappings of symbolic DNA sequences to numerical series, the existing mapping methods do not include the genetic coding features of DNA sequences. We present a novel numerical representation of DNA sequences using genetic codon context (GCC) in which the numerical values are optimized by simulation annealing to maximize the 3-periodicity signal to noise ratio (SNR). The optimized GCC representation is then applied in exon and intron prediction by Short-Time Fourier Transform (STFT) approach. The results show the GCC method enhances the SNR values of exon sequences and thus increases the accuracy of predicting protein coding regions in genomes compared with the commonly used 4D binary representation. In addition, this study offers a novel way to reveal specific features of DNA sequences by optimizing numerical mappings of symbolic DNA sequences. PMID:25491390

  2. Reverse Sample Genome Probing, a New Technique for Identification of Bacteria in Environmental Samples by DNA Hybridization, and Its Application to the Identification of Sulfate-Reducing Bacteria in Oil Field Samples

    PubMed Central

    Voordouw, Gerrit; Voordouw, Johanna K.; Karkhoff-Schweizer, Roxann R.; Fedorak, Phillip M.; Westlake, Donald W. S.

    1991-01-01

    A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a “standard”) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples. Images PMID:16348574

  3. Proceedings, Florida Artificial Intelligence Research Symposium, USA, 1999 Improving Technical Analysis Predictions: An Application of Genetic

    E-print Network

    Boetticher, Gary D.

    Proceedings, Florida Artificial Intelligence Research Symposium, USA, 1999 Improving Technical applications of artificial intelligence. Dr Edward Tsang holds a Bachelor degree in Business Administration Page 2 of 13 1. INTRODUCTION As an approach to financial forecasting, technical analysis is based

  4. Dynamics of the Genetic Diversity of Subsurface Microbial Communities and Their Applications to Contaminated Site Cleanups

    EPA Science Inventory

    When compared to traditional approaches, the utilization of molecular and genomic techniques to soil and groundwater cleanup investigations can reduce inherent parameter variability when conducting bench and pilot-scale investigations or carrying out full-scale field applications...

  5. Properly apply reverse osmosis

    SciTech Connect

    Kucera, J.

    1997-02-01

    Reverse osmosis (RO) is a water purification technique used to reduce the loading of dissolved solids in solution. The popularity of RO for treating boiler feedwater is growing because of the rising cost of ion-exchange-based demineralization as well as safety concerns associated with handling acid and caustic. A properly designed and operated RO-based boiler-feedwater-treatment system can reduce the load to, and costs associated with, ion exchange demineralization. This article discusses RO feedwater quality recommendations, pretreatment techniques, and system monitoring necessary to achieve optimum RO system performance in the most cost-effective manner. Regardless of the application--whether it is the treatment of boiler feedwater, industrial wastewater, or process water--the approach to pretreatment and the other design and operating guidance offered here remains the same.

  6. Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid development of next generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach fo...

  7. Nested Multiplex Polymerase Chain Reaction for the Determination of DNA From Genetically Modified Corn and Soy Beans Using the Agilent 2100 Bioanalyzer Application

    Microsoft Academic Search

    Mark Jensen

    This application note describes how the Agilent Technologies 2100 bioanalyzer and the DNA 500 LabChip can be used to detect polymerase chain reaction products corresponding to genetically modified elements and endogenous sequences in corn and soy beans. The DNA extraction protocol used in the preparation of polymerase chain reaction samples was characterized using the Protein 200 Plus LabChip.

  8. Calibration of neural networks using genetic algorithms, with application to optimal path planning

    NASA Technical Reports Server (NTRS)

    Smith, Terence R.; Pitney, Gilbert A.; Greenwood, Daniel

    1987-01-01

    Genetic algorithms (GA) are used to search the synaptic weight space of artificial neural systems (ANS) for weight vectors that optimize some network performance function. GAs do not suffer from some of the architectural constraints involved with other techniques and it is straightforward to incorporate terms into the performance function concerning the metastructure of the ANS. Hence GAs offer a remarkably general approach to calibrating ANS. GAs are applied to the problem of calibrating an ANS that finds optimal paths over a given surface. This problem involves training an ANS on a relatively small set of paths and then examining whether the calibrated ANS is able to find good paths between arbitrary start and end points on the surface.

  9. Accounting for relatedness in family-based association studies: application to Genetic Analysis Workshop 18 data

    PubMed Central

    2014-01-01

    In the last few years, a bewildering variety of methods/software packages that use linear mixed models to account for sample relatedness on the basis of genome-wide genomic information have been proposed. We compared these approaches as implemented in the programs EMMAX, FaST-LMM, Gemma, and GenABEL (FASTA/GRAMMAR-Gamma) on the Genetic Analysis Workshop 18 data. All methods performed quite similarly and were successful in reducing the genomic control inflation factor to reasonable levels, particularly when the mean values of the observations were used, although more variation was observed when data from each time point were used individually. From a practical point of view, we conclude that it makes little difference to the results which method/software package is used, and the user can make the choice of package on the basis of personal taste or computational speed/convenience. PMID:25519407

  10. Application of carrier testing to genetic counseling for X-linked agammaglobulinemia

    SciTech Connect

    Allen, R.C.; Nachtman, R.G.; Belmont, J.W.; Rosenblatt, H.M.

    1994-01-01

    Bruton X-linked agammaglobulinemia (XLA) is a phenotypically recessive genetic disorder of B lymphocyte development. Female carriers of XLA, although asymptomatic, have a characteristic B cell lineage-specific skewing of the pattern of X inactivation. Skewing apparently results from defective growth and maturation of B cell precursors bearing a mutant active X chromosome. In this study, carrier status was tested in 58 women from 22 families referred with a history of agammaglobulinemia. Primary carrier analysis to examine patterns of X inactivation in CD19[sup +] peripheral blood cells (B lymphocytes) was conducted using quantitative PCR at the androgen-receptor locus. Obligate carriers of XLA demonstrated >95% skewing of X inactivation in peripheral blood CD19[sup +] cells but not in CD19[sup [minus

  11. Application of Genetic Algorithm to Predict Optimal Sowing Region and Timing for Kentucky Bluegrass in China

    PubMed Central

    Peng, Tingting; Jiang, Bo; Guo, Jiangfeng; Lu, Hongfei; Du, Liqun

    2015-01-01

    Temperature is a predominant environmental factor affecting grass germination and distribution. Various thermal-germination models for prediction of grass seed germination have been reported, in which the relationship between temperature and germination were defined with kernel functions, such as quadratic or quintic function. However, their prediction accuracies warrant further improvements. The purpose of this study is to evaluate the relative prediction accuracies of genetic algorithm (GA) models, which are automatically parameterized with observed germination data. The seeds of five P. pratensis (Kentucky bluegrass, KB) cultivars were germinated under 36 day/night temperature regimes ranging from 5/5 to 40/40°C with 5°C increments. Results showed that optimal germination percentages of all five tested KB cultivars were observed under a fluctuating temperature regime of 20/25°C. Meanwhile, the constant temperature regimes (e.g., 5/5, 10/10, 15/15°C, etc.) suppressed the germination of all five cultivars. Furthermore, the back propagation artificial neural network (BP-ANN) algorithm was integrated to optimize temperature-germination response models from these observed germination data. It was found that integrations of GA-BP-ANN (back propagation aided genetic algorithm artificial neural network) significantly reduced the Root Mean Square Error (RMSE) values from 0.21~0.23 to 0.02~0.09. In an effort to provide a more reliable prediction of optimum sowing time for the tested KB cultivars in various regions in the country, the optimized GA-BP-ANN models were applied to map spatial and temporal germination percentages of blue grass cultivars in China. Our results demonstrate that the GA-BP-ANN model is a convenient and reliable option for constructing thermal-germination response models since it automates model parameterization and has excellent prediction accuracy. PMID:26154163

  12. Somatic mosaicism in Wiskott-Aldrich syndrome suggests in vivo reversion by a DNA slippage mechanism

    Microsoft Academic Search

    Taizo Wada; Shepherd H. Schurman; Makoto Otsu; Elizabeth K. Garabedian; Hans D. Ochs; David L. Nelson; Fabio Candotti

    2001-01-01

    Somatic mosaicism caused by in vivo reversion of inherited mutations has been described in several human genetic disorders. Back mutations resulting in restoration of wild-type sequences and second-site mutations leading to compensatory changes have been shown in mosaic individuals. In most cases, however, the precise genetic mechanisms underlying the reversion events have remained unclear, except for the few instances where

  13. Mining genetic epidemiology data with Bayesian networks application to APOE gene variation and plasma lipid levels.

    PubMed

    Rodin, Andrei; Mosley, Thomas H; Clark, Andrew G; Sing, Charles F; Boerwinkle, Eric

    2005-01-01

    There is a critical need for data-mining methods that can identify SNPs that predict among individual variation in a phenotype of interest and reverse-engineer the biological network of relationships between SNPs, phenotypes, and other factors. This problem is both challenging and important in light of the large number of SNPs in many genes of interest and across the human genome. A potentially fruitful form of exploratory data analysis is the Bayesian or Belief network. A Bayesian or Belief network provides an analytic approach for identifying robust predictors of among-individual variation in a disease endpoints or risk factor levels. We have applied Belief networks to SNP variation in the human APOE gene and plasma apolipoprotein E levels from two samples: 702 African-Americans from Jackson, MS, and 854 non-Hispanic whites from Rochester, MN. Twenty variable sites in the APOE gene were genotyped in both samples. In Jackson, MS, SNPs 4036 and 4075 were identified to influence plasma apoE levels. In Rochester, MN, SNPs 3937 and 4075 were identified to influence plasma apoE levels. All three SNPs had been previously implicated in affecting measures of lipid and lipoprotein metabolism. Like all data-mining methods, Belief networks are meant to complement traditional hypothesis-driven methods of data analysis. These results document the utility of a Belief network approach for mining large scale genotype-phenotype association data. PMID:15725730

  14. Time-reversal mirrors

    Microsoft Academic Search

    M. Fink

    1993-01-01

    Time-reversal of ultrasonic fields allows a very efficient approach to focus pulsed ultrasonic waves through inhomogeneous media. Time-reversal mirrors (TRMS) are made of large transducer arrays, allowing the incident acoustic field to be sampled, time-reversed and re-emitted. The paper introduces the time-reversal approach in a discussion of the techniques used in optics for focusing through inhomogeneous media. The discussion is

  15. Genetic Programming for Sensor Networks

    Microsoft Academic Search

    Thomas Weise

    In this paper we present an approach to automated program code generation for sensor nodes and other small devices using Genetic Programming. We give a short introduction to Genetic Algorithms. Our new Distributed Genetic Programming Framework facilitates the development of sensor network applications. Genetic evolution of programs requires program testing. Therefore we use a simulation environment for distributed systems of

  16. Time-reversed acoustics

    Microsoft Academic Search

    Mathias Fink; Didier Cassereau; Arnaud Derode; Claire Prada; Philippe Roux; Mickael Tanter; Jean-Louis Thomas; François Wu

    2000-01-01

    The objective of this paper is to show that time reversal invariance can be exploited in acoustics to create a variety of useful instruments as well as elegant experiments in pure physics. Section 1 is devoted to the description of time reversal cavities and mirrors together with a comparison between time reversal and phase conjugation. To illustrate these concepts, several

  17. A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

    2003-01-01

    In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

  18. Application of genetic algorithms and constructive neural networks for the analysis of microarray cancer data

    PubMed Central

    2014-01-01

    Background Extracting relevant information from microarray data is a very complex task due to the characteristics of the data sets, as they comprise a large number of features while few samples are generally available. In this sense, feature selection is a very important aspect of the analysis helping in the tasks of identifying relevant genes and also for maximizing predictive information. Methods Due to its simplicity and speed, Stepwise Forward Selection (SFS) is a widely used feature selection technique. In this work, we carry a comparative study of SFS and Genetic Algorithms (GA) as general frameworks for the analysis of microarray data with the aim of identifying group of genes with high predictive capability and biological relevance. Six standard and machine learning-based techniques (Linear Discriminant Analysis (LDA), Support Vector Machines (SVM), Naive Bayes (NB), C-MANTEC Constructive Neural Network, K-Nearest Neighbors (kNN) and Multilayer perceptron (MLP)) are used within both frameworks using six free-public datasets for the task of predicting cancer outcome. Results Better cancer outcome prediction results were obtained using the GA framework noting that this approach, in comparison to the SFS one, leads to a larger selection set, uses a large number of comparison between genetic profiles and thus it is computationally more intensive. Also the GA framework permitted to obtain a set of genes that can be considered to be more biologically relevant. Regarding the different classifiers used standard feedforward neural networks (MLP), LDA and SVM lead to similar and best results, while C-MANTEC and k-NN followed closely but with a lower accuracy. Further, C-MANTEC, MLP and LDA permitted to obtain a more limited set of genes in comparison to SVM, NB and kNN, and in particular C-MANTEC resulted in the most robust classifier in terms of changes in the parameter settings. Conclusions This study shows that if prediction accuracy is the objective, the GA-based approach lead to better results respect to the SFS approach, independently of the classifier used. Regarding classifiers, even if C-MANTEC did not achieve the best overall results, the performance was competitive with a very robust behaviour in terms of the parameters of the algorithm, and thus it can be considered as a candidate technique for future studies. PMID:25077572

  19. Applications of High-Performance Computing (HPC) in Plant Breeding, Conservation, and Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasingly powerful and informative DNA sequencing and genotyping techniques, instruments, and software are being developed and used for a wide variety of applications in agriculture. However, the increasing flux and accumulation of data will also require more HPC facilities and expertise. In co...

  20. A reversible nanoconfined chemical reaction.

    PubMed

    Nielsen, Thomas K; Bösenberg, Ulrike; Gosalawit, Rapee; Dornheim, Martin; Cerenius, Yngve; Besenbacher, Flemming; Jensen, Torben R

    2010-07-27

    Hydrogen is recognized as a potential, extremely interesting energy carrier system, which can facilitate efficient utilization of unevenly distributed renewable energy. A major challenge in a future "hydrogen economy" is the development of a safe, compact, robust, and efficient means of hydrogen storage, in particular, for mobile applications. Here we report on a new concept for hydrogen storage using nanoconfined reversible chemical reactions. LiBH4 and MgH2 nanoparticles are embedded in a nanoporous carbon aerogel scaffold with pore size Dmax approximately 21 nm and react during release of hydrogen and form MgB2. The hydrogen desorption kinetics is significantly improved compared to bulk conditions, and the nanoconfined system has a high degree of reversibility and stability and possibly also improved thermodynamic properties. This new scheme of nanoconfined chemistry may have a wide range of interesting applications in the future, for example, within the merging area of chemical storage of renewable energy. PMID:20533850

  1. Application of Genetic Algorithms to Sorting, Swapping and Shimming of the SOLEIL Undulator Magnets

    SciTech Connect

    Chubar, O.; Rudenko, O.; Benabderrahmane, C.; Marcouille, O.; Filhol, J. M.; Couprie, M. E. [Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 GIF-sur-YVETTE CEDEX (France)

    2007-01-19

    Undulators are typically composed of a large number of individual magnets, from tens to many hundreds, depending on undulator type and technology. Characteristics of real magnets often deviate from ideal values, resulting in degradation of the undulator performance. It is known that the imperfections of individual magnets can be mutually compensated, to certain extent, by appropriate sorting of the magnets and/or magnet modules, based on measurements of their individual characteristics, performed before the insertion device (ID) assembly. After the assembly, the quality of the ID magnetic field can be improved by magnet swapping and by shimming, consisting either in small displacements of some of the magnets or in adding small pieces of permanent magnet or soft iron material to appropriate locations of the structure. Mathematically, the magnet sorting, swapping and shimming can be considered as multi-objective constrained optimization problems with large numbers of variables. We show that each of these problems can be efficiently solved by means of Genetic Algorithms with 3D magnetostatics methods and magnetic measurements data used for the fitness calculation. First practical results obtained with three different undulators of the SOLEIL Synchrotron are presented.

  2. Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics.

    PubMed

    Jin, Yan; Shi, Yonggang; Zhan, Liang; Gutman, Boris A; de Zubicaray, Greig I; McMahon, Katie L; Wright, Margaret J; Toga, Arthur W; Thompson, Paul M

    2014-10-15

    To understand factors that affect brain connectivity and integrity, it is beneficial to automatically cluster white matter (WM) fibers into anatomically recognizable tracts. Whole brain tractography, based on diffusion-weighted MRI, generates vast sets of fibers throughout the brain; clustering them into consistent and recognizable bundles can be difficult as there are wide individual variations in the trajectory and shape of WM pathways. Here we introduce a novel automated tract clustering algorithm based on label fusion--a concept from traditional intensity-based segmentation. Streamline tractography generates many incorrect fibers, so our top-down approach extracts tracts consistent with known anatomy, by mapping multiple hand-labeled atlases into a new dataset. We fuse clustering results from different atlases, using a mean distance fusion scheme. We reliably extracted the major tracts from 105-gradient high angular resolution diffusion images (HARDI) of 198 young normal twins. To compute population statistics, we use a pointwise correspondence method to match, compare, and average WM tracts across subjects. We illustrate our method in a genetic study of white matter tract heritability in twins. PMID:24821529

  3. Analysis of a Stochastic Predator-Prey Model with Applications to Intrahost HIV Genetic Diversity

    E-print Network

    Leviyang, Sivan

    2009-01-01

    During an infection, HIV experiences strong selection by immune system T cells. Recent experimental work has shown that MHC escape mutations form an important pathway for HIV to avoid such selection. In this paper, we study a model of MHC escape mutation. The model is a predator-prey model with two prey, composed of two HIV variants, and one predator, the immune system CD8 cells. We assume that one HIV variant is visible to CD8 cells and one is not. The model takes the form of a system of stochastic differential equations. Motivated by well-known results concerning the short life-cycle of HIV intrahost, we assume that HIV population dynamics occur on a faster time scale then CD8 population dynamics. This separation of time scales allows us to analyze our model using an asymptotic approach. Using this model we study the impact of an MHC escape mutation on the population dynamics and genetic evolution of the intrahost HIV population. From the perspective of population dynamics, we show that the competition betw...

  4. Genetic algorithms for the application of Activated Sludge Model No. 1.

    PubMed

    Kim, S; Lee, H; Kim, J; Kim, C; Ko, J; Woo, H; Kim, S

    2002-01-01

    The genetic algorithm (GA) has been integrated into the IWA ASM No. 1 to calibrate important stoichiometric and kinetic parameters. The evolutionary feature of GA was used to configure the multiple local optima as well as the global optimum. The objective function of optimization was designed to minimize the difference between estimated and measured effluent concentrations at the activated sludge system. Both steady state and dynamic data of the simulation benchmark were used for calibration using denitrification layout. Depending upon the confidence intervals and objective functions, the proposed method provided distributions of parameter space. Field data have been collected and applied to validate calibration capacity of GA. Dynamic calibration was suggested to capture periodic variations of inflow concentrations. Also, in order to verify this proposed method in real wastewater treatment plant, measured data sets for substrate concentrations were obtained from Haeundae wastewater treatment plant and used to estimate parameters in the dynamic system. The simulation results with calibrated parameters matched well with the observed concentrations of effluent COD. PMID:11936660

  5. Genetic Algorithms To provide a background and understanding of basic genetic

    E-print Network

    Qu, Rong

    Genetic Algorithms Objectives To provide a background and understanding of basic genetic algorithms and some of their applications. ·a basic genetic algorithm ·the basic discussion ·the applications of the algorithm #12;Genetic Algorithms 1859 Origin of the Species Survival of the Fittest #12;Genetic Algorithms

  6. Accurate whole human genome sequencing using reversible terminator chemistry.

    PubMed

    Bentley, David R; Balasubramanian, Shankar; Swerdlow, Harold P; Smith, Geoffrey P; Milton, John; Brown, Clive G; Hall, Kevin P; Evers, Dirk J; Barnes, Colin L; Bignell, Helen R; Boutell, Jonathan M; Bryant, Jason; Carter, Richard J; Keira Cheetham, R; Cox, Anthony J; Ellis, Darren J; Flatbush, Michael R; Gormley, Niall A; Humphray, Sean J; Irving, Leslie J; Karbelashvili, Mirian S; Kirk, Scott M; Li, Heng; Liu, Xiaohai; Maisinger, Klaus S; Murray, Lisa J; Obradovic, Bojan; Ost, Tobias; Parkinson, Michael L; Pratt, Mark R; Rasolonjatovo, Isabelle M J; Reed, Mark T; Rigatti, Roberto; Rodighiero, Chiara; Ross, Mark T; Sabot, Andrea; Sankar, Subramanian V; Scally, Aylwyn; Schroth, Gary P; Smith, Mark E; Smith, Vincent P; Spiridou, Anastassia; Torrance, Peta E; Tzonev, Svilen S; Vermaas, Eric H; Walter, Klaudia; Wu, Xiaolin; Zhang, Lu; Alam, Mohammed D; Anastasi, Carole; Aniebo, Ify C; Bailey, David M D; Bancarz, Iain R; Banerjee, Saibal; Barbour, Selena G; Baybayan, Primo A; Benoit, Vincent A; Benson, Kevin F; Bevis, Claire; Black, Phillip J; Boodhun, Asha; Brennan, Joe S; Bridgham, John A; Brown, Rob C; Brown, Andrew A; Buermann, Dale H; Bundu, Abass A; Burrows, James C; Carter, Nigel P; Castillo, Nestor; Chiara E Catenazzi, Maria; Chang, Simon; Neil Cooley, R; Crake, Natasha R; Dada, Olubunmi O; Diakoumakos, Konstantinos D; Dominguez-Fernandez, Belen; Earnshaw, David J; Egbujor, Ugonna C; Elmore, David W; Etchin, Sergey S; Ewan, Mark R; Fedurco, Milan; Fraser, Louise J; Fuentes Fajardo, Karin V; Scott Furey, W; George, David; Gietzen, Kimberley J; Goddard, Colin P; Golda, George S; Granieri, Philip A; Green, David E; Gustafson, David L; Hansen, Nancy F; Harnish, Kevin; Haudenschild, Christian D; Heyer, Narinder I; Hims, Matthew M; Ho, Johnny T; Horgan, Adrian M; Hoschler, Katya; Hurwitz, Steve; Ivanov, Denis V; Johnson, Maria Q; James, Terena; Huw Jones, T A; Kang, Gyoung-Dong; Kerelska, Tzvetana H; Kersey, Alan D; Khrebtukova, Irina; Kindwall, Alex P; Kingsbury, Zoya; Kokko-Gonzales, Paula I; Kumar, Anil; Laurent, Marc A; Lawley, Cynthia T; Lee, Sarah E; Lee, Xavier; Liao, Arnold K; Loch, Jennifer A; Lok, Mitch; Luo, Shujun; Mammen, Radhika M; Martin, John W; McCauley, Patrick G; McNitt, Paul; Mehta, Parul; Moon, Keith W; Mullens, Joe W; Newington, Taksina; Ning, Zemin; Ling Ng, Bee; Novo, Sonia M; O'Neill, Michael J; Osborne, Mark A; Osnowski, Andrew; Ostadan, Omead; Paraschos, Lambros L; Pickering, Lea; Pike, Andrew C; Pike, Alger C; Chris Pinkard, D; Pliskin, Daniel P; Podhasky, Joe; Quijano, Victor J; Raczy, Come; Rae, Vicki H; Rawlings, Stephen R; Chiva Rodriguez, Ana; Roe, Phyllida M; Rogers, John; Rogert Bacigalupo, Maria C; Romanov, Nikolai; Romieu, Anthony; Roth, Rithy K; Rourke, Natalie J; Ruediger, Silke T; Rusman, Eli; Sanches-Kuiper, Raquel M; Schenker, Martin R; Seoane, Josefina M; Shaw, Richard J; Shiver, Mitch K; Short, Steven W; Sizto, Ning L; Sluis, Johannes P; Smith, Melanie A; Ernest Sohna Sohna, Jean; Spence, Eric J; Stevens, Kim; Sutton, Neil; Szajkowski, Lukasz; Tregidgo, Carolyn L; Turcatti, Gerardo; Vandevondele, Stephanie; Verhovsky, Yuli; Virk, Selene M; Wakelin, Suzanne; Walcott, Gregory C; Wang, Jingwen; Worsley, Graham J; Yan, Juying; Yau, Ling; Zuerlein, Mike; Rogers, Jane; Mullikin, James C; Hurles, Matthew E; McCooke, Nick J; West, John S; Oaks, Frank L; Lundberg, Peter L; Klenerman, David; Durbin, Richard; Smith, Anthony J

    2008-11-01

    DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications. PMID:18987734

  7. Application of molecular and somatic cell genetics to the study of chromosome 21.

    PubMed

    Law, M L; Van Keuren, M

    1986-01-01

    An extra copy of human chromosome 21 has been known for over twenty years to be the chromosomal abnormality in Down's syndrome; however, the biochemical and molecular basis governing expression of the phenotype is still poorly understood. Using the methods of somatic cell and molecular genetics, we have been studying genes and DNA sequences on chromosome 21 by constructing hamster/human hybrids containing a whole or partial chromosome 21 and assigning their locations on the chromosome. In particular, a family of repetitive sequences, some having only a few thousand copies in the human genome, have been used as cloned DNA markers to define deletions in these somatic cell hybrids. We have shown that this approach can significantly improve the resolution of fine chromosomal structures over the conventional cytogenetic analysis. The rationale behind this approach is the observation that a repetitive sequence probe often forms multiple bands after hybridizing to a Southern blot of digested hybrid DNA, and the band pattern appears to be unique for each human chromosome. Therefore, each band (sequence) can be assigned to a particular region of human chromosome 21 by comparing the band patterns from hybrids containing different portions of the chromosome. Results presented here showed that a 0.58-kb repetitive sequence probe can be used to identify deletions, translocations, and other more complicated rearrangements of chromosome 21 seen in patients with abnormalities of this chromosome. The advantage of using such a repetitive sequence probe over a unique sequence is that it can serve both as a repetitive sequence defining multiple sites (multiple bands on a Southern blot) in the genome and at the same time serve as a unique sequence defining a particular site (individual band). For the detection of deletions and other rearrangements, especially in small chromosomes such as 21, it is the former property that makes it very efficient in the initial assignment of a chromosome location. PMID:2880544

  8. Surface fluid registration of conformal representation: application to detect disease burden and genetic influence on hippocampus.

    PubMed

    Shi, Jie; Thompson, Paul M; Gutman, Boris; Wang, Yalin

    2013-09-01

    In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistent surface fluid registration, and multivariate tensor-based morphometry (mTBM). First, we conformally map a surface onto a planar rectangle space with holomorphic 1-forms. Second, we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface. Third, we align the feature image with a chosen template image via the fluid image registration algorithm, which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization. The inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images. This alignment induces a corresponding deformation on the surface. We tested the system on Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset to study AD symptoms on hippocampus. In our system, by modeling a hippocampus as a 3D parametric surface, we nonlinearly registered each surface with a selected template surface. Then we used mTBM to analyze the morphometry difference between diagnostic groups. Experimental results show that the new system has better performance than two publicly available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E[element of]4 allele (ApoE4), which is considered as the most prevalent risk factor for AD. Our work successfully detected statistically significant difference between ApoE4 carriers and non-carriers in both patients of mild cognitive impairment (MCI) and healthy control subjects. The results show evidence that the ApoE genotype may be associated with accelerated brain atrophy so that our work provides a new MRI analysis tool that may help presymptomatic AD research. PMID:23587689

  9. Response experiments for nonlinear systems with application to reaction kinetics and genetics.

    PubMed

    Vlad, Marcel O; Arkin, Adam; Ross, John

    2004-05-11

    A unified type of response experiment is suggested for complex systems made up of individual species (atoms, molecules, quasi-particles, biological organisms, etc.). We make the following assumptions: (i) some of the species may exist in two forms, labeled and unlabeled, respectively; (ii) the kinetic and transport properties of the labeled and unlabeled species are the same, respectively (neutrality assumption); (iii) the experiment preserves the total input and output fluxes; only the fractions of the labeled compounds in the input and output fluxes are varied. Under these circumstances a linear integral superposition law connects the fractions of labeled species in the input and output fluxes. This linear superposition law is valid for homogeneous and inhomogeneous systems and for systems with intrinsic (hidden) state variables; it arises from the neutrality condition and holds even though the underlying dynamics of the process may be highly nonlinear. Because this response law does not involve the linearization of the evolution equations it has great potential for the analysis of complex physical, chemical, and biological systems. We compare our approach with the linearization techniques used in biochemistry and genetics. We consider a simple reaction network involving replication, transformation, and disappearance steps and study the influence of experimental (measurement) and linearization errors on the evaluated values of rate coefficients. We show that the method involving the linearization of the kinetic equations leads to unpredictable results; because of the interference between measurement and linearization errors, either error compensation or error amplification occurs. Although our approach does not eliminate the effects of measurement errors, it leads to more consistent results. For a broad range of input fractions no error amplification or compensation occurs, and the error range for the rate coefficients is about the same as the error range of the measurements. PMID:15123834

  10. Human genetics

    SciTech Connect

    Carlson, E.A.

    1984-01-01

    This text provides full and balanced coverage of the concepts requisite for a thorough understanding of human genetics. Applications to both the individual and society are integrated throughout the lively and personal narrative, and the essential principles of heredity are clearly presented to prepare students for informed participation in public controversies. High-interest, controversial topics, including recombinant DNA technology, oncogenes, embryo transfer, environmental mutagens and carcinogens, IQ testing, and eugenics encourage understanding of important social issues.

  11. Automatic Synthesis of Active Electronic Networks using Genetic Algorithms IEE/IEEE International Conference on Genetic Algorithms in Engineering Systems: Innovations and Applications

    E-print Network

    Grimbleby, James

    containing a single operational amplifier. Active Network Synthesis using GAs Operational amplifiers haveAutomatic Synthesis of Active Electronic Networks using Genetic Algorithms IEE/IEEE International. In spite of the fact that no expert rules are built into the synthesis program, the networks generated

  12. Scheduling Using Genetic Algorithms Ursula Fissgus

    E-print Network

    Scheduling Using Genetic Algorithms Ursula Fissgus Computer Science Department University Halle memory machine. We present a scheduling derivation step based on the genetic algorithm paradigm, data parallelism, genetic algorithms. 1 Introduction Several applications from scientific computing, e

  13. Institute for Systems Genetics New York, NY

    E-print Network

    Queitsch, Christine

    : human genetics, `omics technologies and their applications, computational sciences, and biological with hypothesis-driven research programs that exploit genetic, `omic, engineering and/or computationally intensive Opportunity Employer. · Human Genetics and Genomics · Computational Biology · Functional Genomics · High

  14. A new multichannel time reversal focusing method for circumferential Lamb waves and its applications for defect detection in thick-walled pipe with large-diameter.

    PubMed

    Liu, Zenghua; Xu, Qinglong; Gong, Yu; He, Cunfu; Wu, Bin

    2014-09-01

    This paper proposes a new multichannel time reversal focusing (MTRF) method for circumferential Lamb waves which is based on modified time reversal algorithm and applies this method for detecting different kinds of defects in thick-walled pipe with large-diameter. The principle of time reversal of circumferential Lamb waves in pipe is presented along with the influence from multiple guided wave modes and propagation paths. Experimental study is carried out in a thick-walled and large-diameter pipe with three artificial defects, namely two axial notches on its inner and outer surface respectively, and a corrosion-like defect on its outer surface. By using the proposed MTRF method, the multichannel signals focus at the defects, leading to the amplitude improvement of the defect scattered signal. Besides, another energy focus arises in the direct signal due to the partial compensation of dispersion and multimode of circumferential Lamb waves, alongside the multichannel focusing, during MTRF process. By taking the direct focus as a time base, accurate defect localization is implemented. Secondly, a new phenomenon is exhibited in this paper that defect scattered wave packet appears just before the right boundary of truncation window after time reversal, and to which two feasible explanations are given. Moreover, this phenomenon can be used as the theoretical basis in the determination of defect scattered waves in time reversal response signal. At last, in order to detect defects without prior knowing their exact position, a large-range truncation window is used in the proposed method. As a result, the experimental operation of MTRF method is simplified and defect detection and localization are well accomplished. PMID:24877582

  15. Cheaper Adjoints by Reversing Address Computations

    DOE PAGESBeta

    Hascoët, L.; Utke, J.; Naumann, U.

    2008-01-01

    The reverse mode of automatic differentiation is widely used in science and engineering. A severe bottleneck for the performance of the reverse mode, however, is the necessity to recover certain intermediate values of the program in reverse order. Among these values are computed addresses, which traditionally are recovered through forward recomputation and storage in memory. We propose an alternative approach for recovery that uses inverse computation based on dependency information. Address storage constitutes a significant portion of the overall storage requirements. An example illustrates substantial gains that the proposed approach yields, and we show use cases in practical applications.

  16. Genetically modified lactic acid bacteria: applications to food or health and risk assessment.

    PubMed

    Renault, Pierre

    2002-11-01

    Lactic acid bacteria have a long history of use in fermented food products. Progress in gene technology allows their modification by introducing new genes or by modifying their metabolic functions. These modifications may lead to improvements in food technology (bacteria better fitted to technological processes, leading to improved organoleptic properties em leader ), or to new applications including bacteria producing therapeutic molecules that could be delivered by mouth. Examples in these two fields will be discussed, at the same time evaluating their potential benefit to society and the possible risks associated with their use. Risk assessment and expected benefits will determine the future use of modified bacteria in the domains of food technology and health. PMID:12595135

  17. Time reversal in multiply scattering media

    Microsoft Academic Search

    Arnaud Derode; Arnaud Tourin; Mathias Fink

    1998-01-01

    The application of time-reversal mirrors (TRM) to media with very high-order multiple scattering is presented. Random sets of up to 2500 steel rods are considered. When a pulsed wave traverses such a medium, it undergoes many scatterings before reaching the TRM. The resulting pressure field spreads in time, up to 300 times the initial pulse duration; it is recorded, time-reversed

  18. Reversible logic for supercomputing.

    SciTech Connect

    DeBenedictis, Erik P.

    2004-12-01

    This paper is about making reversible logic a reality for supercomputing. Reversible logic offers a way to exceed certain basic limits on the performance of computers, yet a powerful case will have to be made to justify its substantial development expense. This paper explores the limits of current, irreversible logic for supercomputers, thus forming a threshold above which reversible logic is the only solution. Problems above this threshold are discussed, with the science and mitigation of global warming being discussed in detail. To further develop the idea of using reversible logic in supercomputing, a design for a 1 Zettaflops supercomputer as required for addressing global climate warming is presented. However, to create such a design requires deviations from the mainstream of both the software for climate simulation and research directions of reversible logic. These deviations provide direction on how to make reversible logic practical

  19. Reversible logic for supercomputing.

    SciTech Connect

    DeBenedictis, Erik P.

    2005-05-01

    This paper is about making reversible logic a reality for supercomputing. Reversible logic offers a way to exceed certain basic limits on the performance of computers, yet a powerful case will have to be made to justify its substantial development expense. This paper explores the limits of current, irreversible logic for supercomputers, thus forming a threshold above which reversible logic is the only solution. Problems above this threshold are discussed, with the science and mitigation of global warming being discussed in detail. To further develop the idea of using reversible logic in supercomputing, a design for a 1 Zettaflops supercomputer as required for addressing global climate warming is presented. However, to create such a design requires deviations from the mainstream of both the software for climate simulation and research directions of reversible logic. These deviations provide direction on how to make reversible logic practical.

  20. Detection of amplified VNTR alleles by direct chemiluminescence: application to the genetic identification of biological samples in forensic cases.

    PubMed

    Decorte, R; Cassiman, J J

    1991-01-01

    Minisatellite or variable number of tandem repeat (VNTR) regions contain such a high degree of polymorphism that they allow one to construct an individual-specific DNA "fingerprint". Analysis of these sequences by Southern blot however, consumes much DNA and is not applicable to degraded DNA samples often recovered from body-fluid stains found at crime scenes. The polymerase chain reaction (PCR) technique may overcome these problems. With oligonucleotide primers flanking the repeat region, amplification of the VNTR alleles followed by direct visualization on ethidium bromide-stained agarose gels is possible. In those cases were the PCR yield is too low for direct visualization, the product can be blotted to a nylon membrane and hybridized with a labelled internal probe. Alternatively, the PCR product can be biotinylated during amplification and visualized by direct chemiluminescence after Southern transfer. The remarkable sensitivity of the PCR technique has allowed the detection of genetic polymorphisms in single cells, hair roots and single sperm. A drawback of this very high sensitivity however is that special precautions have to be taken to prevent accidental contamination resulting in erroneous interpretation of the results. PMID:1831164

  1. Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic

    PubMed Central

    Demongeot, Jacques; Ben Amor, Hedi; Elena, Adrien; Gillois, Pierre; Noual, Mathilde; Sené, Sylvain

    2009-01-01

    Regulatory interaction networks are often studied on their dynamical side (existence of attractors, study of their stability). We focus here also on their robustness, that is their ability to offer the same spatiotemporal patterns and to resist to external perturbations such as losses of nodes or edges in the networks interactions architecture, changes in their environmental boundary conditions as well as changes in the update schedule (or updating mode) of the states of their elements (e.g., if these elements are genes, their synchronous coexpression mode versus their sequential expression). We define the generic notions of boundary, core, and critical vertex or edge of the underlying interaction graph of the regulatory network, whose disappearance causes dramatic changes in the number and nature of attractors (e.g., passage from a bistable behaviour to a unique periodic regime) or in the range of their basins of stability. The dynamic transition of states will be presented in the framework of threshold Boolean automata rules. A panorama of applications at different levels will be given: brain and plant morphogenesis, bulbar cardio-respiratory regulation, glycolytic/oxidative metabolic coupling, and eventually cell cycle and feather morphogenesis genetic control. PMID:20057955

  2. Reverse Transcription-Competitive Multiplex PCR Improves Quantification of mRNA in Clinical Samples—Application to the Low Abundance CFTR mRNA

    Microsoft Academic Search

    Stefan M. Loitsch; Stefan Kippenberger; Nurlan Dauletbaev; Thomas O. F. Wagner; Joachim Bargon

    1999-01-01

    Background: To monitor gene therapy, we wished to quantify cystic fibrosis transmembrane conductance regulator (CFTR) mRNA. We developed a PCR-based method to measure CFTR mRNA in clinical samples. Methods: Expression was determined by reverse transcription-competitive multiplex PCR (RCMP) for CFTR and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) transcripts, and for serial dilutions of two internal cDNA standards consisting of CFTR and GAPDH mutants

  3. Reversible Simulations of Elastic Collisions

    SciTech Connect

    Perumalla, Kalyan S [ORNL; Protopopescu, Vladimir A [ORNL

    2013-01-01

    Consider a system of N identical hard spherical particles moving in a d-dimensional box and undergoing elastic, possibly multi-particle, collisions. We develop a new algorithm that recovers the pre-collision state from the post-collision state of the system, across a series of consecutive collisions, \\textit{with essentially no memory overhead}. The challenge in achieving reversibility for an n-particle collision (where, in general, n<< N) arises from the presence of nd-d-1 degrees of freedom (arbitrary angles) during each collision, as well as from the complex geometrical constraints placed on the colliding particles. To reverse the collisions in a traditional simulation setting, all of the particular realizations of these degrees of freedom (angles) during the forward simulation must be tracked. This requires memory proportional to the number of collisions, which grows very fast with N and d, thereby severely limiting the \\textit{de facto} applicability of the scheme. This limitation is addressed here by first performing a pseudo-randomization of angles, which ensures determinism in the reverse path for any values of n and d. To address the more difficult problem of geometrical and dynamic constraints, a new approach is developed which correctly samples the constrained phase space. Upon combining the pseudo-randomization with correct phase space sampling, perfect reversibility of collisions is achieved, as illustrated for n<=3, d=2, and n=2, d=3. This result enables, for the first time, reversible simulations of elastic collisions with essentially zero memory accumulation. In principle, the approach presented here could be generalized to larger values of n, which would be of definite interest for molecular dynamics simulations at high densities.

  4. Genetic Counseling

    MedlinePLUS

    ... this page It's been added to your dashboard . Genetic counseling Genetic counseling is a service to help ... child care and genetic testing. Who should get genetic counseling? Anyone who has unanswered questions about origins ...

  5. Real-time rapid reverse transcriptase-polymerase chain reaction for intraoperative diagnosis of lymph node micrometastasis: Clinical application for cervical lymph node dissection in esophageal cancers

    Microsoft Academic Search

    Setsuko Yoshioka; Yoshiyuki Fujiwara; Yurika Sugita; Yoshihiro Okada; Masahiko Yano; Shigeyuki Tamura; Takushi Yasuda; Shuji Takiguchi; Hitoshi Shiozaki; Morito Monden

    2002-01-01

    Background. New molecular techniques have been designed to detect cancer micrometastases that are otherwise missed by conventional histologic examination. The aim of this study was to establish a sensitive and rapid genetic assay to detect lymph node micrometastasis and to assess its usefulness clinically for cervical lymphadenectomy in esophageal cancer. We have recently shown that metastasis in the lymph node

  6. Medical genetics

    SciTech Connect

    Nora, J.J.; Fraser, F.C.

    1989-01-01

    This book presents a discussion of medical genetics for the practitioner treating or counseling patients with genetic disease. It includes a discussion of the relationship of heredity and diseases, the chromosomal basis for heredity, gene frequencies, and genetics of development and maldevelopment. The authors also focus on teratology, somatic cell genetics, genetics and cancer, genetics of behavior.

  7. The Application of Hybrid Genetic Particle Swarm Optimization Algorithm in the Distribution Network Reconfigurations Multi-Objective Optimization

    Microsoft Academic Search

    Caiqing Zhang; Jingjing Zhang; Xihua Gu

    2007-01-01

    According to the single performance of most distribution network reconfigurations (DNR), this paper presents the multi-objective distribution network optimization model with the optimal network loss, load balancing, and power supply voltage. Combined with the evolution idea of genetic algorithm (GA) and population intellectual technique of particle swarm optimization (PSO) algorithm, it applies hybrid genetic particle swarm optimization algorithm (HGPSOA) to

  8. Genetic toxicity evaluation of 1,1,1,2,3,3,3- heptatfluoropropane. Volume 1. Results of salmonella typhimurium histidine reversion assay (ames assay). Final report, March-December 1994

    SciTech Connect

    Mitchell, A.D.

    1995-01-01

    Under subcontract to ManTech Environmental Technology, Incorporated, Uenesys Research, Incorporated tested 1,1,12,3,3,3- heptafluoropropane (HFC-227ea) using Billups-Rothenberg exposure chambers for the exposure chamber modification of the Salmonella typhimurium histidine (his) reversion mutagenesis system (the Ames test), a microbial assay that measures his his+ reversion induced by chemicals that cause base changes or frameshift mutations i the genome of this organism. Testing was conducted using five Salmonella strains, with and without metabolic activation. HFC-227ea was tested in a preliminary test and in a mutagenesis assay. HFC-227ea was tested to toxic levels in the mutagenesis assay, but a sufficient number of nontoxic concentrations were tested to determine if HFC-227ea were capable of inducing a dose-related mutagenic response, and the positive control responses were consistent with historical data from the laboratory, and no evidence of a mutagenic response was obtained in any strain without or with activation. Therefore, HFC-227ea was negative in the Salmonella typhimurium histidine reversion mutagenesis test in the presence and absence of metabolic activation.

  9. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    PubMed

    Mascher, Martin; Wu, Shuangye; Amand, Paul St; Stein, Nils; Poland, Jesse

    2013-01-01

    The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop. PMID:24098570

  10. On time reversal mirrors

    Microsoft Academic Search

    Albert C. Fannjiang

    2009-01-01

    The concept of time reversal (TR) of a scalar wave is reexamined from basic principles. Five different time-reversal mirrors (TRMs) are introduced and their relations are analyzed. For the boundary behavior, it is shown that for a paraxial wave only the monopole TR scheme satisfies the exact boundary condition while for the spherical wave only the MD-mode TR scheme satisfies

  11. MIMO time reversal communications

    Microsoft Academic Search

    Hee-chun Song; William S. Hodgkiss; William A. Kuperman

    2007-01-01

    A time reversal mirror (TRM) exploits spatial diversity to achieve spatial and temporal focusing, a useful property for communications in an environment with significant multipath. Temporal focusing (pulse compression) mitigates intersymbol interference (ISI) while spatial focusing enables a straightforward extension to multiple- input\\/multiple-output (MIMO) communications. Furthermore, the time reversal process can be combined with adaptive channel equalization to remove the

  12. Geomagnetism II: Magnetic Reversals

    NSDL National Science Digital Library

    2012-08-03

    This is an activity about the periodic reversals of Earth's magnetic field. Learners will graph the frequency of magnetic pole reversals over the past 800,000 years and investigate answers to questions using the graphed data. This is Activity 8 in the Exploring Magnetism on Earth teachers guide.

  13. Reversibility of laser filamentation

    E-print Network

    Nicolas Berti; Wahb Ettoumi; Jérôme Kasparian; Jean-Pierre Wolf

    2014-09-03

    We investigate the reversibility of laser filamentation, a self-sustained, non-linear propagation regime including dissipation and time-retarded effects. We show that even losses related to ionization marginally affect the possibility of reverse propagating ultrashort pulses back to the initial conditions, although they make it prone to finite-distance blow-up susceptible to prevent backward propagation.

  14. Electrodeposition of mesoscopic Pt-Ru on reticulated vitreous carbon from reverse emulsions and microemulsions: Application to methanol electro-oxidation

    Microsoft Academic Search

    Tommy T. Cheng; El?d L. Gyenge

    2006-01-01

    High surface area Pt-Ru (between 120 and 400cm2mg?1) meso-sized particles and mesoporous coatings were electrodeposited on reticulated vitreous carbon (RVC) three-dimensional electrodes using reverse emulsions and microemulsions. The organic phase of the colloidal media was composed of cyclohexane, Triton X-100 non-ionic surfactant and tetrabutylammonium perchlorate (for ionic conductivity) while the aqueous phase contained H2PtCl6 and RuCl3 (or (NH4)2RuCl6). For microemulsification

  15. Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

    PubMed Central

    Martínez-García, Pedro J.; Parfitt, Dan E.; Bostock, Richard M.; Fresnedo-Ramírez, Jonathan; Vazquez-Lobo, Alejandra; Ogundiwin, Ebenezer A.; Gradziel, Thomas M.; Crisosto, Carlos H.

    2013-01-01

    The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot. PMID:24244329

  16. Low Cost Reversible fuel cell systems

    SciTech Connect

    Technology Management Inc.

    2003-12-30

    This final report summarizes a 3-phase program performed from March 2000 through September 2003 with a particular focus on Phase III. The overall program studied TMI's reversible solid oxide stack, system concepts, and potential applications. The TMI reversible (fuel cell-electrolyzer) system employs a stack of high temperature solid-oxide electrochemical cells to produce either electricity (from a fuel and air or oxygen) or hydrogen (from water and supplied electricity). An atmospheric pressure fuel cell system operates on natural gas (or other carbon-containing fuel) and air. A high-pressure reversible electrolyzer system is used to make high-pressure hydrogen and oxygen from water and when desired, operates in reverse to generate electricity from these gases.

  17. Application of a reverse dot blot DNA-DNA hydridization method to quantify host-feeding tendencies of two sibling species in the Anopheles gambiae complex.

    PubMed

    Fritz, M L; Miller, J R; Bayoh, M N; Vulule, J M; Landgraf, J R; Walker, E D

    2013-12-01

    A DNA-DNA hybridization method, reverse dot blot analysis (RDBA), was used to identify Anopheles gambiae s.s. and Anopheles arabiensis (Diptera: Culicidae) hosts. Of 299 blood-fed and semi-gravid An. gambiae s.l. collected from Kisian, Kenya, 244 individuals were identifiable to species; of these, 69.5% were An. arabiensis and 29.5% were An. gambiae s.s. Host identifications with RDBA were comparable with those of conventional polymerase chain reaction (PCR) followed by direct sequencing of amplicons of the vertebrate mitochondrial cytochrome b gene. Of the 174 amplicon-producing samples used to compare these two methods, 147 were identifiable by direct sequencing and 139 of these were identifiable by RDBA. Anopheles arabiensis bloodmeals were mostly (94.6%) bovine in origin, whereas An. gambiae s.s. fed upon humans more than 91.8% of the time. Tests by RDBA detected that two of 112 An. arabiensis contained blood from more than one host species, whereas PCR and direct sequencing did not. Recent use of insecticide-treated bednets in Kisian is likely to have caused the shift in the dominant vector species from An. gambiae s.s. to An. arabiensis. Reverse dot blot analysis provides an opportunity to study changes in host-feeding by members of the An. gambiae complex in response to the broadening distribution of vector control measures targeting host-selection behaviours. PMID:24188164

  18. Enriching Reverse Engineering with Annotations

    E-print Network

    Nierstrasz, Oscar

    Enriching Reverse Engineering with Annotations Masterarbeit der Philosophisch Successful reverse engineering needs to take into account human knowledge about architecture, about features to the automatically reverse engineered model and should be taken into account by analyses. Typically, when we want

  19. Introduction Reverse Engineering MIFARE Classic

    E-print Network

    Garcia, Flavio D.

    Introduction Reverse Engineering MIFARE Classic Cryptanalysis of MIFARE Classic Conclusions MIFARE Classic #12;Introduction Reverse Engineering MIFARE Classic Cryptanalysis of MIFARE Classic Conclusions Outline 1 Introduction Timeline RFID MIFARE 2 Reverse Engineering MIFARE Classic Characteristics

  20. The Application of a Genetic Algorithm to Estimate Material Properties for Fire Modeling from Bench-Scale Fire Test Data 

    E-print Network

    Lautenberger, Chris; Rein, Guillermo; Fernandez-Pello, Carlos

    A methodology based on an automated optimization technique that uses a genetic algorithm (GA) is developed to estimate the material properties needed for CFD-based fire growth modeling from bench-scale fire test data. ...

  1. MULTI-OBJECTIVE OPTIMAL DESIGN OF GROUNDWATER REMEDIATION SYSTEMS: APPLICATION OF THE NICHED PARETO GENETIC ALGORITHM (NPGA). (R826614)

    EPA Science Inventory

    A multiobjective optimization algorithm is applied to a groundwater quality management problem involving remediation by pump-and-treat (PAT). The multiobjective optimization framework uses the niched Pareto genetic algorithm (NPGA) and is applied to simultaneously minimize the...

  2. The application of genetic algorithm and nonlinear fuzzy programming for water pollution control in a river basin

    Microsoft Academic Search

    Ni-Bin Chang; H. W. Chen

    1996-01-01

    This paper presents a modified formulation of a fuzzy multiobjective programming model in order to illustrate the tendency of nonlinearity in many environmental problems. The genetic algorithm is described as a tool to solve a typical water pollution control problem

  3. Application of somatic embryogenesis in high-value clonal forestry: Deployment, genetic control, and stability of cryopreserved clones

    Microsoft Academic Search

    Y. S. Park; J. D. Barrett; J. M. Bonga

    1998-01-01

    Summary  The most important advantage of cloning conifers by somatic embryogenesis (SE) is that the embryogenic tissue can be cryopreserved\\u000a without changing its genetic make-up and without loss of juvenility. This offers an opportunity to develop high-value clonal\\u000a varieties by defrosting and repropagating cryopreserved clones after genetic testing has shown which clones are the best performers.\\u000a In the current absence of

  4. Medical genetics

    SciTech Connect

    Jorde, L.B.; Carey, J.C.; White, R.L.

    1995-10-01

    This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.

  5. Genetics and genomics of root symbiosis

    Microsoft Academic Search

    Jens Stougaard

    2001-01-01

    Model genetics and genomics have been developed as tools for studying the third largest family of flowering plants, the Leguminosae, which includes important crop plants. Functional genomics strategies for the global analysis of gene expression, the elucidation of pathways and reverse genetics are established. These approaches provide new possibilities for investigating rhizobial as well as mycorrhizal endosymbiosis. Plant genes with

  6. Reverse Transcription-PCR

    NSDL National Science Digital Library

    American Society For Microbiology

    2003-05-12

    This Flash animation shows how the method of reverse transcription-PCR is performed and some sample data are produced. It uses sound and mouse-over identification to help students learn more and retain the information.

  7. Reverse Shoulder Replacement

    MedlinePLUS

    Reverse Shoulder Replacement You must have Javascript enabled in your web browser. View Program Transcript Click Here to view the OR-Live, Inc. Privacy Policy and Legal Notice © 2010 OR-Live, Inc. All rights reserved.

  8. Combination of 15 N Reverse Labeling and Afterglow Spectroscopy for Assigning Membrane Protein Spectra by Magic-Angle-Spinning Solid-State NMR: Application to the Multidrug Resistance Protein EmrE

    PubMed Central

    Banigan, James R.; Gayen, Anindita; Traaseth, Nathaniel J.

    2013-01-01

    Magic-angle-spinning (MAS) solid-state NMR spectroscopy has emerged as a viable method to characterize membrane protein structure and dynamics. Nevertheless, the spectral resolution for uniformly labeled samples is often compromised by redundancy of the primary sequence and the presence of helical secondary structure that results in substantial resonance overlap. The ability to simplify the spectrum in order to obtain unambiguous site-specific assignments is a major bottleneck for structure determination. To address this problem, we used a combination of 15N reverse labeling and afterglow spectroscopic techniques that dramatically improved the ability to resolve peaks in a crowded spectrum. This was demonstrated using the polytopic membrane protein EmrE, an efflux pump involved in multidrug resistance. Residues preceding the 15N reverse labeled amino acid were imaged using a 3D NCOCX afterglow experiment and those following were recorded using a frequency-selective dephasing experiment. Our approach reduced the spectral congestion and provided a sensitive way to obtain chemical shift assignments for a membrane protein where no high-resolution structure is available. This MAS methodology is widely applicable to the study of other polytopic membrane proteins in functional lipid bilayer environments. PMID:23539118

  9. Combination of ¹?N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE.

    PubMed

    Banigan, James R; Gayen, Anindita; Traaseth, Nathaniel J

    2013-04-01

    Magic-angle-spinning (MAS) solid-state NMR spectroscopy has emerged as a viable method to characterize membrane protein structure and dynamics. Nevertheless, the spectral resolution for uniformly labeled samples is often compromised by redundancy of the primary sequence and the presence of helical secondary structure that results in substantial resonance overlap. The ability to simplify the spectrum in order to obtain unambiguous site-specific assignments is a major bottleneck for structure determination. To address this problem, we used a combination of (15)N reverse labeling, afterglow spectroscopic techniques, and frequency-selective dephasing experiments that dramatically improved the ability to resolve peaks in crowded spectra. This was demonstrated using the polytopic membrane protein EmrE, an efflux pump involved in multidrug resistance. Residues preceding the (15)N reverse labeled amino acid were imaged using a 3D NCOCX afterglow experiment and those following were recorded using a frequency-selective dephasing experiment. Our approach reduced the spectral congestion and provided a sensitive way to obtain chemical shift assignments for a membrane protein where no high-resolution structure is available. This MAS methodology is widely applicable to the study of other polytopic membrane proteins in functional lipid bilayer environments. PMID:23539118

  10. On time reversal mirrors

    Microsoft Academic Search

    Albert C. Fannjiang

    2009-01-01

    The concept of time reversal (TR) of scalar wave is reexamined from basic\\u000aprinciples. Five different time reversal mirrors (TRM) are introduced and their\\u000arelations are analyzed. For the boundary behavior, it is shown that for\\u000aparaxial wave only the monopole TR scheme satisfies the exact boundary\\u000acondition while for spherical wave only one of the mixed mode TR scheme,

  11. Investigation of Microflow Reversal by AC Electrokinetics in Orthogonal Electrodes for Micropump Design

    E-print Network

    Wu, Jayne

    1 Investigation of Microflow Reversal by AC Electrokinetics in Orthogonal Electrodes for Micropump microflows when excited by AC signals, showing potential for micropumping applications. This paper investigates the microflow reversal phenomena in such orthogonal electrode micropumps. Three types of microflow

  12. Genetic Algorithms

    Microsoft Academic Search

    Kumara Sastry; David Goldberg; Graham Kendall

    Genetic algorithms (GAs) are search methods based on principles of natural selection and genetics (Fraser, 1957;Bremermann, 1958;Holland, 1975). We start with a brief introduction to simple genetic algorithms and associated terminology.

  13. Genetic Counseling

    MedlinePLUS

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  14. Genetic Networks and Soft Computing

    Microsoft Academic Search

    Sushmita Mitra; Ranajit Das; Yoichi Hayashi

    2011-01-01

    The analysis of gene regulatory networks provides enormous information on various fundamental cellular processes involving growth, development, hormone secretion, and cellular communication. Their extraction from available gene expression profiles is a challenging problem. Such reverse engineering of genetic networks offers insight into cellular activity toward prediction of adverse effects of new drugs or possible identification of new drug targets. Tasks

  15. Rotating Reverse-Osmosis for Water Purification

    NASA Technical Reports Server (NTRS)

    Lueptow, RIchard M.

    2004-01-01

    A new design for a water-filtering device combines rotating filtration with reverse osmosis to create a rotating reverse- osmosis system. Rotating filtration has been used for separating plasma from whole blood, while reverse osmosis has been used in purification of water and in some chemical processes. Reverse- osmosis membranes are vulnerable to concentration polarization a type of fouling in which the chemicals meant not to pass through the reverse-osmosis membranes accumulate very near the surfaces of the membranes. The combination of rotating filtration and reverse osmosis is intended to prevent concentration polarization and thereby increase the desired flux of filtered water while decreasing the likelihood of passage of undesired chemical species through the filter. Devices based on this concept could be useful in a variety of commercial applications, including purification and desalination of drinking water, purification of pharmaceutical process water, treatment of household and industrial wastewater, and treatment of industrial process water. A rotating filter consists of a cylindrical porous microfilter rotating within a stationary concentric cylindrical outer shell (see figure). The aqueous suspension enters one end of the annulus between the inner and outer cylinders. Filtrate passes through the rotating cylindrical microfilter and is removed via a hollow shaft. The concentrated suspension is removed at the end of the annulus opposite the end where the suspension entered.

  16. Genetic network identification using convex programming A. Agung Julius1,

    E-print Network

    Genetic network identification using convex programming A. Agung Julius1, , Michael Zavlanos1@stanford.edu Introduction Genes in living cells regulate various cellular biochemical processes through genetic regu- latory in a large scale network. In the literature, this is sometimes called reverse engineering the genetic network

  17. Visa Type Alien Number (If Applicable) FPd Which of the following categories best describes you? Response is voluntary. See notes on reverse side for explanation.

    E-print Network

    Qiu, Weigang

    COLLEGE USE ONLY DIV FEE GRPADM CURRICULUM RESIDENCY STP YR MO Visa Type Alien Number (If of application . 3. Permanent residents of the United States will be required to present their Alien Registration

  18. Returnable containers: an example of reverse logistics

    Microsoft Academic Search

    Leo Kroon; Gaby Vrijens

    1995-01-01

    Considers the application of returnable containers as an example of reverse logistics. A returnable container is a type of secondary packaging that can be used several times in the same form, in contrast with traditional cardboard boxes. For this equipment to be used, a system for the return logistics of the containers should be available: this system should guarantee that

  19. Concentration of blackcurrant juice by reverse osmosis

    Microsoft Academic Search

    N. Pap; Sz. Kertész; E. Pongrácz; L. Myllykoski; R. L. Keiski; Gy. Vatai; Zs. László; C. Hodúr

    2009-01-01

    The aim of this study was to examine the applicability of reverse osmosis (RO) for the concentration of blackcurrant juice by AFC-80 polyamide tubular membrane that has a salt rejection greater than 80%. The fresh juice had a total soluble solids content of about 16.5°Brix. The effect of centrifugation followed by depectinization with two commercially available pectinase enzyme preparations (Panzym

  20. Reverse mutations in fragile X syndrome

    SciTech Connect

    Brown, W.T.; Nolin, S.; Houck, G.E. [and others

    1994-09-01

    The fragile X syndrome is the most common inherited form of mental retardation. Yet new mutations have not been described and no affected child has been born to a carrier mother having less than 60 FMR-1 CGG triplet repeats. Reverse mutations also appear to be very rare. We have previously identified the daughter of a premutation mother (95 CGGs) who inherited a normal repeat size of 35 as a reverse mutation. In the process of carrier testing by PCR, we have now identified two additional females with reverse mutations. All three of these reverse mutation women were previously tested by linkage as part of known fragile X families (subsequently confirmed by direct analysis), and assigned a > 99% risk as a carrier. In the second family, the mother carries a premutation allele of 95 repeats and the daughter inherited a 43 repeat allele. Prior to direct DNA testing, she had a positive prenatal diagnosis by linkage (> 99% risk) and cytogenetics with 3/450 cells apparently positive. Subsequent retesting of the products of conception by PCR now reveals a 43 repeat allele from her carrier mother with an 82 repeat allele. Testing with close CA markers (FRAXAC1 and DXS548) confirmed that these women inherited the same chromosome and their full mutation brothers. Further analysis is pending. These examples of reverse mutations are the only ones we have identified in our study of offspring of more than 200 carriers (400+ meioses) examined to date. Therefore, we conclude the frequency of fragile X back mutations is likely to be less than 1%. Retesting of linkage positive carriers is recommended to detect reverse mutations and assure accurate genetic counseling.

  1. Evaluation of estimated genetic values and their application to genome-wide investigation of systolic blood pressure

    PubMed Central

    2014-01-01

    The concept of breeding values, an individual's phenotypic deviation from the population mean as a result of the sum of the average effects of the genes they carry, is of great importance in livestock, aquaculture, and cash crop industries where emphasis is placed on an individual's potential to pass desirable phenotypes on to the next generation. As breeding or genetic values (as referred to here) cannot be measured directly, estimated genetic values (EGVs) are based on an individual's own phenotype, phenotype information from relatives, and, increasingly, genetic data. Because EGVs represent additive genetic variation, calculating EGVs in an extended human pedigree is expected to provide a more refined phenotype for genetic analyses. To test the utility of EGVs in genome-wide association, EGVs were calculated for 847 members of 20 extended Mexican American families based on 100 replicates of simulated systolic blood pressure. Calculations were performed in GAUSS to solve a variation on the standard Best Linear Unbiased Predictor (BLUP) mixed model equation with age, sex, and the first 3 principal components of sample-wide genetic variability as fixed effects and the EGV as a random effect distributed around the relationship matrix. Three methods of calculating kinship were considered: expected kinship from pedigree relationships, empirical kinship from common variants, and empirical kinship from both rare and common variants. Genome-wide association analysis was conducted on simulated phenotypes and EGVs using the additive measured genotype approach in the SOLAR software package. The EGV-based approach showed only minimal improvement in power to detect causative loci. PMID:25519398

  2. --Guest Editorial --Software Reverse Engineering

    E-print Network

    van Deursen, Arie

    -- Guest Editorial -- Software Reverse Engineering Arie van Deursen a,b Liz Burd c aCWI, P.O. Box, UK Introduction Reverse engineering aims at obtaining high level representations of programs. Reverse just given, source code, architectural views, or use cases, respectively). Reverse engineering methods

  3. The logic of time reversal

    Microsoft Academic Search

    E. J. Post

    1979-01-01

    Active time reversal in the sense of ``object reversal'' and passive time reversal in the sense of a frame reversal of time are discussed separately and then together so as to bring out their dual nature. An understanding of that duality makes it unavoidable to contrast symmetry properties of matter with symmetry properties to be assigned to antimatter. Only frame

  4. The logic of time reversal

    Microsoft Academic Search

    E. J. Post

    1979-01-01

    Active time reversal in the sense of object reversal and passive time reversal in the sense of a frame reversal of time are discussed separately and then together so as to bring out their dual nature. An understanding of that duality makes it unavoidable to contrast symmetry properties of matter with symmetry properties to be assigned to antimatter. Only frame

  5. Reversibly immobilized biological materials in monolayer films on electrodes

    DOEpatents

    Weaver, P.F.; Frank, A.J.

    1993-05-04

    Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

  6. Reversible effects of permeation enhancers on human skin

    Microsoft Academic Search

    L. Kang; A. L. Poh; S. K. Fan; P. C. Ho; Y. W. Chan; S. Y. Chan

    2007-01-01

    This study outlines a systematic approach for investigating a desired characteristic of chemicals used to facilitate the permeation of drugs across the skin that is, the reversibility of the permeation enhancement effect. This implies that the vital skin barrier function is restored and not permanently impaired after the application of these enhancers. The reversible effects of two terpene enhancers, (R)-(?)-carvone

  7. Analysis of Cocoa Proanthocyanidins Using Reversed Phase High-Performance Liquid Chromatography and Electrochemical Detection: Application to Studies on the Effect of Alkaline Processing.

    PubMed

    Stanley, Todd H; Smithson, Andrew T; Neilson, Andrew P; Anantheswaran, Ramaswamy C; Lambert, Joshua D

    2015-07-01

    Flavan-3-ols and proanthocyanidins play a key role in the health beneficial effects of cocoa. Here, we developed a new reversed phased high-performance liquid chromatography-electrochemical detection (HPLC-ECD) method for the analysis of flavan-3-ols and proanthocyanidins of degree of polymerization (DP) 2-7. We used this method to examine the effect of alkalization on polyphenol composition of cocoa powder. Treatment of cocoa powder with NaOH (final pH 8.0) at 92 °C for up to 1 h increased catechin content by 40%, but reduced epicatechin and proanthocyanidins by 23-66%. Proanthocyanidin loss could be modeled using a two-phase exponential decay model (R(2) > 0.7 for epicatchin and proanthocyanidins of odd DP). Alkalization resulted in a significant color change and 20% loss of total polyphenols. The present work demonstrates the first use of HPLC-ECD for the detection of proanthocyanidins up to DP 7 and provides an initial predictive model for the effect of alkali treatment on cocoa polyphenols. PMID:26042917

  8. Synchronized separation of seven medications representing most commonly prescribed antihypertensive classes by using reversed-phase liquid chromatography: Application for analysis in their combined formulations.

    PubMed

    Ebeid, Walid M; Elkady, Ehab F; El-Zaher, Asmaa A; El-Bagary, Ramzia I; Patonay, Gabor

    2014-04-01

    A reversed-phase high-performance liquid chromatography method was developed for the simultaneous determination of the diuretic, hydrochlorothiazide, along with six drugs representing the most commonly prescribed antihypertensive pharmacological classes such as atenolol, a selective ?1 blocker, amlodipine besylate, a calcium channel blocker, moexipril hydrochloride, an angiotensin-converting-enzyme inhibitor, valsartan and candesartan cilexetil, which are angiotensin II receptor blockers, and aliskiren hemifumarate, a renin inhibitor, using irbesartan as an internal standard. The chromatographic separation was achieved using acetonitrile/sodium phosphate dibasic buffer (0.02 M, pH 5.5) at a flow rate of 1 mL/min in gradient elution mode at ambient temperature on a stationary phase composed of an Eclipse XDB-C18 (4.6 × 150 mm, 5 ?m) column. UV detection was carried out at 220 nm. The method was validated according to ICH guidelines. Linearity, accuracy, and precision were satisfactory over the concentration ranges of 2-40 ?g/mL for hydrochlorothiazide and candesartan cilexetil, 20-120, 10-160, 5-40, 20-250, and 5-50 ?g/mL for atenolol, valsartan, moexipril hydrochloride, aliskiren hemifumarate, and amlodipine besylate, respectively. The method was successfully applied for the determination of each of the studied drugs in their combined formulations with hydrochlorothiazide. The developed method is suitable for the quality control and routine analysis of the cited drugs in their pharmaceutical dosage forms. PMID:24482404

  9. Validation and Application of a New Reversed Phase HPLC Method for In Vitro Dissolution Studies of Rabeprazole Sodium in Delayed-Release Tablets

    PubMed Central

    Nawaz, Md. Saddam

    2013-01-01

    The purpose of this study was to develop and validate a new reversed phase high performance liquid chromatographic (RP-HPLC) method to quantify in vitro dissolution assay of rabeprazole sodium in pharmaceutical tablet dosage form. Method development was performed on C 18, 100 × 4.6?mm ID, and 10??m particle size column, and injection volume was 20??L using a diode array detector (DAD) to monitor the detection at 280?nm. The mobile phase consisted of buffer: acetonitrile at a ratio of 60?:?40 (v/v), and the flow rate was maintained at 1.0?mL/min. The method was validated in terms of suitability, linearity, specificity, accuracy, precision, stability, and sensitivity. Linearity was observed over the range of concentration 0.05–12.0??g/mL, and the correlation coefficient was found excellent >0.999. The method was specific with respect to rabeprazole sodium, and the peak purity was found 99.99%. The method was precise and had relative standard deviations (RSD) less than 2%. Accuracy was found in the range of 99.9 to 101.9%. The method was robust in different variable conditions and reproducible. This proposed fast, reliable, cost-effective method can be used as quality control tool for the estimation of rabeprazole sodium in routine dissolution test analysis. PMID:24062966

  10. In Peter Aiken and Elizabeth Burd, editors, Proc. 8th Working Conference on Reverse Engineering. IEEE, Los Alamitos, 2001 Application of UML Associations and Their Adornments in Design Recovery

    E-print Network

    Gogolla, Martin - Fachbereich 3

    In Peter Aiken and Elizabeth Burd, editors, Proc. 8th Working Conference on Reverse Engineering fkollmannjgogollag@informatik.uni­bremen.de Abstract Many CASE tools support reverse engineering and the UML. However advanced features of UML notations are not commonly supported in reverse engineering. In this paper, we

  11. MINI REVIEW TUMOR REVERSION: CORRECTION OF MALIGNANT BEHAVIOR BY

    E-print Network

    Kenny, Paraic

    MINI REVIEW TUMOR REVERSION: CORRECTION OF MALIGNANT BEHAVIOR BY MICROENVIRONMENTAL CUES Paraic A that is intimately linked to, and controlled by, reciprocal signaling between the genetically altered tumor defects can revert tumor cells to a normal phenotype, both in vivo and in culture, even when the tumor

  12. Genetics Home Reference: Genetic Consultation

    MedlinePLUS

    ... Mutations and Health Inheritance Traits Consultation Testing Therapy Human Genome Project Genomic Research Precision Medicine Next Handbook > Genetic Consultation Finding and visiting a genetic counselor or ...

  13. Design of a reversible single precision floating point subtractor.

    PubMed

    Anantha Lakshmi, Av; Sudha, Gf

    2014-01-01

    In recent years, Reversible logic has emerged as a major area of research due to its ability to reduce the power dissipation which is the main requirement in the low power digital circuit design. It has wide applications like low power CMOS design, Nano-technology, Digital signal processing, Communication, DNA computing and Optical computing. Floating-point operations are needed very frequently in nearly all computing disciplines, and studies have shown floating-point addition/subtraction to be the most used floating-point operation. However, few designs exist on efficient reversible BCD subtractors but no work on reversible floating point subtractor. In this paper, it is proposed to present an efficient reversible single precision floating-point subtractor. The proposed design requires reversible designs of an 8-bit and a 24-bit comparator unit, an 8-bit and a 24-bit subtractor, and a normalization unit. For normalization, a 24-bit Reversible Leading Zero Detector and a 24-bit reversible shift register is implemented to shift the mantissas. To realize a reversible 1-bit comparator, in this paper, two new 3x3 reversible gates are proposed The proposed reversible 1-bit comparator is better and optimized in terms of the number of reversible gates used, the number of transistor count and the number of garbage outputs. The proposed work is analysed in terms of number of reversible gates, garbage outputs, constant inputs and quantum costs. Using these modules, an efficient design of a reversible single precision floating point subtractor is proposed. Proposed circuits have been simulated using Modelsim and synthesized using Xilinx Virtex5vlx30tff665-3. The total on-chip power consumed by the proposed 32-bit reversible floating point subtractor is 0.410 W. PMID:24455466

  14. The genetics of the epilepsies.

    PubMed

    El Achkar, Christelle M; Olson, Heather E; Poduri, Annapurna; Pearl, Phillip L

    2015-07-01

    While genetic causes of epilepsy have been hypothesized from the time of Hippocrates, the advent of new genetic technologies has played a tremendous role in elucidating a growing number of specific genetic causes for the epilepsies. This progress has contributed vastly to our recognition of the epilepsies as a diverse group of disorders, the genetic mechanisms of which are heterogeneous. Genotype-phenotype correlation, however, is not always clear. Nonetheless, the developments in genetic diagnosis raise the promise of a future of personalized medicine. Multiple genetic tests are now available, but there is no one test for all possible genetic mutations, and the balance between cost and benefit must be weighed. A genetic diagnosis, however, can provide valuable information regarding comorbidities, prognosis, and even treatment, as well as allow for genetic counseling. In this review, we will discuss the genetic mechanisms of the epilepsies as well as the specifics of particular genetic epilepsy syndromes. We will include an overview of the available genetic testing methods, the application of clinical knowledge into the selection of genetic testing, genotype-phenotype correlations of epileptic disorders, and therapeutic advances as well as a discussion of the importance of genetic counseling. PMID:26008807

  15. A risk prediction algorithm based on family history and common genetic variants: application to prostate cancer with potential clinical impact.

    PubMed

    Macinnis, Robert J; Antoniou, Antonis C; Eeles, Rosalind A; Severi, Gianluca; Al Olama, Ali Amin; McGuffog, Lesley; Kote-Jarai, Zsofia; Guy, Michelle; O'Brien, Lynne T; Hall, Amanda L; Wilkinson, Rosemary A; Sawyer, Emma; Ardern-Jones, Audrey T; Dearnaley, David P; Horwich, Alan; Khoo, Vincent S; Parker, Christopher C; Huddart, Robert A; Van As, Nicholas; McCredie, Margaret R; English, Dallas R; Giles, Graham G; Hopper, John L; Easton, Douglas F

    2011-09-01

    Genome wide association studies have identified several single nucleotide polymorphisms (SNPs) that are independently associated with small increments in risk of prostate cancer, opening up the possibility for using such variants in risk prediction. Using segregation analysis of population-based samples of 4,390 families of prostate cancer patients from the UK and Australia, and assuming all familial aggregation has genetic causes, we previously found that the best model for the genetic susceptibility to prostate cancer was a mixed model of inheritance that included both a recessive major gene component and a polygenic component (P) that represents the effect of a large number of genetic variants each of small effect, where . Based on published studies of 26 SNPs that are currently known to be associated with prostate cancer, we have extended our model to incorporate these SNPs by decomposing the polygenic component into two parts: a polygenic component due to the known susceptibility SNPs, , and the residual polygenic component due to the postulated but as yet unknown genetic variants, . The resulting algorithm can be used for predicting the probability of developing prostate cancer in the future based on both SNP profiles and explicit family history information. This approach can be applied to other diseases for which population-based family data and established risk variants exist. PMID:21769933

  16. A risk prediction algorithm based on family history and common genetic variants: application to prostate cancer with potential clinical impact

    PubMed Central

    MacInnis, Robert J; Antoniou, Antonis C; Eeles, Rosalind A; Severi, Gianluca; Olama, Ali Amin Al; McGuffog, Lesley; Kote-Jarai, Zsofia; Guy, Michelle; O'Brien, Lynne T; Hall, Amanda L; Wilkinson, Rosemary A; Sawyer, Emma; Ardern-Jones, Audrey T; Dearnaley, David P.; Horwich, Alan; Khoo, Vincent S.; Parker, Christopher C.; Huddart, Robert A.; Van As, Nicholas; McCredie, Margaret R; English, Dallas R; Giles, Graham G; Hopper, John L; Easton, Douglas F

    2014-01-01

    Genome Wide Association Studies have identified several Single Nucleotide Polymorphisms (SNPs) that are independently associated with small increments in risk of prostate cancer, opening up the possibility for using such variants in risk prediction. Using segregation analysis of population-based samples of 4390 families of prostate cancer patients from the UK and Australia, and assuming all familial aggregation has genetic causes, we previously found that the best model for the genetic susceptibility to prostate cancer was a mixed model of inheritance that included both a recessive major gene component and a polygenic component (P) that represents the effect of a large number of genetic variants each of small effect, where P?N(0,?P2). Based on published studies of 26 SNPs that are currently known to be associated with prostate cancer, we have extended our model to incorporate these SNPs by decomposing the polygenic component into two parts: a polygenic component due to the known susceptibility SNPs, PK?N(0,?K2), and the residual polygenic component due to the postulated but as yet unknown genetic variants, PU?N(0,?U2). The resulting algorithm can be used for predicting the probability of developing prostate cancer in the future based on both SNP profiles and explicit family history information. This approach can be applied to other diseases for which population-based family data and established risk variants exist. PMID:21769933

  17. Successful application of new cost-effective procedures for genotyping pearl millets for genetic diversity and linkage mapping

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In spite of technology advancement, procedures of DNA extraction and genotyping of large plant populations are cumbersome and expensive. Therefore, in order to genotype large mapping populations for studying genetic diversity, and linkage/QTL mapping for disease and pest resistance in pearl millet (...

  18. Single nucleotide primer extension to detect genetic diseases: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes

    Microsoft Academic Search

    M. N. Kuppuswamy; J. W. Hoffmann; S. G. Spitzer; S. L. Groce; S. P. Bajaj; C. K. Kasper

    1991-01-01

    In this report, the authors describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then

  19. The application of alterable parameter genetic algorithm in optimum firepower distribution for caboodle of air defense force

    Microsoft Academic Search

    Wang Yunfeng; Pan Wei; Diao Huazong; Wang Dezhi

    2011-01-01

    Optimum firepower distribution model for caboodle of air defense force based on genetic algorithm is established by using the battlefield object value and air defense firepower distribution. The model can exert the highest point of firepower unit efficiency of weapon and realize the most damage effect. The steps includes adopting real number to code, creating original community through building chromosome;

  20. APPLICATION OF A PLAN TEST SYSTEM IN THE IDENTIFICATION OF POTENTIAL GENETIC HAZARDS AT CHEMICAL WASTE SITES

    EPA Science Inventory

    We have utilized the Tradescantia micronucleus (Trad-MCN) assay for evaluating genetic hazards at a chemical waste site contaminated with agricultural insecticides scheduled for clean-up under the Superfund program. he chemical analysis of soil samples from the site indicates pre...