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1

TILLING without a plough: a new method with applications for reverse genetics  

E-print Network

TILLING without a plough: a new method with applications for reverse genetics Erin J Gilchrist and George W Haughn TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful reverse genetic. TILLING is currently being used for the detection of both induced and natural variation in several plant

Haughn, George

2

Reverse genetics technology for Rift Valley fever virus: current and future applications for the development of therapeutics and vaccines.  

PubMed

The advent of reverse genetics technology has revolutionized the study of RNA viruses, making it possible to manipulate their genomes and evaluate the effects of these changes on their biology and pathogenesis. The fundamental insights gleaned from reverse genetics-based studies over the last several years provide a new momentum for the development of designed therapies for the control and prevention of these viral pathogens. This review summarizes the successes and stumbling blocks in the development of reverse genetics technologies for Rift Valley fever virus and their application to the further dissection of its pathogenesis and the design of new therapeutics and safe and effective vaccines. PMID:19682499

Bouloy, Michele; Flick, Ramon

2009-11-01

3

Reverse genetics of influenza virus.  

PubMed

Reverse genetics is the creation of a virus from a full-length cDNA copy of the viral genome, referred to as an "infectious clone," and is one of the most powerful genetic tools in modern virology. Since its development in 1999, plasmid-based reverse genetics has been effectively applied to numerous aspects of influenza studies which include revolutionizing the production of seasonal and pandemic influenza vaccine seed strains. Although continual improvement in reverse genetics system is being made in different laboratories for the efficient rescue of the influenza virus, the basic concept of synthesizing viral RNA using RNA polymerase I remains the same. Coupled with in vitro mutagenesis, reverse genetics can be applied widely to accelerate progress in understanding the influenza virus life cycle, the generation of customized vaccine seed strains, development of live-attenuated vaccines, and the use of influenza virus as vaccine and gene delivery vectors. PMID:24899418

Lee, Chang-Won

2014-01-01

4

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

PubMed Central

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

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

2004-01-01

5

Reverse genetics for mammalian reovirus  

Microsoft Academic Search

Mammalian orthoreoviruses (reoviruses) are highly tractable models for studies of viral replication and pathogenesis. The versatility of reovirus as an experimental model has been enhanced by development of a plasmid-based reverse genetics system. Infectious reovirus can be recovered from cells transfected with plasmids encoding cDNAs of each reovirus gene segment using a strategy that does not require helper virus and

Karl W. Boehme; Mine´ Ikizler; Takeshi Kobayashi; Terence S. Dermody

2011-01-01

6

Genetic Programming for Reverse Engineering Mark Harman, William B. Langdon and Westley Weimer  

E-print Network

Genetic Programming for Reverse Engineering Mark Harman, William B. Langdon and Westley Weimer of Genetic Programming (GP) and Genetic Improvement (GI) to reverse engineering. Section II presents that form part of a `GP4RE' research agenda; genetic programming applications for reverse engineering. II

Harman, Mark

7

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

PubMed Central

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

Barkley, N.A; Wang, M.L

2008-01-01

8

Reverse genetics: Its origins and prospects  

SciTech Connect

The nucleotide sequence of a gene and its flanking segments alone will not tell us how its expression is regulated during development and differentiation, or in response to environmental changes. To comprehend the physiological significance of the molecular details requires biological analysis. Recombinant DNA techniques provide a powerful experimental approach. A strategy termed reverse genetics' utilizes the analysis of the activities of mutant and normal genes and experimentally constructed mutants to explore the relationship between gene structure and function thereby helping elucidate the relationship between genotype and phenotype.

Berg, P. (Stanford Univ., CA (United States))

1991-04-01

9

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

Microsoft Academic Search

With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequenc- ing 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

N. A. Barkley; M. L. Wang

2008-01-01

10

Arenavirus reverse genetics for vaccine development  

PubMed Central

Arenaviruses are important human pathogens with no Food and Drug Administration (FDA)-licensed vaccines available and current antiviral therapy being limited to an off-label use of the nucleoside analogue ribavirin of limited prophylactic efficacy. The development of reverse genetics systems represented a major breakthrough in arenavirus research. However, rescue of recombinant arenaviruses using current reverse genetics systems has been restricted to rodent cells. In this study, we describe the rescue of recombinant arenaviruses from human 293T cells and Vero cells, an FDA-approved line for vaccine development. We also describe the generation of novel vectors that mediate synthesis of both negative-sense genome RNA and positive-sense mRNA species of lymphocytic choriomeningitis virus (LCMV) directed by the human RNA polymerases I and II, respectively, within the same plasmid. This approach reduces by half the number of vectors required for arenavirus rescue, which could facilitate virus rescue in cell lines approved for human vaccine production but that cannot be transfected at high efficiencies. We have shown the feasibility of this approach by rescuing both the Old World prototypic arenavirus LCMV and the live-attenuated vaccine Candid#1 strain of the New World arenavirus Junín. Moreover, we show the feasibility of using these novel strategies for efficient rescue of recombinant tri-segmented both LCMV and Candid#1. PMID:23364194

Ortiz-Riano, Emilio; Cheng, Benson Yee Hin; Carlos de la Torre, Juan

2013-01-01

11

Biol Cell . Author manuscript Reverse genetics in eukaryotes  

E-print Network

Biol Cell . Author manuscript Page /1 20 Reverse genetics in eukaryotes Serge Hardy , Vincent Abstract Reverse genetics consists in the modification of the activity and will help decipher gene functions in the post-genome era. MESH Keywords Animals ; Animals, Genetically

Paris-Sud XI, Université de

12

Development and application of a positive-negative selectable marker system for use in reverse genetics in Plasmodium  

Microsoft Academic Search

A limitation of transfection of malaria parasites is the availability of only a low number of positive selectable markers for selection of transformed mutants. This is exacerbated for the rodent parasite Plasmodium berghei as selection of mutants is performed in vivo in laboratory rodents. We here report the development and application of a negative selection system based upon transgenic expression

Joanna A. M. Braks; Blandine Franke-Fayard; Hans Kroeze; Chris J. Janse; Andrew P. Waters

2006-01-01

13

TILLING is an effective reverse genetics technique for Caenorhabditis elegans  

Microsoft Academic Search

BACKGROUND: TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetic technique based on the use of a mismatch-specific enzyme that identifies mutations in a target gene through heteroduplex analysis. We tested this technique in Caenorhabditis elegans, a model organism in which genomics tools have been well developed, but limitations in reverse genetics have restricted the number of heritable

Erin J Gilchrist; Nigel J O'Neil; Ann M Rose; Monique C Zetka; George W Haughn

2006-01-01

14

Towards Reverse Engineering of Genetic Regulatory Networks Zelmina Lubovac  

E-print Network

1 Towards Reverse Engineering of Genetic Regulatory Networks Zelmina Lubovac , Björn Olsson understanding of reverse engineering of regulatory networks. One of the aspects that have not been considered to a great extent in the development of reverse engineering approaches is combinatorial regulation

Chang, Joseph T.

15

Reverse genetics approaches to combat pathogenic arenaviruses  

PubMed Central

Several arenaviruses cause hemorrhagic fever (HF) in humans, and evidence indicates that the worldwide-distributed prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a neglected human pathogen of clinical significance. Moreover, arenaviruses pose a biodefense threat. No licensed anti-arenavirus vaccines are available, and current anti-arenavirus therapy is limited to the use of ribavirin, which is only partially effective and is associated with anemia and other side effects. Therefore, it is important to develop effective vaccines and better antiviral drugs to combat the dual threats of naturally occurring and intentionally introduced arenavirus infections. The development of arenavirus reverse genetic systems is allowing investigators to conduct a detailed molecular characterization of the viral cis-acting signals and trans-acting factors that control each of the steps of the arenavirus life cycle, including RNA synthesis, packaging and budding. Knowledge derived from these studies is uncovering potential novel targets for therapeutic intervention, as well as facilitating the establishment of assays to identify and characterize candidate antiviral drugs capable of interfering with specific steps of the virus life cycle. Likewise, the ability to generate predetermined specific mutations within the arenavirus genome and analyze their phenotypic expression would significantly contribute to the elucidation of arenavirus-host interactions, including the basis of their ability to cause severe HF. This, in turn, could lead to the development of novel, potent and safe arenavirus vaccines. PMID:18782590

de la Torre, Juan C.

2008-01-01

16

Reverse genetics by chemical mutagenesis in Caenorhabditis elegans.  

PubMed

Traditional reverse genetics on yeast, mice and other organisms uses homologous recombination with transgenic DNA to interrupt a target gene. Here we report that target-selected gene inactivation can be be achieved in Caenorhabditis elegans with the use of chemical mutagens. We use PCR to selectively visualize deletions in genes of interest; the method is sensitive enough to permit detection of a single mutant among more than 15,000 wild types. A permanent frozen mutant collection of more than a million mutagenized animals has been established, and deletion mutants of several G-protein genes were isolated from it. The approach is suitable to be scaled up for systematic inactivation of all 17,000 C. elegans genes. Because it requires no transgenesis or cell culturing, it may also be applicable to small organisms usually considered to be outside the realm of reverse genetics (for example, other nematodes and insects). Any sequenced gene in any organism that can be handled in very large numbers can possibly be targeted in this way. PMID:9288111

Jansen, G; Hazendonk, E; Thijssen, K L; Plasterk, R H

1997-09-01

17

Reverse Hillclimbing, Genetic Algorithms and the Busy Beaver Problem  

Microsoft Academic Search

This paper introduces a new analysis tool called {\\\\it reverse hillclimbing}, and demonstrates how it can be used to evaluate the performance of a genetic algorithm. Using reverse hillclimbing, one can calculate the exact probability that hillclimbing will attain some point in a landscape. From this, the expected number of evaluations before the point is found by hillclimbing can be

Terry Jones; Gregory J. E. Rawlins

1993-01-01

18

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling  

E-print Network

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling Jesper contained in the genetic circuit. A natural plan of attack is to use a forward engineering approach, wherebyDynamics and Department of Biomedical Engineering, Boston University, Boston, MA 02215; Division of Computational Biology

Babu, M. Madan

19

Bayesian Networks Applications in Genetics  

E-print Network

Bayesian Networks Applications in Genetics Segregation, IBD and Linkage from the Perspective the Perspective of BNT #12;Bayesian Networks Applications in Genetics Outline 1 Bayesian Networks Model and Notations Belief Propagation Exact Inference 2 Applications in Genetics Segregation IBD Linkage G. NUEL

Nuel, Gregory

20

Reverse HillclimbingGenetic Algorithms and the Busy Beaver Problem  

Microsoft Academic Search

This paper introduces a new analysis tool called reverse hillclimbing, and demonstrateshow it can be used to evaluate the performance of a genetic algorithm. Usingreverse hillclimbing, one can calculate the exact probability that hillclimbing will attainsome point in a landscape. From this, the expected number of evaluations before thepoint is found by hillclimbing can be calculated. This figure can be

Terry Jones; Gregory J. E. Rawlins

1993-01-01

21

NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications  

PubMed Central

Background TILLING (Targeting Induced Local Lesions in Genomes) is a reverse genetics procedure for identifying point mutations in selected gene(s) amplified from a mutagenized population using high-throughput detection platforms such as slab gel electrophoresis, capillary electrophoresis or dHPLC. One essential pre-requisite for TILLING is genomic DNA isolation from a large population for PCR amplification of selected target genes. It also requires multiplexing of genomic DNA isolated from different individuals (pooling) in typically 8-fold pools, for mutation scanning, and to minimize the number of PCR amplifications, which is a strenuous and long-drawn-out work. We describe here a simplified procedure of multiplexing, NEATTILL (Nucleic acid Extraction from Arrayed Tissue for TILLING), which is rapid and equally efficient in assisting mutation detection. Results The NEATTILL procedure was evaluated for the tomato TILLING platform and was found to be simpler and more efficient than previously available methods. The procedure consisted of pooling tissue samples, instead of nucleic acid, from individual plants in 96-well plates, followed by DNA isolation from the arrayed samples by a novel protocol. The three variants of the NEATTILL procedure (vast, in-depth and intermediate) can be applied across various genomes depending upon the population size of the TILLING platform. The 2-D pooling ensures the precise confirmation of the coordinates of the positive mutant line while scanning complementary plates. Choice of tissue for arraying and nucleic acid isolation is discussed in detail with reference to tomato. Conclusion NEATTILL is a convenient procedure that can be applied to all organisms, the genomes of which have been mutagenized and are being scanned for multiple alleles of various genes by TILLING for understanding gene-to-phenotype relationships. It is a time-saving, less labour intensive and reasonably cost-effective method. Tissue arraying can cut costs by up to 90% and minimizes the risk of exposing the DNA to nucleases. Before arraying, different tissues should be evaluated for DNA quality, as the case study in tomato showed that cotyledons rather than leaves are better suited for DNA isolation. The protocol described here for nucleic acid isolation can be generally adapted for large-scale projects such as insertional mutagenesis, transgenic confirmation, mapping and fingerprinting which require isolation of DNA from large populations. PMID:20181012

2010-01-01

22

An improved reverse genetics system for mammalian orthoreoviruses  

Microsoft Academic Search

Mammalian orthoreoviruses (reoviruses) are highly useful models for studies of double-stranded RNA virus replication and pathogenesis. We previously developed a strategy to recover prototype reovirus strain T3D from cloned cDNAs transfected into murine L929 fibroblast cells. Here, we report the development of a second-generation reovirus reverse genetics system featuring several major improvements: (1) the capacity to rescue prototype reovirus strain

Takeshi Kobayashi; Laura S. Ooms; Mine Ikizler; James D. Chappell; Terence S. Dermody

2010-01-01

23

Feline Genetics: Clinical Applications and Genetic Testing  

PubMed Central

DNA testing for domestic cat diseases and appearance traits is a rapidly growing asset for veterinary medicine. Approximately thirty-three genes contain fifty mutations that cause feline health problems or alterations in the cat’s appearance. A variety of commercial laboratories can now perform cat genetic diagnostics, allowing both the veterinary clinician and the private owner to obtain DNA test results. DNA is easily obtained from a cat via a buccal swab using a standard cotton bud or cytological brush, allowing DNA samples to be easily sent to any laboratory in the world. The DNA test results identify carriers of the traits, predict the incidence of traits from breeding programs, and influence medical prognoses and treatments. An overall goal of identifying these genetic mutations is the correction of the defect via gene therapies and designer drug therapies. Thus, genetic testing is an effective preventative medicine and a potential ultimate cure. However, genetic diagnostic tests may still be novel for many veterinary practitioners and their application in the clinical setting needs to have the same scrutiny as any other diagnostic procedure. This article will review the genetic tests for the domestic cat, potential sources of error for genetic testing, and the pros and cons of DNA results in veterinary medicine. Highlighted are genetic tests specific to the individual cat, which are a part of the cat’s internal genome. PMID:21147473

Lyons, Leslie A.

2010-01-01

24

The application of reverse genetics technology in the study of rabies virus (RV) pathogenesis and for the development of novel RV vaccines  

Microsoft Academic Search

Rabies is a central nervous system (CNS) disease that is almost invariably fatal. Neurotropism, neuroinvasiveness, and transsynaptic\\u000a spread are the main features that determine the pathogenesis of rabies. Recent advances in rabies virus (RV) research, which\\u000a made direct genetic manipulations of the RV genome possible, greatly improved the understanding of the role of different viral\\u000a and host cell factors in

Matthias J. Schnell; Gene S. Tan; Bernhard Dietzschold

2005-01-01

25

Chloroquine Susceptibility and Reversibility in a Plasmodium falciparum Genetic Cross  

PubMed Central

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

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

26

REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING  

E-print Network

REVERSE ENGINEERING OF METABOLIC PATHWAYS FROM OBSERVED DATA USING GENETIC PROGRAMMING John R. Koza Biomedical Informatics, Department of Medicine Department of Electrical Engineering Stanford University, Stanford, California, koza@stanford.edu William Mydlowec Genetic Programming Inc., Los Altos, California

Fernandez, Thomas

27

REVERSE ENGINEERING BY MEANS OF GENETIC PROGRAMMING OF METABOLIC PATHWAYS FROM OBSERVED DATA  

E-print Network

REVERSE ENGINEERING BY MEANS OF GENETIC PROGRAMMING OF METABOLIC PATHWAYS FROM OBSERVED DATA John R, to automatically reverse engineer the network from the data. Genetic programming (Koza, Bennett, Andre, and Keane. Koza Biomedical Informatics, Department of Medicine Department of Electrical Engineering Stanford

Fernandez, Thomas

28

Reverse genetics plasmid for cloning unstable Influenza A virus gene segments  

Microsoft Academic Search

Reverse genetics approaches that enable the generation of recombinant influenza A viruses entirely from plasmids are invaluable for studies on virus replication, morphogenesis, pathogenesis, or transmission. Furthermore, influenza virus reverse genetics is now critical for the development of new vaccines for this human and animal pathogen. Periodically, influenza gene segments are unstable within plasmids in bacteria. The PB2 gene segment

Bin Zhou; Greta Jerzak; Derek T. Scholes; Matthew E. Donnelly; Yan Li; David E. Wentworth

2011-01-01

29

Genetic algorithms and their applications  

Microsoft Academic Search

This article introduces the genetic algorithm (GA) as an emerging optimization algorithm for signal processing. After a discussion of traditional optimization techniques, it reviews the fundamental operations of a simple GA and discusses procedures to improve its functionality. The properties of the GA that relate to signal processing are summarized, and a number of applications, such as IIR adaptive filtering,

K. S. Tang; K. F. Man; S. Kwong; Q. He

1996-01-01

30

Live vaccines for human metapneumovirus designed by reverse genetics.  

PubMed

Human metapneumovirus (HMPV) was first described in 2001 and has quickly become recognized as an important cause of respiratory tract disease worldwide, especially in the pediatric population. A vaccine against HMPV is required to prevent severe disease associated with infection in infancy. The primary strategy is to develop a live-attenuated virus for intranasal immunization, which is particularly well suited against a respiratory virus. Reverse genetics provides a means of developing highly characterized 'designer' attenuated vaccine candidates. To date, several promising vaccine candidates have been developed, each using a different mode of attenuation. One candidate involves deletion of the G glycoprotein, providing attenuation that is probably based on reduced efficiency of attachment. A second candidate involves deletion of the M2-2 protein, which participates in regulating RNA synthesis and whose deletion has the advantageous property of upregulating transcription and increasing antigen synthesis. A third candidate involves replacing the P protein gene of HMPV with its counterpart from the related avian metapneumovirus, thereby introducing attenuation owing to its chimeric nature and host range restriction. Another live vaccine strategy involves using an attenuated parainfluenza virus as a vector to express HMPV protective antigens, providing a bivalent pediatric vaccine. Additional modifications to provide improved vaccines will also be discussed. PMID:17181442

Buchholz, Ursula J; Nagashima, Kunio; Murphy, Brian R; Collins, Peter L

2006-10-01

31

Reversible Hydrogels from Self-Assembling Genetically Engineered Protein Block Copolymers  

E-print Network

Reversible Hydrogels from Self-Assembling Genetically Engineered Protein Block Copolymers Chunyu Xu-soluble polyelectrolyte segment flanked by two coiled-coil domains was synthesized by genetic engineering methods antibodies that can form complexes with antigens,20 and genetically engineered proteins containing coiled

Breedveld, Victor

32

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

E-print Network

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 strongly on females. Here, we use a DNA-based study of parentage in the Gulf pipe¢sh Syngnathus scovelli

Avise, John

33

Methods for reverse genetic screening in zebrafish by resequencing and TILLING  

Microsoft Academic Search

Animal models provide an in vivo system to study gene function by transgenic and knockout approaches. Targeted knockout approaches have been very successful in mice, but are currently not feasible in zebrafish due to the inability to grow embryonic stem cells. As an alternative, a reverse genetic approach that utilizes screening by resequencing and\\/or TILLING (Targeting Induced Local Lesions INGenomes)

Raman Sood; Milton A. English; MaryPat Jones; James Mullikin; Duen-Mei Wang; Maria Anderson; Dongying Wu; Settara C. Chandrasekharappa; Jun Yu; Jinghui Zhang; P. Paul Liu

2006-01-01

34

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

PubMed Central

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

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

35

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

Microsoft Academic Search

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

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

2003-01-01

36

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 and indirect job losses among communities near aquaculture operations. The goal of this project was to develop a reverse genetics system for ISAV to construct live viral particles from plasmid DNA molecules

37

APPLICATION OF REVERSE ENGINEERING FOR DEVELOPMENT OF SURFACES OUTPOSTS  

Microsoft Academic Search

Reverse Engineering (RE) is a rapidly evolving discipline, which covers a multitude of activities. The objective of the RE is to obtain data from an product of public access, with the purpose of determining of what it is done, what makes work and how it was made. Within the most outstanding applications of the RE they are possible to mention

Víctor APERRIBAY; Iñaki MARTIN; José Javier; SAN MARTÍN; José Ignacio

38

Biological applications of expanded genetic codes.  

PubMed

Substantial efforts in the past decade have resulted in the systematic expansion of genetic codes, allowing for the direct ribosomal incorporation of ?100 unnatural amino acids into bacteria, yeast, mammalian cells, and animals. Here, we illustrate the versatility of expanded genetic codes in biology and bioengineering, focusing on the application of expanded genetic codes to problems in protein, cell, synthetic, and experimental evolutionary biology. As the expanded genetic code field continues to develop, its place as a foundational technology in the whole of biological sciences will solidify. PMID:25171489

Li, Xiang; Liu, Chang C

2014-11-01

39

Imaging-Genetics Applications in Child Psychiatry  

PubMed Central

Objective To place imaging–genetics research in the context of child psychiatry. Method A conceptual overview is provided, followed by discussion of specific research examples. Results Imaging–genetics research is described linking brain function to two specific genes, for the serotonin-reuptake-transporter protein and a monoamine oxidase enzyme. Work is then described on phenotype selection in imaging genetics. Conclusions Child psychiatry applications of imaging genetics are only beginning to emerge. The approach holds promise for advancing understandings of pathophysiology and therapeutics. PMID:20643311

Pine, Daniel S.; Ernst, Monique; Leibenluft, Ellen

2010-01-01

40

Genetically modified industrial yeast ready for application.  

PubMed

Tremendous progress in the genetic engineering of yeast had been achieved at the end of 20th century, including the complete genome sequence, genome-wide gene expression profiling, and whole gene disruption strains. Nevertheless, genetically modified (GM) baking, brewing, wine, and sake yeasts have not, as yet, been used commercially, although numerous industrial recombinant yeasts have been constructed. The recent progress of genetic engineering for the construction of GM yeast is reviewed and possible requirements for their application are discussed. 'Self-cloning' yeast will be the most likely candidate for the first commercial application of GM microorganisms in food and beverage industries. PMID:16233347

Akada, Rinji

2002-01-01

41

Reveal, a general reverse engineering algorithm for inference of genetic network architectures.  

PubMed

Given the immanent gene expression mapping covering whole genomes during development, health and disease, we seek computational methods to maximize functional inference from such large data sets. Is it possible, in principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables? We investigated this possibility using binary models of genetic networks. Trajectories, or state transition tables of Boolean nets, resemble time series of gene expression. By systematically analyzing the mutual information between input states and output states, one is able to infer the sets of input elements controlling each element or gene in the network. This process is unequivocal and exact for complete state transition tables. We implemented this REVerse Engineering ALgorithm (REVEAL) in a C program, and found the problem to be tractable within the conditions tested so far. For n = 50 (elements) and k = 3 (inputs per element), the analysis of incomplete state transition tables (100 state transition pairs out of a possible 10(15)) reliably produced the original rule and wiring sets. While this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi-state models, essentially allowing direct application to realistic biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields. PMID:9697168

Liang, S; Fuhrman, S; Somogyi, R

1998-01-01

42

Prospects for fusion applications of reversed-field pinches  

SciTech Connect

The applicability of the Reversed-Field Pinch (RFP) as a source of fusion neutrons for use in developing key fusion nuclear technologies is examined. This Fusion Test Facility (FTF) would emphasize high neutron wall loading, small plasma volume, low fusion and driver powers, and steady-state operation. Both parametric tradeoffs based on present-day physics understanding and a conceptual design based on an approx.1-MW/mS (neutron) driven operation are reported. 10 refs.

Bathke, C.G.; Krakowski, R.A.; Hagenson, R.L.

1985-01-01

43

Repository of Eurasian influenza A virus hemagglutinin and neuraminidase reverse genetics vectors and recombinant viruses.  

PubMed

Reverse genetics can be used to produce recombinant influenza A viruses containing virtually every desired combination of hemagglutinin (HA) and neuraminidase (NA) genes using the virus backbone of choice. Here, a repository of plasmids and recombinant viruses representing all contemporary Eurasian HA and NA subtypes, H1-H16 and N1-N9, was established. HA and NA genes were selected based on sequence analyses of influenza virus genes available from public databases. Prototype Eurasian HA and NA genes were cloned in bidirectional reverse genetics plasmids. Recombinant viruses based on the virus backbone of A/PR/8/34, and containing a variety of HA and NA genes were produced in 293T cells. Virus stocks were produced in MDCK cells and embryonated chicken eggs. These plasmids and viruses may be useful for numerous purposes, including influenza virus research projects, vaccination studies, and to serve as reference reagents in diagnostic settings. PMID:20600474

Keawcharoen, J; Spronken, M I J; Vuong, O; Bestebroer, T M; Munster, V J; Osterhaus, A D M E; Rimmelzwaan, G F; Fouchier, R A M

2010-08-16

44

Molecular modeling, organ culture and reverse genetics for a newly identified human rhinovirus C  

Microsoft Academic Search

A recently recognized human rhinovirus species C (HRV-C) is associated with up to half of HRV infections in young children. Here we propagated two HRV-C isolates ex vivo in organ culture of nasal epithelial cells, sequenced a new C15 isolate and developed the first, to our knowledge, reverse genetics system for HRV-C. Using contact points for the known HRV receptors,

Ann C Palmenberg; Wai-Ming Lee; Jennifer A Rathe; Svetlana P Amineva; Xin Sun; Thomas R Pasic; Nizar N Jarjour; Stephen B Liggett; James E Gern; Yury A Bochkov

2011-01-01

45

Development of a reverse genetics system for a human rabies virus vaccine strain employed in China  

Microsoft Academic Search

The CTN rabies virus was isolated from a human in China in 1953 and subsequently attenuated by multiple passaging to a vaccine strain now approved by the WHO. In this study, we describe the development of a reverse genetics system for the CTN rabies virus strain. The recombinant full-length genomic cDNA was flanked by a hammerhead ribozyme (HamRz) and the

Ying Huang; Qing Tang; Susan A. Nadin-Davis; Shoufeng Zhang; Craig D. Hooper; Pinggang Ming; Jialiang Du; Xiaoyan Tao; Rongliang Hu; Guodong Liang

2010-01-01

46

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

Microsoft Academic Search

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

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

1999-01-01

47

Genetic engineering applications in animal breeding  

Microsoft Academic Search

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,

Hugo H. Montaldo

2006-01-01

48

[Applications of genetically modified animals].  

PubMed

The first transgenic animals, mice, were obtained in 1980. The techniques of gene transfer had to be adapted to obtain transgenic animals with an acceptable yield in about fifteen species. When the yield is low (low rate of random integration and targeted integration via homologous recombination), genetic modifications must be achieved in intermediate cells able to participate to the development of chimeric transgenic animals (ES cells, EG cells, iPS obtained by the dedifferentiation of somatic cells) or in somatic cells used as nuclear donor to generate transgenic clones. Various tools make possible a marked increase of homologous recombination efficiency (meganucleases and ZFN), or a gene inactivation at the genome level (direct or conditional knock out) or at the mRNA level (interfering RNAs). Vectors allow a more reliable transgene expression. Genetically modified animals are used mainly to obtain information on biological functions and human diseases. Transgenic animals produce recombinant pharmaceutical proteins in milk and soon in egg white. Pig organs adapted to be tolerated by patients might be tested in humans in five years. The projects based on the use of transgenesis to improve animal production are presently few. Transgenic salmon with accelerated growth might be on the market when their possible escape in oceans will be controlled. PMID:20122391

Houdebine, Louis-Marie

2009-01-01

49

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

PubMed

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

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

2014-03-01

50

Mobile Timekeeping Application Built on Reverse-Engineered JPL Infrastructure  

NASA Technical Reports Server (NTRS)

Every year, non-exempt employees cumulatively waste over one man-year tracking their time and using the timekeeping Web page to save those times. This app eliminates this waste. The innovation is a native iPhone app. Libraries were built around a reverse- engineered JPL API. It represents a punch-in/punch-out paradigm for timekeeping. It is accessible natively via iPhones, and features ease of access. Any non-exempt employee can natively punch in and out, as well as save and view their JPL timecard. This app is built on custom libraries created by reverse-engineering the standard timekeeping application. Communication is through custom libraries that re-route traffic through BrowserRAS (remote access service). This has value at any center where employees track their time.

Witoff, Robert J.

2013-01-01

51

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

PubMed Central

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

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

2013-01-01

52

Applications of Genetic Programming to Building Decision Cezary Z Janikow  

E-print Network

Applications of Genetic Programming to Building Decision Trees Cezary Z Janikow Dept Programming, Constrained Genetic Programming, Decision Trees, Classification, Data Mining Conference GEM11 effective. Genetic Programming methods have also been used to generate decision trees. In this case, which

He, Wenjie

53

Introduction to Genetic Engineering and Its Applications  

NSDL National Science Digital Library

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.

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

54

Statistical Applications in Genetics and Molecular Biology  

E-print Network

.gilks@mrc-bsu.cam.ac.uk Medical Research Council Laboratory of Molecular Biology, madanm@mrc-lmb.cam.ac.uk Medical ResearchStatistical Applications in Genetics and Molecular Biology Volume 5, Issue 1 2006 Article 5 Walter R. Gilks M. Madan Babu Sarah Teichmann Medical Research Council Biostatistics Unit, thomas

Babu, M. Madan

55

Increased Genetic and Phenotypic Stability of a Promising Live-Attenuated Respiratory Syncytial Virus Vaccine Candidate by Reverse Genetics  

PubMed Central

Human respiratory syncytial virus (RSV) is the most important viral cause of serious pediatric respiratory illness worldwide. Currently, the most promising live-attenuated vaccine candidate is a temperature-sensitive (ts) cDNA-derived virus named rA2cp248/404/1030?SH, in reference to its set of attenuating mutations. In a previous clinical study, more than one-third of postvaccination nasal wash isolates exhibited partial loss of the ts phenotype. Most of this instability appeared to be due to reversion at a missense point mutation called 1030. This 1030 mutation is a single-nucleotide tyrosine-to-asparagine substitution at position 1321 (Y1321N) of the polymerase L protein that contributes to the ts and attenuation phenotypes of the vaccine candidate. The goals of the present study were to identify a reversion-resistant codon at position 1321 conferring a comparable level of attenuation and to use this to develop a genetically stable version of the vaccine virus. We modified wild-type (wt) RSV to insert each of the 20 possible amino acids at position 1321; 19 viruses were recoverable. We also investigated small deletions at or near this position, but these viruses were not recoverable. Phenotypic analysis identified alternative attenuating amino acids for position 1321. Several of these amino acids were predicted, based on the genetic code, to be refractory to deattenuation. Classical genetics, using temperature stress tests in vitro combined with nucleotide sequencing, confirmed this stability but identified a second site with a compensatory mutation at position 1313. It was possible to stabilize the 1313 site as well, providing a stable 1030 mutation. Further stress tests identified additional incidental mutations, but these did not reverse the ts/attenuation phenotype. An improved version of the vaccine candidate virus was constructed and validated in vitro by temperature stress tests and in vivo by evaluation of attenuation in seronegative chimpanzees. In addition to developing an improved version of this promising live-attenuated RSV vaccine candidate, this study demonstrated the propensity of an RNA virus to escape from attenuation but also showed that, through systematic analysis, genetics can be used to cut off the routes of escape. PMID:22837193

Luongo, Cindy; Winter, Christine C.; Collins, Peter L.

2012-01-01

56

Natural genetic variation of Xanthomonas campestris pv. campestris pathogenicity on arabidopsis revealed by association and reverse genetics.  

PubMed

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. IMPORTANCE The identification and understanding of the genetic determinants of bacterial virulence are essential to be able to design efficient protection strategies for infected plants. The recent availability of genomic resources for a limited number of pathogen isolates and host genotypes has strongly biased our research toward genotype-specific approaches. Indeed, these do not consider the natural variation in both pathogens and hosts, so their applied relevance should be challenged. In our study, we exploited the genetic diversity of Xanthomonas campestris pv. campestris, the causal agent of black rot on Brassicaceae (e.g., cabbage), to mine for pathogenicity determinants. This work evidenced the contribution of known and unknown loci to pathogenicity relevant at the pathovar level and identified these virulence determinants as prime targets for breeding resistance to X. campestris pv. campestris in Brassicaceae. PMID:23736288

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

57

Identification of host genes involved in geminivirus infection using a reverse genetics approach.  

PubMed

Geminiviruses, like all viruses, rely on the host cell machinery to establish a successful infection, but the identity and function of these required host proteins remain largely unknown. Tomato yellow leaf curl Sardinia virus (TYLCSV), a monopartite geminivirus, is one of the causal agents of the devastating Tomato yellow leaf curl disease (TYLCD). The transgenic 2IRGFP N. benthamiana plants, used in combination with Virus Induced Gene Silencing (VIGS), entail an important potential as a tool in reverse genetics studies to identify host factors involved in TYLCSV infection. Using these transgenic plants, we have made an accurate description of the evolution of TYLCSV replication in the host in both space and time. Moreover, we have determined that TYLCSV and Tobacco rattle virus (TRV) do not dramatically influence each other when co-infected in N. benthamiana, what makes the use of TRV-induced gene silencing in combination with TYLCSV for reverse genetic studies feasible. Finally, we have tested the effect of silencing candidate host genes on TYLCSV infection, identifying eighteen genes potentially involved in this process, fifteen of which had never been implicated in geminiviral infections before. Seven of the analyzed genes have a potential anti-viral effect, whereas the expression of the other eleven is required for a full infection. Interestingly, almost half of the genes altering TYLCSV infection play a role in postranslational modifications. Therefore, our results provide new insights into the molecular mechanisms underlying geminivirus infections, and at the same time reveal the 2IRGFP/VIGS system as a powerful tool for functional reverse genetics studies. PMID:21818318

Lozano-Durán, Rosa; Rosas-Díaz, Tábata; Luna, Ana P; Bejarano, Eduardo R

2011-01-01

58

Establishment of a reverse genetics system for Schmallenberg virus, a newly emerged orthobunyavirus in Europe  

PubMed Central

Schmallenberg virus (SBV) is a newly emerged orthobunyavirus that has caused widespread disease in cattle, sheep and goats in Europe. Like other orthobunyaviruses, SBV is characterized by a tripartite negative-sense RNA genome that encodes four structural and two non-structural proteins. This study showed that SBV has a wide in vitro host range, and that BHK-21 cells are a convenient host for both SBV propagation and assay by plaque titration. The SBV genome segments were cloned as cDNA and a three-plasmid rescue system was established to recover infectious virus. Recombinant virus behaved similarly in cell culture to authentic virus. The ORF for the non-structural NSs protein, encoded on the smallest genome segment, was disrupted by introduction of translation stop codons in the appropriate cDNA, and when this plasmid was used in reverse genetics, a recombinant virus that lacked NSs expression was recovered. This virus had reduced capacity to shut-off host-cell protein synthesis compared with the wild-type virus. In addition, the NSs-deleted virus induced interferon (IFN) in cells, indicating that, like other orthobunyaviruses, NSs functions as an IFN antagonist, most probably by globally inhibiting host-cell metabolism. The development of a robust reverse genetics system for SBV will facilitate investigation of its pathogenic mechanisms as well as the creation of attenuated strains that could be candidate vaccines. PMID:23255627

Blakqori, Gjon; van Knippenberg, Ingeborg C.; Koudriakova, Elina; Li, Ping; McLees, Angela; Shi, Xiaohong; Szemiel, Agnieszka M.

2013-01-01

59

A Stabilized Respiratory Syncytial Virus Reverse Genetics System Amenable to Recombination Mediated Mutagenesis  

PubMed Central

We describe the first example of combining bacterial artificial chromosome (BAC) recombination-mediated mutagenesis with reverse genetics for a negative strand RNA virus. A BAC-based respiratory syncytial virus (RSV) rescue system was established. An important advantage of this system is that RSV antigenomic cDNA was stabilized in the BAC vector. The RSV genotype chosen was A2-line19F, a chimeric strain previously shown to recapitulate in mice key features of RSV pathogenesis. We recovered two RSV reporter viruses, one expressing the red fluorescent protein monomeric Katushka 2 (A2-K-line19F) and one expressing Renilla luciferase (A2-RL-line19F). As proof of principle, we efficiently generated a RSV gene deletion mutant (A2-line19F?NS1/NS2) and a point mutant (A2-K-line19F-I557V) by recombination-mediated BAC mutagenesis. Together with sequence-optimized helper expression plasmids, BAC-RSV is a stable, versatile, and efficient reverse genetics platform for generation of a recombinant Pneumovirus. PMID:23062737

Hotard, Anne L.; Shaikh, Fyza Y.; Lee, Sujin; Yan, Dan; Teng, Michael N.; Plemper, Richard K.; Crowe, James E.; Moore, Martin L.

2012-01-01

60

Applications of Time-Reversal Processing for Planetary Surface Communications  

NASA Technical Reports Server (NTRS)

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

Barton, Richard J.

2007-01-01

61

Delay of the reverse pedicled venous island flap: clinical applications.  

PubMed

In patients with hand or foot injuries, the delay procedure of the reverse pedicled venous flap was applied, including the loose areolar tissue around the pedicle vein. As preliminary clinical observations, five patients were treated with delay and the results compared with those of four patients without delay. The delay procedures were two types: type 1 was circumferential incision with ligature of the proximal vein, and type 2 was a bipedicled flap without ligature of the pedicle vein. Two weeks later, the flap was transferred to the defect. In the patients treated without delay, the maximum limit of the perfectly survived flap sizes was 4.0 × 2.0 cm. However, in the patients treated with delay, the perfectly survived sizes were 5.0 × 3.0 cm and 10 × 4.0 cm in type 1 delay and 12 × 5.0 cm in type 2 delay. The delay procedure appeared to stabilise the reverse pedicled venous flap and to expand its clinical applications. PMID:23710795

Ueda, Koichi; Nuri, Takashi; Akamatsu, Jun; Sugita, Naoya; Otani, Kazuhiro; Yamada, Akira

2013-10-01

62

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

NASA Astrophysics Data System (ADS)

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.

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

63

Application of Genetic Algorithms in Seismic Tomography  

NASA Astrophysics Data System (ADS)

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.

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

2010-05-01

64

DEVELOPMENT OF NONLINEAR TIME REVERSED ACOUSTICS (NLTRA) FOR APPLICATIONS TO CRACK DETECTION IN SOLIDS  

E-print Network

DEVELOPMENT OF NONLINEAR TIME REVERSED ACOUSTICS (NLTRA) FOR APPLICATIONS TO CRACK DETECTION of Nondestructive Evaluation (NDE) exhibit extremely high sensitivity to the presence of cracks. Time Reverse. These are the first measurements we are aware of combining elastic nonlinearity and time reversal in solids

65

The Application of Reverse Genetics to Polyploid Plant Species  

Microsoft Academic Search

Polyploidy events (polyploidization) followed by progressive loss of redundant genome components are a major feature of plant evolution, with new evidence suggesting that all flowering plants possess ancestral genome duplications. Furthermore, many of our most important crop plants have undergone additional, relatively recent, genome duplication events. Recent advances in DNA sequencing have made vast amounts of new genomic data available

Timothy L. Fitzgerald; Kemal Kazan; John M. Manners

2012-01-01

66

Arenavirus Reverse Genetics: New Approaches for the Investigation of Arenavirus Biology and Development of Antiviral Strategies  

PubMed Central

Several arenaviruses, chiefly Lassa virus, cause hemorrhagic fever disease in humans and pose a significant public health problem in their endemic regions. On the other hand the prototypic arenavirus LCMV is a superb workhorse for the investigation of virus-host interactions and associated disease. The development of novel antiviral strategies to combat pathogenic arenaviruses would be facilitated by a detailed understanding of the arenavirus molecular and cell biology. To this end, the development of reverse genetics systems for several arenaviruses has provided investigators with novel and powerful approaches to dissect the functions of arenavirus proteins and their interactions with host factors required to complete each of the steps of the virus life cycle, as well as to cause disease. PMID:21324503

Emonet, Sebastien E.; Urata, Shuzo; de la Torre, Juan C.

2011-01-01

67

Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120.  

PubMed

Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. Thirteen 1.5-2.8 kb fragments contiguously spanning the virus genome were amplified and cloned into pMD19-T. Transcription grade complete length cDNA was acquired by a modified "No See'm" ligation strategy, which employed restriction enzyme Bsa I and BsmB I and ligated more than two fragments in one T4 ligase reaction. The full-length genomic cDNA was transcribed and its transcript was transfected by electroporation into BHK-21 together with the transcript of nucleocapsid gene. At 48 h post transfection, the medium to culture the transfected BHK-21 cells was harvested and inoculated into 10-days old SPF embryonated chicken eggs (ECE) to replicate the rescued virus. After passage of the virus in ECE five times, the rescued H120 virus (R-H120) was successfully recovered. R-H120 was subsequently identified to possess the introduced silent mutation site in its genome. Some biological characteristics of R-H120 such as growth curve, EID50 and HA titers, were tested and all of them were very similar to its parent strain H120. In addition, both R-H120 and H120 induced a comparable titer of HA inhibition (HI) antibody in immunized chickens and also provided up to 85% of immune protection to the chickens that were challenged with Mass41 IBV strain. The present study demonstrated that construction of infectious clone from IBV vaccine strain H120 is possible and IBV-H120 can be use as a vaccine vector for the development of novel vaccines through molecular recombination and the modified reverse genetics approach. PMID:22999521

Zhou, Ying Shun; Zhang, Yi; Wang, Hong Ning; Fan, Wen Qiao; Yang, Xin; Zhang, An Yun; Zeng, Fan Ya; Zhang, Zhi Kun; Cao, Hai Peng; Zeng, Cheng

2013-02-22

68

Convexity of reverse coherent information capacity and its application  

NASA Astrophysics Data System (ADS)

Reverse coherent information, as a symmetric counterpart of the coherent information, has been firstly defined by R. García-Patrón et al. This quantity allows to define reverse coherent information capacity which is additive. In this Letter, we prove the convexity of such capacity for a general quantum channel, and investigate the effect of convex decomposition of quantum channel on its (reverse) coherent information. Finally, we apply the convexity property to provide an upper bound on the reverse coherent information capacity for some important channels.

Wang, MinJie; Pan, Wei

2011-07-01

69

Genetically modified plants for tactical systems applications  

NASA Astrophysics Data System (ADS)

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.

Stewart, C. Neal, Jr.

2002-08-01

70

A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia.  

PubMed

Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes. PMID:24554834

Berenschot, Amanda S; Quecini, Vera

2014-01-01

71

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

PubMed Central

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

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

2014-01-01

72

Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes  

PubMed Central

Liu et al. recently described a group of related temperate bacteriophages that infect Bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (Liu et al., Science 295: 2091-2094, 2002). Tropism switching results from the introduction of single nucleotide substitutions at defined locations in the VR1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria. In this report, we describe the complete nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA genomes of three related phage isolates and characterize two additional regions of variability. Forty-nine coding sequences were identified. Of these coding sequences, bbp36 contained VR2 (variable region 2), which is highly dynamic and consists of a variable number of identical 19-bp repeats separated by one of three 5-bp spacers, and bpm encodes a DNA adenine methylase with unusual site specificity and a homopolymer tract that functions as a hotspot for frameshift mutations. Morphological and sequence analysis suggests that these Bordetella phage are genetic hybrids of P22 and T7 family genomes, lending further support to the idea that regions encoding protein domains, single genes, or blocks of genes are readily exchanged between bacterial and phage genomes. Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection. PMID:14973019

Liu, Minghsun; Gingery, Mari; Doulatov, Sergei R.; Liu, Yichin; Hodes, Asher; Baker, Stephen; Davis, Paul; Simmonds, Mark; Churcher, Carol; Mungall, Karen; Quail, Michael A.; Preston, Andrew; Harvill, Eric T.; Maskell, Duncan J.; Eiserling, Frederick A.; Parkhill, Julian; Miller, Jeff F.

2004-01-01

73

New Generation Live Vaccines against Human Respiratory Syncytial Virus Designed by Reverse Genetics  

PubMed Central

Development of a live pediatric vaccine against human respiratory syncytial virus (RSV) is complicated by the need to immunize young infants and the difficulty in balancing attenuation and immunogenicity. The ability to introduce desired mutations into infectious virus by reverse genetics provides a method for identifying and designing highly defined attenuating mutations. These can be introduced in combinations as desired to achieve gradations of attenuation. Attenuation is based on several strategies: multiple independent temperature-sensitive point mutations in the polymerase, a temperature-sensitive point mutation in a transcription signal, a set of non–temperature-sensitive mutations involving several genes, deletion of a viral RNA synthesis regulatory protein, and deletion of viral IFN ?/? antagonists. The genetic stability of the live vaccine can be increased by judicious choice of mutations. The virus also can be engineered to increase the level of expression of the protective antigens. Protective antigens from antigenically distinct RSV strains can be added or swapped to increase the breadth of coverage. Alternatively, the major RSV protective antigens can be expressed from transcription units added to an attenuated parainfluenza vaccine virus, making a bivalent vaccine. This would obviate the difficulties inherent in the fragility and inefficient in vitro growth of RSV, simplifying vaccine design and use. PMID:16113487

Collins, Peter L.; Murphy, Brian R.

2005-01-01

74

Applications for the 2014 Kenyon Award Each year, the Department of Genetics recognizes a graduating Genetics major with the  

E-print Network

of Genetics recognizes a graduating Genetics major with the Cynthia Kenyon Outstanding on a plaque that hangs in the Genetics office. This year students are invited. The applications will be reviewed by the Undergraduate Affairs Committee of the Genetics

Arnold, Jonathan

75

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

Microsoft Academic Search

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

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

2002-01-01

76

Hybrid genetic algorithm research and its application in problem optimization  

Microsoft Academic Search

There is a lot of research in genetic algorithm about structural optimization. But as far as the large multi-goal program is concerned, it limits the application of genetic algorithm for the reason of its specialty and large calculation. In order to explore a new resolution, the author proposed a combining algorithm for structural optimization, which is based on genetic algorithm

Weijin Jiang I; Dingti Luol; Yusheng Xu; Xingming Sun

2004-01-01

77

INTERNAL/INTRACAMPUS TRANSFER APPLICATION NCSU Department of Genetics  

E-print Network

INTERNAL/INTRACAMPUS TRANSFER APPLICATION NCSU Department of Genetics If you are currently a student at NCSU and wish to transfer into the Department of Genetics, complete this form and submit deadlines are listed at http://genetics.ncsu.edu/undergrad. Students will be notified of the admission

Langerhans, Brian

78

Application of Genetic Programming to Induction of Linear Classification Trees  

E-print Network

an optimal decision tree for a given dataset is NP­complete. Genetic programming (GP) [5] is used as a stochastic search technique for find­ ing accurate decision trees. Genetic programming [5] is a techniqueApplication of Genetic Programming to Induction of Linear Classification Trees Martijn Bot William

Fernandez, Thomas

79

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

PubMed Central

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

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

80

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)

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. All data gathered in this investigation are contained in the CD-ROM.

Asbury, Scott C.; Yetter, Jeffrey A.

2000-01-01

81

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)

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.

Asbury, Scott C.; Yetter, Jeffrey A.

2000-01-01

82

Genetic Algorithms and Genetic Programming for Multiscale Modeling: Applications in Materials  

E-print Network

Genetic Algorithms and Genetic Programming for Multiscale Modeling: Applications in Materials FOR MULTISCALE MODELING: APPLICATIONS IN MATERIALS SCIENCE AND CHEMISTRY AND ADVANCES IN SCALABILITY BY KUMARA multiscale modeling is essential to advance both the science and synthesis in a wide array of fields

Fernandez, Thomas

83

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering  

NASA Technical Reports Server (NTRS)

Advances in molecular biological, analytical, and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-duster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e., who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting, and bioengineering.

Dhaeseleer, Patrik; Liang, Shoudan; Somogyi, Roland

2000-01-01

84

Genetic inactivation of D-amino acid oxidase enhances extinction and reversal learning in mice  

PubMed Central

Activation of the N-methyl-d-aspartate receptor (NMDAR) glycine site has been shown to accelerate adaptive forms of learning that may benefit psychopathologies involving cognitive and perseverative disturbances. In this study, the effects of increasing the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic inactivation of its catabolic enzyme D-amino acid oxidase (DAO), were examined in behavioral tests of learning and memory. In the Morris water maze task (MWM), mice carrying the hypofunctional Dao1G181R mutation demonstrated normal acquisition of a single platform location but had substantially improved memory for a new target location in the subsequent reversal phase. Furthermore, Dao1G181R mutant animals exhibited an increased rate of extinction in the MWM that was similarly observed following pharmacological administration of D-serine (600 mg/kg) in wild-type C57BL/6J mice. In contextual and cued fear conditioning, no alterations were found in initial associative memory recall; however, extinction of the contextual fear memory was facilitated in mutant animals. Thus, an augmented level of D-serine resulting from reduced DAO activity promotes adaptive learning in response to changing conditions. The NMDAR glycine site and DAO may be promising therapeutic targets to improve cognitive flexibility and inhibitory learning in psychiatric disorders such as schizophrenia and anxiety syndromes. PMID:19117914

Labrie, Viviane; Duffy, Steven; Wang, Wei; Barger, Steven W.; Baker, Glen B.; Roder, John C.

2009-01-01

85

Systematic Reverse Genetics of Transfer-DNA-Tagged Lines of Arabidopsis1  

PubMed Central

We have developed an efficient reverse-genetics protocol that uses expedient pooling and hybridization strategies to identify individual transfer-DNA insertion lines from a collection of 6000 independently transformed lines in as few as 36 polymerase chain reactions. We have used this protocol to systematically isolate Arabidopsis lines containing insertional mutations in individual cytochrome P450 genes. In higher plants P450 genes encode enzymes that perform an exceptionally wide range of functions, including the biosynthesis of primary metabolites necessary for normal growth and development, the biosynthesis of secondary products, and the catabolism of xenobiotics. Despite their importance, progress in assigning enzymatic function to individual P450 gene products has been slow. Here we report the isolation of the first 12 such lines, including one (CYP83B1-1) that displays a runt phenotype (small plants with hooked leaves), and three insertions in abundantly expressed genes. The DNAs used in this study are publicly available and can be used to systematically isolate mutants in Arabidopsis. PMID:9808718

Winkler, Rodney G.; Frank, Michael R.; Galbraith, David W.; Feyereisen, Rene; Feldmann, Kenneth A.

1998-01-01

86

A vaccine candidate of attenuated genotype VII Newcastle disease virus generated by reverse genetics.  

PubMed

Genotype VII Newcastle disease virus (NDV) has been documented as the predominant epidemic genotype in China and some other Asian countries since 1990s. Recent work has demonstrated that NDV vaccines phylogenetically closer to epidemic viruses provide better protection than conventional vaccines in terms of reducing virus shedding and transmission. Since there is currently no available vaccine which possesses a close antigenic relationship to the prevalent virulent NDV, a new vaccine to protect against the infection of this genotype NDV is in urgent need. Here, we describe the generation of a pathogenicity-attenuated genotype VII NDV (NDV/ZJ1HN) from a velogenic NDV by mutating the velogenic amino acid motif at the F protein cleavage site using reverse genetics techniques. The attenuated-pathogenicity of NDV/ZJ1HN was confirmed by examination of mean death time (MDT) in embryonated eggs and intracerebral pathogenicity index (ICPI) in day-old chickens. Subsequently, 2 weeks old birds were immunized with live and inactivated NDV/ZJ1HN-based vaccines and challenged 3 or 4 weeks post-immunization with a lethal dose of a virulent genotype VII NDV strain. Results showed that NDV/ZJ1HN effectively protected the vaccinated birds from morbidity and mortality against genotype VII virus challenge and significantly reduced virus shedding from the vaccinated birds when compared with La Sota vaccinated animals, suggesting that NDV/ZJ1HN is a promising vaccine candidate for the control of current ND epidemic in China. PMID:19095026

Hu, Shunlin; Ma, Huailiang; Wu, Yantao; Liu, Wenbo; Wang, Xiaoquan; Liu, Yuliang; Liu, Xiufan

2009-02-01

87

The application of reversible chemical reactions to solar thermal energy systems  

Microsoft Academic Search

It has been proposed to use reversible thermochemical reactions as a means for storing thermal energy in solar energy systems. The considered approach involves the storage of thermal energy in the form of chemicals created by endothermic reactions. In addition to the storage applications, there is also interest in applying reversible reactions to solar thermal energy transport and solar thermal

R. Mar

1980-01-01

88

Compositional reversed Markov processes, with applications to G-networks  

Microsoft Academic Search

Stochastic networks dened by a collection of cooperating agents are solved for their equilibrium state probability distribution by a new compositional method. The agents are processes formalised in a Markovian Process Alge- bra, which enables the reversed stationary Markov process of a cooperation to be determined symbolically under appropriate conditions. From the re- versed process, a separable (compositional) solution follows

Peter G. Harrison

2004-01-01

89

Genetic model compensation: Theory and applications  

NASA Astrophysics Data System (ADS)

The adaptive filtering algorithm known as Genetic Model Compensation (GMC) was originally presented in the author's Master's Thesis. The current work extends this earlier work. GMC uses a genetic algorithm to optimize filter process noise parameters in parallel with the estimation of the state and based only on the observational information available to the filter. The original stochastic state model underlying GMC was inherited from the antecedent, non-adaptive Dynamic Model Compensation (DMC) algorithm. The current work develops the stochastic state model from a linear system viewpoint, avoiding the simplifications and approximations of the earlier development, and establishes Riemann sums as unbiased estimators of the stochastic integrals which describe the evolution of the random state components. These are significant developments which provide GMC with a solid theoretical foundation. Orbit determination is the area of application in this work, and two types of problems are studied: real-time autonomous filtering using absolute GPS measurements and precise post-processed filtering using differential GPS measurements. The first type is studied in a satellite navigation simulation in which pseudorange and pseudorange rate measurements are processed by an Extended Kalman Filter which incorporates both DMC and GMC. Both estimators are initialized by a geometric point solution algorithm. Using measurements corrupted by simulated Selective Availability errors, GMC reduces mean RSS position error by 6.4 percent, reduces mean clock bias error by 46 percent, and displays a marked improvement in covariance consistency relative to DMC. To study the second type of problem, GMC is integrated with NASA Jet Propulsion Laboratory's Gipsy/Oasis-II (GOA-II) precision orbit determination program creating an adaptive version of GOA-II's Reduced Dynamic Tracking (RDT) process noise formulation. When run as a sequential estimator with GPS measurements from the TOPEX satellite and ground station network, this adaptive version of GOA-II reduces mean RSS position error by 5.9 percent and mean RSS velocity error by 3.7 percent relative to non-adaptive RDT. The success of this integration effort establishes GMC as a viable and widely applicable adaptive filtering algorithm. Standard hypothesis testing techniques are used in both studies to establish the statistical significance of GMC's apparent superiority over conventional non-adaptive process noise formulations.

Cruickshank, David Raymond

90

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

E-print Network

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 ...

Lu, Rongrong

2008-01-01

91

A new approach to an Influenza virus live vaccine: Modification of eleavage site of the haemagglu reverse genetics  

Microsoft Academic Search

A promising approach to reduce the impact of influenza is the use of an attenuated live virus as a vaccine. Using reverse genetics, we generated a mutant of strain A\\/WSN\\/33 with a modified cleavage site within its haemagglutinin which depends on proteolytic activation by elastase. Unlike the wild-type requiring trypsin, this mutant is strictly dependent on elastase. Both viruses grow

Holger Garn; Hans-Dieter Klenk; Jürgen Stech

92

Molecular genetics and clinical applications for RH  

PubMed Central

Rhesus is the clinically most important protein-based blood group system. It represents the largest number of antigens and the most complex genetics of the 30 known blood group systems. The RHD and RHCE genes are strongly homologous. Some genetic complexity is explained by their close chromosomal proximity and unusual orientation, with their tail ends facing each other. The antigens are expressed by the RhD and the RhCE proteins. Rhesus exemplifies the correlation of genotype and phenotype, facilitating the understanding of general genetic mechanisms. For clinical purposes, genetic diagnostics of Rhesus antigens will improve the cost-effective development of transfusion medicine. PMID:21277262

Flegel, Willy A.

2011-01-01

93

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

NASA Astrophysics Data System (ADS)

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.

Monser, George J.

1995-01-01

94

Genetic loss of D-amino acid oxidase activity reverses schizophrenia-like phenotypes in mice.  

PubMed

Reduced function of the N-methyl-d-aspartate receptor (NMDAR) has been implicated in the pathophysiology of schizophrenia. The NMDAR contains a glycine binding site in its NR1 subunit that may be a useful target for the treatment of schizophrenia. In this study, we assessed the therapeutic potential of long-term increases in the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic inactivation of its catabolic enzyme D-amino acid oxidase (DAO) in mice. The effects of eliminating DAO function were investigated in mice that display schizophrenia-related behavioral deficits due to a mutation (Grin 1(D481N)) in the NR1 subunit that results in a reduction in NMDAR glycine affinity. Grin 1(D481N) mice show deficits in sociability, prolonged latent inhibition, enhanced startle reactivity and impaired spatial memory. The hypofunctional Dao 1(G181R) mutation elevated brain levels of D-serine, but alone it did not affect performance in the behavioral measures. Compared to animals with only the Grin 1(D481N) mutation, mice with both the Dao1(G181R) and Grin 1(D481N) mutations displayed an improvement in social approach and spatial memory retention, as well as a reversal of abnormally persistent latent inhibition and a partial normalization of startle responses. Thus, an increased level of D-serine resulting from decreased catalysis corrected the performance of mice with deficient NMDAR glycine site activation in behavioral tasks relevant to the negative and cognitive symptoms of schizophrenia. Diminished DAO activity and elevations in D-serine may serve as an effective therapeutic intervention for the treatment of psychiatric symptoms. PMID:19751394

Labrie, V; Wang, W; Barger, S W; Baker, G B; Roder, J C

2010-02-01

95

Genetic loss of D-amino acid oxidase activity reverses schizophrenia-like phenotypes in mice  

PubMed Central

Reduced function of the N-methyl-D-aspartate receptor (NMDAR) has been implicated in the pathophysiology of schizophrenia. The NMDAR contains a glycine binding site in its NR1 subunit that may be a useful target for the treatment of schizophrenia. In this study, we assessed the therapeutic potential of long-term increases in the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic inactivation of its catabolic enzyme D-amino acid oxidase (DAO) in mice. The effects of eliminating DAO function were investigated in mice that display schizophrenia-related behavioral deficits due to a mutation (Grin1D481N) in the NR1 subunit that results in a reduction in NMDAR glycine affinity. Grin1D481N mice show deficits in sociability, prolonged latent inhibition, enhanced startle reactivity, and impaired spatial memory. The hypofunctional Dao1G181R mutation elevated brain levels of D-serine, but alone it did not affect performance in the behavioral measures. Compared to animals with only the Grin1D481N mutation, mice with both the Dao1G181R and Grin1D481N mutations displayed an improvement in social approach and spatial memory retention, as well as a reversal of abnormally persistent latent inhibition and a partial normalization of startle responses. Thus, an increased level of D-serine resulting from decreased catalysis corrected the performance of mice with deficient NMDAR glycine site activation in behavioral tasks relevant to the negative and cognitive symptoms of schizophrenia. Diminished DAO activity and elevations in D-serine may serve as an effective therapeutic intervention for the treatment of psychiatric symptoms. PMID:19751394

Labrie, V.; Wang, W.; Barger, S. W.; Baker, G. B.; Roder, J. C.

2009-01-01

96

Imaging-Genetics Applications in Child Psychiatry  

ERIC Educational Resources Information Center

Objective: To place imaging-genetics research in the context of child psychiatry. Method: A conceptual overview is provided, followed by discussion of specific research examples. Results: Imaging-genetics research is described linking brain function to two specific genes, for the serotonin-reuptake-transporter protein and a monoamine oxidase…

Pine, Daniel S.; Ernst, Monique; Leibenluft, Ellen

2010-01-01

97

Applications of terpene analysis in forest genetics  

Microsoft Academic Search

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

James W. Hanover

1992-01-01

98

Application of flux reversal principle for axial flux permanent magnet machines  

NASA Astrophysics Data System (ADS)

Applications of flux reversal machine can be found both for linear and radial flux machines. For axial flux machines, only one application is reported considering a two phase machine. In general, flux reversal effect can produce higher back electromotive forces than other topologies for the less amount of permanent magnets and thus can increase the performance of the machine. Combining the axial structure with the flux reversal effect feature allows higher power density machines suitable for high speed or low speed direct drive applications. Proposed model has a 12-slot stator and a 16-pole variable reluctance rotor. Nd-Fe-B magnets are fixed on the surface of the pole of the stator. The objective of this article is to present an effective method for the design and performance prediction for the axial flux reversal configuration. Basic dimension equations are presented and a two-dimensional equivalent model based on finite element analysis is used for the reduction of the simulation time.

Topor, Marcel; Chun, Yon-Do; Koo, Dae-Hyun; Han, Pil-Wan; Woo, Byung-Chul; Boldea, Ion

2008-04-01

99

ORIGINAL ARTICLE A new scoring system in cancer genetics: application  

E-print Network

ORIGINAL ARTICLE A new scoring system in cancer genetics: application to criteria for BRCA1 November 2013 To cite: Bonaïti B, Alarcon F, Andrieu N, et al. J Med Genet Published Online First: [please of cancer due to mutations of genes such as BRCA1 and BRCA2, methods have been proposed to predict

Paris-Sud XI, Université de

100

Time-reversal imaging of seismic sources and application to the great Sumatra earthquake  

E-print Network

Time-reversal imaging of seismic sources and application to the great Sumatra earthquake Carene and therighttime of the earthquake. When TR is applied to the Sumatra-Andaman earthquake (26 Dec. 2004 sources and application to the great Sumatra earthquake, Geophys. Res. Lett., 33, L19312, doi:10

Montagner, Jean-Paul

101

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

E-print Network

PWP-073 Stochastic Models of Energy Commodity Prices and Their Applications: Mean.ucei.berkeley.edu/ucei #12;Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps-switching and stochastic volatility into these models in order to capture the salient features of energy commodity prices

California at Berkeley. University of

102

Polyglot Programming in Applications Used for Genetic Data Analysis  

PubMed Central

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.

Nowak, Robert M.

2014-01-01

103

Polyglot programming in applications used for genetic data analysis.  

PubMed

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

Nowak, Robert M

2014-01-01

104

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

National Technical Information Service (NTIS)

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...

J. A. Yetter, S. C. Asbury

2000-01-01

105

Differential Equation Models and Numerical Methods for Reverse Engineering Genetic Regulatory Networks.  

E-print Network

??This dissertation develops and analyzes differential equation-based mathematical models and efficient numerical methods and algorithms for genetic regulatory network identification. The primary objectives of the… (more)

Yoon, Mi Un

2010-01-01

106

Intermediate-Type Vancomycin Resistance (VISA) in Genetically-Distinct Staphylococcus aureus Isolates Is Linked to Specific, Reversible Metabolic Alterations  

PubMed Central

Intermediate (VISA-type) vancomycin resistance in Staphylococcus aureus has been associated with a range of physiologic and genetic alterations. Previous work described the emergence of VISA-type resistance in two clonally-distinct series of isolates. In both series (the first belonging to MRSA clone ST8-USA300, and the second to ST5-USA100), resistance was conferred by a single mutation in yvqF (a negative regulator of the vraSR two-component system associated with vancomycin resistance). In the USA300 series, resistance was reversed by a secondary mutation in vraSR. In this study, we combined systems-level metabolomic profiling with statistical modeling techniques to discover specific, reversible metabolic alterations associated with the VISA phenotype. PMID:24817125

Alexander, Elizabeth L.; Gardete, Susana; Bar, Haim Y.; Wells, Martin T.; Tomasz, Alexander; Rhee, Kyu Y.

2014-01-01

107

Network model and optimization of reverse logistics by hybrid genetic algorithm  

Microsoft Academic Search

The interest about recovery of used products and materials have been increased. Therefore, reverse logistics network problem (rLNP) will be powerful and get a great potential for winning consumers in a more competitive context in the future.We formulate a mathematical model of remanufacturing system as three-stage logistics network model for minimizing the total of costs to reverse logistics shipping cost

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

2009-01-01

108

Applications of genetic engineering in veterinary medicine  

Microsoft Academic Search

A mutation of just one gene will cause abnormal cell behavior leading to the synthesis of a dysfunctional protein. This mutation will inevitably result in the cell functioning only marginally or not at all. Other genetic mutations interfere with the cell’s normal life cycle, especially the cell-division cycle. The goal behind recombinant DNA technology is to deliver the correct version

Kadriye Ciftci; Peter Trovitch

2000-01-01

109

Statistical Applications in Genetics and Molecular Biology  

E-print Network

be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical Genetic research has identified a number of genes for which inherited mutations confer a significantly and de la Chapelle 1999), which accounts for up to 5% of all diagnoses of colorectal cancer in the US

Broman, Karl W.

110

Applications of graph theory to landscape genetics  

Microsoft Academic Search

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

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

2008-01-01

111

Reversibility of a quantum channel: General conditions and their applications to Bosonic linear channels  

SciTech Connect

The method of complementary channel for analysis of reversibility (sufficiency) of a quantum channel with respect to families of input states (pure states for the most part) are considered and applied to Bosonic linear (quasi-free) channels, in particular, to Bosonic Gaussian channels. The obtained reversibility conditions for Bosonic linear channels have clear physical interpretation and their sufficiency is also shown by explicit construction of reversing channels. The method of complementary channel gives possibility to prove necessity of these conditions and to describe all reversed families of pure states in the Schrodinger representation. Some applications in quantum information theory are considered. Conditions for existence of discrete classical-quantum subchannels and of completely depolarizing subchannels of a Bosonic linear channel are presented.

Shirokov, M. E. [Steklov Mathematical Institute, Moscow (Russian Federation)] [Steklov Mathematical Institute, Moscow (Russian Federation)

2013-11-15

112

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

NASA Technical Reports Server (NTRS)

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.

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

1974-01-01

113

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

NASA Technical Reports Server (NTRS)

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.

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

1974-01-01

114

Applications of Genetic Programming in Cancer Research  

PubMed Central

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

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

2012-01-01

115

Efficient rescue of infectious bursal disease virus using a simplified RNA polymerase II-based reverse genetics strategy.  

PubMed

We describe a simplified RNA polymerase II-based reverse genetics approach that allows for the efficient rescue of high-titer infectious bursal disease virus (IBDV) from cloned cDNAs of genomic segments A and B. Unlike the previously reported RNA polymerase II-based methods, the developed strategy does not necessitate the introduction of a ribozyme sequence at both ends of the genomic cDNA sequences. This was achieved by fusing the 5' terminal sequence of the cDNA of each segment to the transcription start site of the immediate early cytomegalovirus promoter, while a ribozyme sequence was only introduced at the 3' end. Using this strategy, and without complementing with IBDV structural proteins, titers as high as 10(11) tissue culture infectious dose 50 were reproducibly obtained in chicken embryo fibroblast cells immediately upon co-transfection with cDNAs of both segments. We anticipate that this modification could improve reverse genetics for any other RNA virus and may be beneficial for vaccine development and dissection of the viral life cycle. PMID:18392769

Ben Abdeljelil, N; Khabouchi, N; Mardassi, H

2008-01-01

116

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

SciTech Connect

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.

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

1994-09-01

117

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

E-print Network

Stochastic Models of Energy Commodity Prices and Their Applications: Mean-reversion with Jumps usion models to describe energy commodity spot prices. We incorporate multiple jumps, regime-switching and stochastic volatility in these models. Prices of various energy commodity derivatives are obtained under each

118

A specialised speech synthesis technique for application to automatic reverse directory service  

Microsoft Academic Search

This paper describes a specialised version of Eloquens, the CSELT's text-to-speech synthesiser, which has been conceived to achieve a substantial improvement for what concerns not only intelligibility, but also speech naturalness in the synthesis of messages in an automatic reverse directory service. This result has been obtained taking advantage of the peculiarities of the application domain, namely the possibility, or

Luciano Nebbia; Silvia Quazza; Pier Luigi Salza

1998-01-01

119

Applications of graph theory to landscape genetics  

PubMed Central

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.

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

2008-01-01

120

Statistical Applications in Genetics and Molecular Biology  

E-print Network

Robert J. Tibshirani Stanford University, dwitten@stanford.edu Stanford University, tibs Correlation Analysis with Applications to Genomic Data Daniela M. Witten and Robert J. Tibshirani Abstract and Engineering Graduate Fellowship. Robert Tibshirani was partially supported by National Science Foundation

Tibshirani, Robeert

121

Time-Reversal Imaging of seismic sources and application to recent large Earthquakes  

NASA Astrophysics Data System (ADS)

The occurrence of the disastrous Sumatra-Andaman earthquake on dec. 26, 2004 makes it necessary to develop innovative techniques for studying the complex spatio-temporal characteristics of rupture. The concept of time-reversal (hereafter referred to as TR) was previously successfully applied for acoustic waves in many fields such as medical imaging, underwater acoustics and non destructive testing. The increasing power of computers and numerical methods (such as spectral element methods) enables one to simulate more and more accurately the propagation of seismic waves in heterogeneous media and to develop new applications, in particular time reversal in the three-dimensional Earth. We present here the first applications at the global scale of TR with associated reverse movies of seismic waves propagation by sending back time--reversed seismograms. We show that seismic wave energy is refocused at the right location and the right time of the earthquake. When TR is applied to the Sumatra-- Andaman earthquake (26 dec. 2004), the migration of the rupture from the south towards the north is retrieved. All corresponding movies can be downloaded at the following webpage: http://www.gps.caltech.edu/~carene Other applications to recent smaller earthquakes will be also shown. Therefore, the technique of TR is potentially interesting for automatically locating earthquakes in space and time and for constraining the spatio-temporal history of complex earthquakes .

Montagner, J.; Larmat, C.; Fink, M.; Capdeville, Y.; Tourin, A.

2006-12-01

122

Genetic Inactivation of D-Amino Acid Oxidase Enhances Extinction and Reversal Learning in Mice  

ERIC Educational Resources Information Center

Activation of the N-methyl-d-aspartate receptor (NMDAR) glycine site has been shown to accelerate adaptive forms of learning that may benefit psychopathologies involving cognitive and perseverative disturbances. In this study, the effects of increasing the brain levels of the endogenous NMDAR glycine site agonist D-serine, through the genetic

Labrie, Viviane; Duffy, Steven; Wang, Wei; Barger, Steven W.; Baker, Glen B.; Roder, John C.

2009-01-01

123

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

Microsoft Academic Search

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

Karen L. Wiebe; Bart Kempenaers

2009-01-01

124

Statistical Applications in Genetics and Molecular Biology  

E-print Network

Mellon University, cg09@andrew.cmu.edu Copyright c 2004 by the authors. All rights reserved. No part of the publisher, bepress, which has been given certain exclusive rights by the author. Statistical Applications of significant cross-hybridization in expressed sequence tags (EST) IMAGE clones used on a commercially available

Spirtes, Peter

125

Genetic Algorithm Application in Optimization of Wireless Sensor Networks  

PubMed Central

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

Norouzi, Ali; Zaim, A. Halim

2014-01-01

126

Decision Tree Construction for Genetic Applications Based on Association Rules  

Microsoft Academic Search

A decision tree is an effective means of data classification from which rules can be both expressive and precise. However decision tree is only applicable in the applications that the data is expressed with attribute-value pairs. Since genetic data are not attribute-pairs, the only method that we know of to make decision-tree for them is based on a greedy graph-based

Ashkan Sami; Makoto Takahashi

2005-01-01

127

Genetic algorithms and their applications in accelerator physics  

SciTech Connect

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.

Hofler, Alicia S. [JLAB

2013-12-01

128

Application of a hybrid genetic algorithm to airline crew scheduling  

Microsoft Academic Search

This paper discusses the development and application of a hybrid genetic algorithmto airline crew scheduling problems. The hybrid algorithm consists of a steady-stategenetic algorithm and a local search heuristic. The hybrid algorithm was tested on a set of fortyreal-world problems. It found the optimal solution for half the problems, and good solutionsfor nine others. The results were compared to those

David Levine

1996-01-01

129

Genetic engineering applications to biotechnology in the genus Bacillus  

SciTech Connect

This review presents a global picture of current applications and capabilities of genetic engineering to biotechnology in Bacillus, particularly B. subtilis, so that the academic biotechnologist, the industrial microbiologist, and the manager may turn to one source to study this subject. 236 references.

Workman, W.E.; McLinden, J.H.; Dean, D.H.

1986-06-09

130

Genetic Susceptibility and Survival: Application to Breast Cancer  

E-print Network

Genetic Susceptibility and Survival: Application to Breast Cancer Edwin S. IVERSEN, JR., Giovanni are known to confer an elevated risk of both breast and ovarian cancers. The effect of carrying such a mutation on survival after developing breast or ovarian cancer is less well understood. We investigate

West, Mike

131

Application of Genetic Programming to Induction of Linear Classification Trees  

E-print Network

Application of Genetic Programming to Induction of Linear Classification Trees Martijn C.J. Bot 1 decision trees with a linear combination of variables in each func­ tion node. A new representation of decision trees using Strong Typing in GP is introduced. With this representation it is now possible to let

Fernandez, Thomas

132

Reverse Engineering Financial Markets with Majority and Minority Games using Genetic Algorithms  

E-print Network

Using virtual stock markets with artificial interacting software investors, aka agent-based models (ABMs), we present a method to reverse engineer real-world financial time series. We model financial markets as made of a large number of interacting boundedly rational agents. By optimizing the similarity between the actual data and that generated by the reconstructed virtual stock market, we obtain parameters and strategies, which reveal some of the inner workings of the target stock market. We validate our approach by out-of-sample predictions of directional moves of the Nasdaq Composite Index.

Wiesinger, J; Satinover, J

2010-01-01

133

Adaptable Constrained Genetic Programming: Extensions and Applications  

NASA Technical Reports Server (NTRS)

An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.

Janikow, Cezary Z.

2005-01-01

134

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

PubMed

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

Lamparter, T; Hughes, J; Hartmann, E

1998-09-01

135

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

PubMed

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

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

2014-05-19

136

Quantitative genetic versions of Hamilton's rule with empirical applications  

PubMed Central

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

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

2014-01-01

137

Genetic ablation of vitamin D activation pathway reverses biochemical and skeletal anomalies in Fgf-23-null animals.  

PubMed

Fibroblast growth factor-23 (FGF-23) is one of the circulating phosphaturic factors associated with renal phosphate wasting. Fgf-23-/- animals show extremely high serum levels of phosphate and 1,25-dihydroxyvitamin D3, along with abnormal bone mineralization and soft tissue calcifications. To determine the role of vitamin D in mediating altered phosphate homeostasis and skeletogenesis in the Fgf-23-/- mice, we generated mice lacking both the Fgf-23 and 1alpha-hydroxylase genes (Fgf-23-/-/1alpha(OH)ase-/-). In the current study, we have identified the cellular source of Fgf-23 in adult mice. In addition, loss of vitamin D activities from Fgf-23-/- mice reverses the severe hyperphosphatemia to hypophosphatemia, attributable to increased urinary phosphate wasting in Fgf-23-/-/1alpha(OH)ase-/- mice, possibly as a consequence of decreased expression of NaPi2a. Ablation of vitamin D from Fgf-23-/- mice resulted in further reduction of total bone mineral content and bone mineral density and reversed ectopic calcification of skeleton and soft tissues, suggesting that abnormal mineral ion homeostasis and impaired skeletogenesis in Fgf-23-/- mice are mediated through enhanced vitamin D activities. In conclusion, using genetic manipulation studies, we have provided evidence for an in vivo inverse correlation between Fgf-23 and vitamin D activities and for the severe skeletal and soft tissue abnormalities of Fgf-23-/- mice being mediated through vitamin D. PMID:17148678

Sitara, Despina; Razzaque, Mohammed S; St-Arnaud, René; Huang, Wei; Taguchi, Takashi; Erben, Reinhold G; Lanske, Beate

2006-12-01

138

Genetic correction using engineered nucleases for gene therapy applications.  

PubMed

Genetic mutations in humans are associated with congenital disorders and phenotypic traits. Gene therapy holds the promise to cure such genetic disorders, although it has suffered from several technical limitations for decades. Recent progress in gene editing technology using tailor-made nucleases, such as meganucleases (MNs), zinc finger nucleases (ZFNs), TAL effector nucleases (TALENs) and, more recently, CRISPR/Cas9, has significantly broadened our ability to precisely modify target sites in the human genome. In this review, we summarize recent progress in gene correction approaches of the human genome, with a particular emphasis on the clinical applications of gene therapy. PMID:24329887

Li, Hongmei Lisa; Nakano, Takao; Hotta, Akitsu

2014-01-01

139

Identification of Genes Important for Cutaneous Function Revealed by a Large Scale Reverse Genetic Screen in the Mouse  

PubMed Central

The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

DiTommaso, Tia; Jones, Lynelle K.; Cottle, Denny L.; Gerdin, Anna-Karin; Vancollie, Valerie E.; Watt, Fiona M.; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P.; Sundberg, John P.; White, Jacqueline K.; Smyth, Ian M.

2014-01-01

140

A colorimetric temperature sensor of a cyanine dye supramolecule and its application in reversible switch  

NASA Astrophysics Data System (ADS)

A colorimetric temperature sensor is constructed based on the thermo-responsive switch of a cyanine dye supramolecule. With rising temperature, the supramolecule switches from J- to H-aggregate which is accompanied by obvious changes of absorption spectra and colour. This process can be accurately regulated by changing the concentrations of cyanine dye and metal ions, and it is also reproducible undergo multiple cycles. The results provide an application of cyanine dye supramolecules as a temperature sensor and reversible switch.

Sun, Hongxia; Xiang, Junfeng; Zhang, Xiufeng; Chen, Hongbo; Shi, Yunhua; Yu, Lijia; Yang, Qianfan; Li, Qian; Guan, Aijiao; Tang, Yalin

2014-08-01

141

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

E-print Network

Water: Optimization, Process Control, and Renewable Energy Application. (August 2006) Brett Mareth, B.S., Texas A&M University Chair of Advisory Committee: Dr. Maria Barrufet Fresh water resources in many of the world?s oil producing regions... technology developed to treat produced water by reverse osmosis and other means to render it suitable for agricultural or industrial use, while simultaneously reducing disposal costs. Pilot testing of the process thus far has demonstrated the technology?s...

Mareth, Brett

2009-06-02

142

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

PubMed Central

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

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

2014-01-01

143

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

PubMed Central

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

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

144

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

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

Renn, Susan C.P.

145

Application of quantile regression to recent genetic and -omic studies.  

PubMed

This paper provides a review of recent applications of quantile regression to the fields of genetic and the emerging -omic studies. It begins with a general background about this statistical approach following the seminal paper of Koenker and Bassett (Econometrica 46:33-50, 1978). Applications are described, as diverse as genetic association studies, penetrance estimation, gene expression, CGH array experiments, RNAseq experiments, methylation data and proteomics. This paper also introduces recent extensions of quantile regression with a particular focus on the Copula-quantile regression, an approach we recently proposed for sib-pair analysis. A real data example from eQTL analysis is then presented and the [Formula: see text] codes, which run the analyses are provided. Finally, we conclude with some statistical software presentation and some general statements about the potential and interests of quantile regression in modern biological experiments. PMID:24770874

Briollais, Laurent; Durrieu, Gilles

2014-08-01

146

Reversible Thermal Denaturation of a 60-kDa Genetically Engineered ?-Sheet Polypeptide  

PubMed Central

A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)3GY(GA)3GE(GA)3GH(GA)3GK, forms large ?-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of ?-sheet formation yielding intimate folding information that is otherwise difficult to obtain and may inform folding studies of naturally occurring materials. The polypeptide assumes a fully folded antiparallel ?-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125°C, adopting a predominant polyproline II conformation. Deep ultraviolet Raman spectroscopy indicated that melting/refolding occurred without any spectroscopically distinct intermediates, yet the relaxation kinetics depend on the initial polypeptide state, as would be indicative of a non-two-state process. Thermal denaturation and refolding on cooling appeared to be monoexponential with characteristic times of ?1 and ?60 min, respectively, indicating no detectable formation of hairpin-type nuclei in the millisecond timescale that could be attributed to nonlocal “nonnative” interactions. The polypeptide folding dynamics agree with a general property of ?-sheet proteins, i.e., initial collapse precedes secondary structure formation. The observed folding is much faster than expected for a protein of this size and could be attributed to a less frustrated free-energy landscape funnel for folding. The polypeptide sequence suggests an important balance between the absence of strong nonnative contacts (salt bridges or hydrophobic collapse) and limited repulsion of charged side chains. PMID:16891363

Lednev, Igor K.; Ermolenkov, Vladimir V.; Higashiya, Seiichiro; Popova, Ludmila A.; Topilina, Natalya I.; Welch, John T.

2006-01-01

147

Cross flow filtration for radwaste applications reverse osmosis demonstration case studies  

SciTech Connect

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.

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

1995-05-01

148

Novel and potential application of cryopreservation to plant genetic transformation.  

PubMed

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

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

2012-01-01

149

Sub-population policies for a parallel multiobjective genetic algorithm with applications to wing design  

E-print Network

Sub-population policies for a parallel multiobjective genetic algorithm with applications to wing. 2. GENETIC ALGORITHM WITH SUB-POPULATIONS The algorithm here described, that will be called Virtual Sub- population Genetic Algorithm (VSGA), is an extension of the multi-objective genetic algorithm

Coello, Carlos A. Coello

150

Designing application-specific neural networks using the structured genetic algorithm  

Microsoft Academic Search

Presents a different type of genetic algorithm called the structured genetic algorithm (SGA) for the design of application-specific neural networks. The novelty of this new genetic approach is that it can determine the network structures and their weights solely by an evolutionary process. This is made possible for the SGA primarily due to its redundant genetic material and a gene

Dipankar Dasgupta; Douglas R. Mcgregor

1992-01-01

151

Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation.  

PubMed

Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions. PMID:25135455

Posavi, Marijan; Gelembiuk, Gregory William; Larget, Bret; Lee, Carol Eunmi

2014-11-01

152

Protective efficacy of a high-growth reassortant swine H3N2 inactivated vaccine constructed by reverse genetic manipulation.  

PubMed

Novel reassortant H3N2 swine influenza viruses (SwIV) with the matrix gene from the 2009 H1N1 pandemic virus have been isolated in many countries as well as during outbreaks in multiple states in the United States, indicating that H3N2 SwIV might be a potential threat to public health. Since southern China is the world's largest producer of pigs, efficient vaccines should be developed to prevent pigs from acquiring H3N2 subtype SwIV infections, and thus limit the possibility of SwIV infection at agricultural fairs. In this study, a high-growth reassortant virus (GD/PR8) was generated by plasmid-based reverse genetics and tested as a candidate inactivated vaccine. The protective efficacy of this vaccine was evaluated in mice by challenging them with another H3N2 SwIV isolate [A/Swine/Heilongjiang/1/05 (H3N2) (HLJ/05)]. Prime and booster inoculation with GD/PR8 vaccine yielded high-titer serum hemagglutination inhibiting antibodies and IgG antibodies. Complete protection of mice against H3N2 SwIV was observed, with significantly reduced lung lesion and viral loads in vaccine-inoculated mice relative to mock-vaccinated controls. These results suggest that the GD/PR8 vaccine may serve as a promising candidate for rapid intervention of H3N2 SwIV outbreaks in China. PMID:24675833

Wen, Feng; Ma, Ji-Hong; Yu, Hai; Yang, Fu-Ru; Huang, Meng; Zhou, Yan-Jun; Li, Ze-Jun; Tong, Guang-Zhi

2014-09-01

153

Protective efficacy of a high-growth reassortant swine H3N2 inactivated vaccine constructed by reverse genetic manipulation  

PubMed Central

Novel reassortant H3N2 swine influenza viruses (SwIV) with the matrix gene from the 2009 H1N1 pandemic virus have been isolated in many countries as well as during outbreaks in multiple states in the United States, indicating that H3N2 SwIV might be a potential threat to public health. Since southern China is the world's largest producer of pigs, efficient vaccines should be developed to prevent pigs from acquiring H3N2 subtype SwIV infections, and thus limit the possibility of SwIV infection at agricultural fairs. In this study, a high-growth reassortant virus (GD/PR8) was generated by plasmid-based reverse genetics and tested as a candidate inactivated vaccine. The protective efficacy of this vaccine was evaluated in mice by challenging them with another H3N2 SwIV isolate [A/Swine/Heilongjiang/1/05 (H3N2) (HLJ/05)]. Prime and booster inoculation with GD/PR8 vaccine yielded high-titer serum hemagglutination inhibiting antibodies and IgG antibodies. Complete protection of mice against H3N2 SwIV was observed, with significantly reduced lung lesion and viral loads in vaccine-inoculated mice relative to mock-vaccinated controls. These results suggest that the GD/PR8 vaccine may serve as a promising candidate for rapid intervention of H3N2 SwIV outbreaks in China. PMID:24675833

Wen, Feng; Ma, Ji-Hong; Yang, Fu-Ru; Huang, Meng; Zhou, Yan-Jun; Li, Ze-Jun

2014-01-01

154

Genomic and Biological Characterization of Aggressive and Docile Strains of LCMV Rescued from a Plasmid-Based Reverse Genetics System  

PubMed Central

Arenaviruses include several causative agents of hemorrhagic fever disease in humans. In addition, the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) is a superb model for the study of virus-host interactions, including the basis of viral persistence and associated diseases. The molecular mechanisms concerning the regulation and specific role of viral proteins in modulating arenavirus-host cell interactions associated either with an acute or persistent infection and associated disease remain little understood. Here we report the genomic and biological characterization of LCMV strains Docile (persistent) and Aggressive (not persistent) recovered from cloned cDNA via reverse genetics. Our results confirmed that the cloned viruses accurately recreated the in vivo phenotypes associated with the corresponding natural Docile and Aggressive viral isolates. In addition, we provide evidence that the ability of the Docile strain to persist is determined by the nature of both S and L RNA segments. Thus, our findings provide the foundation for studies aimed at gaining a detailed understanding of viral determinants of LCMV persistence in its natural host that may aid in the development of vaccines to prevent or treat the diseases caused by arenaviruses in humans. PMID:18474558

Chen, Minjie; Lan, Shuiyun; Ou, Rong; Price, Graeme E.; Jiang, Hong; de la Torre, Juan Carlos; Moskophidis, Demetrius

2008-01-01

155

Structure-Specified Real Coded Genetic Algorithms with Applications  

Microsoft Academic Search

Absract This chapter intends to present a brief review of genetic search algorithms and introduce a new type of genetic algorithms (GAs) called the real coded structural genetic algorithm (RSGA) for function optimization. The new genetic model combines the advantages of traditional real genetic algorithm (RGA) with structured genetic algorithm (SGA). This specific feature makes it able to solve more

Chun-Liang Lin; Ching-Huei Huang; Chih-Wei Tsai

156

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

E-print Network

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 ...

Hoop, Martijn de

2005-01-01

157

Applications of a formal approach to decipher discrete genetic networks  

PubMed Central

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

2010-01-01

158

Virus-induced gene silencing for Asteraceae--a reverse genetics approach for functional genomics in Gerbera hybrida.  

PubMed

Virus-induced gene silencing (VIGS) is a natural defence mechanism in plants which leads to sequence-specific degradation of viral RNA. For identifying gene functions, Tobacco rattle virus (TRV)-based VIGS has been applied for silencing of endogenous genes in many plant species. Gerbera hybrida (Asteraceae) has emerged as a novel model for studies in flower development and secondary metabolism. For this highly heterozygous species, functional studies have been conducted through reverse genetic methods by producing stable transgenic lines, which, however, is labour-intensive and time-consuming. For the development of TRV-based VIGS system for gerbera, and for the first time for an Asteraceaeous species, we screened several gerbera cultivars and optimized the agroinfiltration methods for efficient silencing. Gene fragments for gerbera phytoene desaturase (GPDS) and Mg-chelatase subunits (GChl-H and GChl-I), expressed from a TRV vector, induced silencing phenotypes in leaves, scapes, and involucral bracts indicating their feasibility as markers for green tissues. In addition, robust silencing symptoms were achieved in gerbera floral tissues by silencing the anthocyanin pathway gene for chalcone synthase (GCHS1) and a gerbera B-type MADS-box gene globosa (GGLO1), confirming the phenotypes previously observed in stable transgenic lines. Unexpectedly, photobleaching induced by GPDS and GChl-H or GChl-I silencing, or by the herbicide norflurazon, resulted in silencing of the polyketide synthase gene G2PS1, which has no apparent connections to carotenoid or chlorophyll biosynthesis. We have shown feasibility of VIGS for functional studies in gerbera, but our results also show that selection of the marker gene for silencing must be critically evaluated. PMID:22805353

Deng, Xianbao; Elomaa, Paula; Nguyen, Cuong X; Hytönen, Timo; Valkonen, Jari P T; Teeri, Teemu H

2012-10-01

159

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

PubMed Central

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

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

2014-01-01

160

Two applications of time reversal mirrors: seismic radio and seismic radar.  

PubMed

Two seismic applications of time reversal mirrors (TRMs) are introduced and tested with field experiments. The first one is sending, receiving, and decoding coded messages similar to a radio except seismic waves are used. The second one is, similar to radar surveillance, detecting and tracking a moving object(s) in a remote area, including the determination of the objects speed of movement. Both applications require the prior recording of calibration Green's functions in the area of interest. This reference Green's function will be used as a codebook to decrypt the coded message in the first application and as a moving sensor for the second application. Field tests show that seismic radar can detect the moving coordinates (x(t), y(t), z(t)) of a person running through a calibration site. This information also allows for a calculation of his velocity as a function of location. Results with the seismic radio are successful in seismically detecting and decoding coded pulses produced by a hammer. Both seismic radio and radar are highly robust to signals in high noise environments due to the super-stacking property of TRMs. PMID:21973353

Hanafy, Sherif M; Schuster, Gerard T

2011-10-01

161

Reverse boundary layer capacitor model in glass/ceramic composites for energy storage applications  

NASA Astrophysics Data System (ADS)

Reverse boundary layer capacitor (RBLC) configuration model, where the grain boundary has a higher electrical conductivity than the grain, is proposed in glass/ceramic composites for dielectric energy storage applications. By introducing glass additives as grain boundaries with electrical conductivity higher than ceramic grains, the steady electric field across grains can be larger than grain boundaries as desired due to the conductivity difference. The breakdown field is thus expected to increase in the RBLC-type brick wall model because of the field distribution. The equivalent circuit, grain boundary conductivity dependence of energy density, low-loss frequency range of the RBLC model are discussed. The simulation results suggest that the RBLC approach has advantages in overall energy density, compared with normal insulating glass phase composites.

Wei, Xiaoyong; Yan, Haixue; Wang, Tong; Hu, Qingyuan; Viola, G.; Grasso, Salvatore; Jiang, Qinghui; Jin, Li; Xu, Zhuo; Reece, Michael J.

2013-01-01

162

The multi-niche crowding genetic algorithm: Analysis and applications  

SciTech Connect

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.

Cedeno, W.

1995-09-01

163

Engineering Applications of Artificial Intelligence 13 (2000) 611623 Genetic adaptive state estimation$  

E-print Network

Engineering Applications of Artificial Intelligence 13 (2000) 611­623 Genetic adaptive state in a nonlinear jet engine. Our main conclusion is that the genetic adaptive state estimator has the potential Ltd. All rights reserved. Keywords: Estimation; Genetic algorithms; Jet engine surge=stall control 1

164

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

E-print Network

for technical analysis tools, but to show how genetic programming (GP) (Koza 1992), a decision-tree-based method decision trees as opposed to strings in genetic algorithms. This allows one to handle rule sets of variableStock Portfolio Evaluation: An Application of Genetic- Programming-Based Technical Analysis Liad

Fernandez, Thomas

165

Innovative Applications of Genetic Algorithms to Problems in Accelerator Physics  

SciTech Connect

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.

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

166

Innovative applications of genetic algorithms to problems in accelerator physics  

NASA Astrophysics Data System (ADS)

The genetic algorithm (GA) is a powerful technique that implements the principles nature uses in biological evolution 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 Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion Collider at Jefferson Lab, and a radio frequency 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, include a newly devised enhancement which leads to improved convergence to the optimum, and make recommendations for future GA developments and accelerator applications.

Hofler, Alicia; Terzi?, Balša; Kramer, Matthew; Zvezdin, Anton; Morozov, Vasiliy; Roblin, Yves; Lin, Fanglei; Jarvis, Colin

2013-01-01

167

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

NASA Astrophysics Data System (ADS)

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.

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

2006-08-01

168

Review of proteomics with applications to genetic epidemiology.  

PubMed

Mapping of the human genome has the potential to transform the traditional methods of genetic epidemiology. The complete draft sequence of the 3.3 billion nucleotides comprising the genome is now available over the Internet, including the location and nearly complete sequence of the 26,000 to 31,000 protein-encoding genes. However, aside from water, almost everything in the human body is either made of, or by, proteins. Although the DNA code provides the instructions for their amino acid sequence, there are an estimated 1.5 million proteins. Thus, the correlation between DNA sequence and protein is low, reflecting alternate splicing as well as post-translational modification. The purpose of this article is to explore ways in which the emerging field of proteomics, the study of proteins in a cell, may inform our approach to gene mapping. This article reviews the various technical approaches currently available for proteomics. Technologies are available to quantify protein expression (and compare normal versus disease states), identify proteins through comparison with sequence information in databases or direct sequencing (which can then be mapped to chromosomal locations to ensure appropriate markers), elucidate protein-protein interactions (which may underlie disease), determine localization of proteins within the cell (abnormal trafficking of proteins could have an inherited basis), and characterize modifications of proteins (which is relevant to modifier gene candidates). Several examples are presented to illustrate the potential application of proteomics to the field of genetic epidemiology, and we conclude with various considerations regarding design and analysis. PMID:12548670

Sellers, Thomas A; Yates, John R

2003-02-01

169

Genetic Applications of an Inverse Polymerase Chain Reaction  

Microsoft Academic Search

A method is presented for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. The method uses the polymerase chain reaction (PCR), but it has the primers oriented in the reverse direction of the usual orientation. The template for the reverse primers is a restriction fragment that has been ligated upon itself to form

Howard Ochman; Anne S. Gerber; Daniel L. Hart

170

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

NASA Technical Reports Server (NTRS)

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.

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

1999-01-01

171

Reversible Programmable Logic Array (RPLA) using Feynman & MUX Gates for Low Power Industrial Applications  

E-print Network

This paper present the research work directed towards the design of reversible programmable logic array using very high speed integrated circuit hardware description language (VHDL). Reversible logic circuits have significant importance in bioinformatics, optical information processing, CMOS design etc. In this paper the authors propose the design of new RPLA using Feynman & MUX gate.VHDL based codes of reversible gates with simulating results are shown .This proposed RPLA may be further used to design any reversible logic function or Boolean function (Adder, subtractor etc.) which dissipate very low or ideally no heat.

Singla, Pradeep

2012-01-01

172

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

PubMed

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

Porteri, Corinna

2013-08-01

173

Controlled reversal of Co/Pt Dots for nanomagnetic logic applications  

SciTech Connect

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.

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

174

Investigations on the Suitability of Coated Steel Piping System for High Pressure Seawater Reverse Osmosis Application  

NASA Astrophysics Data System (ADS)

This study deals with the investigations concerning with the suitability of coated steel piping system as an economically viable alternative to costly stainless steel piping for high pressure seawater reverse osmosis (SWRO) application. The piping system selected for investigation is a carbon steel piping coated internally and externally with thermoplastic coating (coating powder Plascoat PPA 571). The performance of thermoplastic coating was investigated by conducting SWRO pilot plant test, salt spray test, mechanical tests and testing of the coating under crevices (both in pilot plant and laboratory), and for leachable organics and inorganics (both in laboratory and pilot plant test). The testing of coating in the pilot plant resulted in the formation of some blisters on the internal surface of the pipes. The blisters were broken causing the corrosion of underneath steel. The coating showed a poor resistance to salt fog test. In general, the coating performed satisfactorily under the crevices but showed blistering on either side of the test panels. The adhesive strength of the coating was found to be poor; however, it showed good flexibility. The results of chemical analysis did not show the leaching of organic or inorganic pollutants from the coating.

Mobin, Mohammad

2010-03-01

175

Genetic mapping of the autosomal region involved in XX sex-reversal and horn development in goats  

Microsoft Academic Search

Contrary to other genetic disorders, the genetic study of sex determination anomalies in humans stumbles over the difficulty\\u000a in observing large pedigrees. In goats, abnormalities in sex determination are intimately linked to a dominant Mendelian gene\\u000a coding for the “polled” (hornless) character, which could render this species an interesting animal model for the rare human\\u000a cases of SRY-negative XX males.

D. Vaiman; O. Koutita; A. Oustry; J.-M. Elsen; E. Manfredi; M. Fellous; E. P. Cribiu

1996-01-01

176

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

NASA Astrophysics Data System (ADS)

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.

Luo, Xiaofan

177

A genetic algorithm-based heuristic for the dynamic integrated forward\\/reverse logistics network for 3PLs  

Microsoft Academic Search

Today's competitive business environment has resulted in increasing cooperation among individual companies as members of a supplychain. Accordingly , third partylogistics providers (3PLs) must operate supplychains for a number of different clients who want to improve their logistics operations for both forward and reverse flows. As a result of the dynamic environment in which these supply chains must operate, 3PLs

Hyun Jeung Ko; Gerald W. Evans

2007-01-01

178

Expression of AMH, SF1, and SOX9 in gonads of genetic female chickens during sex reversal induced by an aromatase inhibitor.  

PubMed

Aromatase inhibitors administered prior to histological signs of gonadal sex differentiation can induce sex reversal of genetic female chickens. Under the effects of Fadrozole (CGS 16949A), a nonsteroidal aromatase inhibitor, the right gonad generally becomes a testis, and the left gonad a testis or an ovotestis. We have compared the expression pattern of the genes encoding AMH (the anti-Müllerian hormone), SF1 (steroidogenic factor 1), and SOX9 (a transcription factor related to SRY) in these sex-reversed gonads with that in control testes and ovaries, using in situ hybridization with riboprobes on gonadal sections. In control males, the three genes are expressed in Sertoli cells of testicular cords; however, only SOX9 is male specific, since as observed previously AMH and SF1 but not SOX9 are expressed in the control female gonads. In addition to testicular-like cords, sex-reversed gonads present many lacunae with a composite, thick and flat epithelium. We show that during embryonic and postnatal development, AMH, SF1 and SOX9 are expressed in the epithelium of testicular-like cords and in the thickened part but not in the flattened part of the epithelium of composite lacunae. AMH and SF1 but not SOX9 are expressed in follicular cells of ovotestes. Coexpression of the three genes, of which SOX9 is a specific Sertoli-cell marker, provides strong evidence for the transdifferentiation of ovarian into testicular epithelium in gonads of female chickens treated with Fadrozole. PMID:11668600

Vaillant, S; Magre, S; Dorizzi, M; Pieau, C; Richard-Mercier, N

2001-10-01

179

Genetically engineered antibodies and their application to brain delivery  

Microsoft Academic Search

Techniques of genetic engineering and expression have been applied to the production of antibodies in a variety of expression systems. Combinatorial libraries produced in bacteriophage may present an alternative to animal immunization as a source of antigen-binding specificities. Transfectomas which express genetically engineered antibody genes provide one approach to overcoming some of the limitations inherent in classical monoclonal antibodies. Novel

Sherie L. Morrison; Seung-Uon Shin

1995-01-01

180

On the applicability of genetic algorithms to protein folding  

Microsoft Academic Search

Discusses the protein folding problem and suggests the use of genetic algorithms for protein folding simulations. The issues of protein energy functions, search algorithms, and folding pathways are discussed. The authors review the current approaches to the protein folding problem, point out the limitations of the approaches, and present the genetic algorithm method, which is based on viewing evolution as

Ron Unger; J. Moult

1993-01-01

181

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

Microsoft Academic Search

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

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

182

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

E-print Network

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 ...

deHoop, Maarten V.

2006-03-01

183

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

PubMed

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

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

2014-01-01

184

Designing a Multistage Supply Chain in Cross-Stage Reverse Logistics Environments: Application of Particle Swarm Optimization Algorithms  

PubMed Central

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), VMax 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

Chiang, Tzu-An; Che, Z. H.

2014-01-01

185

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

NASA Technical Reports Server (NTRS)

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.

Fiebrich, Rolf-Dieter

1987-01-01

186

The Applications of Genetic Algorithms in Stock Market Data Mining Optimisation  

E-print Network

, NSW 2007, Australia Capital Market CRC, Sydney NSW 2000, Australia Abstract In stock marketThe Applications of Genetic Algorithms in Stock Market Data Mining Optimisation Li Lin, Longbing: Technical trading rule; Genetic Algorithm; sub-domain; Parameter combination; 1 Introduction In stock market

Cao, Longbing

187

THE APPLICATION OF A GENETIC ALGORITHM FOR A TWO LINK PENDULUM PROGRAMMED STIMULATION  

Microsoft Academic Search

Natural evolution is intrinsically a robust search and optimization mechanism. Genetic algorithm uses operators taken from natural evolution. This method is fundamentally iterative operating on a set of candidate solutions, which is called a population. All the population evolves toward better candidate solutions. As subject for the genetic algorithm application is a two link pendulum, which tried to be a

Sergiu-Boris CONONOVICI

188

Adaptive-intelligent control by neural-network and genetic-algorithm systems and its application  

Microsoft Academic Search

As a attempt towards brain-computing, adaptive-intelligent controls by neural-network and genetic-algorithm systems are studied. As an application the computer-simulation system for nano-structured materials is constructed

Y. Yamazaki; V. Aiyoshin; J. Krasilnikova; I. Krasilnikov

1998-01-01

189

Application of Bayesian Hierarchical Models in Genetic Data Analysis  

E-print Network

. 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...

Zhang, Lin

2012-08-15

190

Genetically engineered phage fibers and coatings for antibacterial applications  

E-print Network

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 ...

Mao, Joan Y

2009-01-01

191

Inducible and Reversible Enhancement of Learning, Memory, and Long-Term Potentiation by Genetic Inhibition of Calcineurin  

Microsoft Academic Search

The threshold for hippocampal-dependent synaptic plasticity and memory storage is thought to be determined by the balance between protein phosphorylation and dephosphorylation mediated by the kinase PKA and the phosphatase calcineurin. To establish whether endogenous calcineurin acts as an inhibitory constraint in this balance, we examined the effect of genetically inhibiting calcineurin on plasticity and memory. Using the doxycycline-dependent rtTA

Gaël Malleret; Ursula Haditsch; David Genoux; Matthew W. Jones; Tim V. P. Bliss; Amanda M. Vanhoose; Carl Weitlauf; Eric R. Kandel; Danny G. Winder; Isabelle M. Mansuy

2001-01-01

192

Reverse micelle mediated synthesis, processing, mechanical and biological characterization of hydroxyapatite nanopowders for bone graft application  

NASA Astrophysics Data System (ADS)

Hydroxyapatite (HA) is the most widely used bioceramic material in bone graft applications because of its compositional similarity with natural bone. However, synthetic HA does not show similar mechanical and biological properties to the inorganic component of bone. Properties of ceramic material depend on starting materials, processing techniques, densification and microstructure of the final product. The objective of this research was to process HA whisker reinforced HA composite using HA nanopowders and whiskers. HA nanopowders with different length scale and morphology were synthesized by reverse micelle system using NP5 and NP12 as surfactants and cyclohexane as organic solvent. The lowest average aspect ratio was 1.357+/-0.39 with average particle size of 66 nm and the highest average aspect ratio was 7.277+/-3.227 with average length of 150 nm and width of 20 nm, were synthesized. Micron sized HA whiskers with aspect ratio between 20 and 50, average particle length of 15 mum and width of 400 nm was synthesized using urea as a precipitating agent. Desired microstructure was obtained after sintering with spherical HA nanopowder and whiskers along with dopants. Addition of whiskers decreased density of the sintered compacts. However, at 10 wt% whisker content sample showed microhardness and fracture toughness of 3.6 GPa and 1.5 MPa.m1/2, respectively, and a compressive strength of 80 MPa was obtained. Mineralization study in simulated body fluid (SBF) showed formation of apatite layer on the dense HA compacts indicating a good tendency of bond formation with natural bone. Cytotoxicity results showed excellent cell attachment on the HA surface. In the Appendices, 3 journal articles have been attached which describe synthesis, processing and characterization of undoped and doped PZT nanopowders. Free standing and agglomerated PZT nanopowders were synthesized by the sucrose templated method and the citrate nitrate autocombustion method. Particle size in the range of 50 to 90 nm was obtained. The effect of dopants on sintering and dielectric properties was studied by varying the amount of ZnO, SrO and La2O3 addition in PZT nanopowders. Sintering temperature of the bulk PZT was reduced to 900°C compared to the conventional sintering temperature of 1285°C and the highest dielectric constant of about 2100 was obtained.

Banerjee, Ashis

193

Noise of model target type thrust reversers for engine-over-the-wing applications  

NASA Technical Reports Server (NTRS)

The results of experiments on the noise generated by V-gutter and semicylindrical target reversers with circular and short-aspect-ratio slot nozzles having diameters of about 5 cm are presented. The experiments were conducted with cold-flow jets at velocities from 190-290 m/sec. The reversers at subsonic jet velocities had a more uniform noise distribution and higher frequency than the nozzles alone. The reverser shape was shown to be more important than the nozzle shape in determining the noise characteristics. The maximum sideline pressure level varied with the sixth power of the jet velocity, and the data were correlated for angles along the sideline. An estimate of the noise level along the 152 m sideline for an engine-over-the-wing powered-lift airplane was made.

Stone, J. R.; Gutierrez, O. A.

1974-01-01

194

Clinical Application of Genetics in Management of Colorectal Cancer  

PubMed Central

The extensive study of genetic alterations in colorectal cancer (CRC) has led to molecular diagnostics playing an increasingly important role in CRC diagnosis and treatment. Currently, it is believed that CRC is a consequence of the accumulation of both genetic and epigenetic genomic alterations. It is known that there are at least 3 major pathways that lead to colorectal carcinogenesis: (1) the chromosomal instability pathway, (2) the microsatellite instability pathway, and (3) the cytosine-phospho-guanine island methylator phenotype pathway. With recent advances in CRC genetics, the identification of specific molecular alterations responsible for CRC pathogenesis has directly influences clinical care. Patients at high risk for developing CRC can be identified by genetic testing for specific molecular alterations, and the use of molecular biomarkers for predictive and prognostic purposes is also increasing. This is clearly supported by the recent advances in genetic testing for CRC whereby specific molecular alterations are identified for the purpose of guiding treatment with targeting therapies such as anti-endothelial growth factor receptor monoclonal antibodies. PMID:25349592

Kim, Eun Ran

2014-01-01

195

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

PubMed

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

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

2010-09-01

196

Approximation for the enhancement factor applicable to reversible reactions of finite rate in chemically loaded solutions  

Microsoft Academic Search

A new explicit relation is proposed for the prediction of the enhancement factor for reversible reactions of finite rate in chemically loaded solutions which also allows for unequal diffusivities. The relation for the enhancement factor is not based on an approximation of the absorption process, but is derived from a similarity which can be observed between the results of the

J. A. Hogendoorn; R. D. Vas Bhat; J. A. M. Kuipers; W. P. M. van Swaaij; G. F. Versteeg

1997-01-01

197

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...

198

A field-reversed magnetic configuration and applications of high-temperature FRC plasma  

SciTech Connect

As applied to a tokomak, a magnetic trap for confinement of a plasma with an inverted field or a magnetic field reversed configuration (FRC) is one of the most promising alternatives of the systems with high {beta}. A brief review of the latest data on FRC and potential directions of using such configurations in addition to energy generation in thermonuclear reactors (TNRs) is proposed.

Ryzhkov, S. V., E-mail: ryzhkov@power.bmstu.ru [Bauman Moscow State Technical University (Russian Federation)

2011-12-15

199

Reverse Correlation in Neurophysiology  

ERIC Educational Resources Information Center

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…

Ringach, Dario; Shapley, Robert

2004-01-01

200

Asymmetry in Family History Implicates Nonstandard Genetic Mechanisms: Application to the Genetics of Breast Cancer  

PubMed Central

Genome-wide association studies typically target inherited autosomal variants, but less studied genetic mechanisms can play a role in complex disease. Sex-linked variants aside, three genetic phenomena can induce differential risk in maternal versus paternal lineages of affected individuals: 1. maternal effects, reflecting the maternal genome's influence on prenatal development; 2. mitochondrial variants, which are inherited maternally; 3. autosomal genes, whose effects depend on parent of origin. We algebraically show that small asymmetries in family histories of affected individuals may reflect much larger genetic risks acting via those mechanisms. We apply these ideas to a study of sisters of women with breast cancer. Among 5,091 distinct families of women reporting that exactly one grandmother had breast cancer, risk was skewed toward maternal grandmothers (p<0.0001), especially if the granddaughter was diagnosed between age 45 and 54. Maternal genetic effects, mitochondrial variants, or variant genes with parent-of-origin effects may influence risk of perimenopausal breast cancer. PMID:24651610

Weinberg, Clarice R.; Shi, Min; DeRoo, Lisa A.; Taylor, Jack A.; Sandler, Dale P.; Umbach, David M.

2014-01-01

201

Application of Genetic Algorithm in Architectural Conceptual Design  

Microsoft Academic Search

A genetic algorithm for supporting architectural conceptual design is presented in this paper. The algorithm adopts mathematical expression binary tree based coded approach, corresponding crossover and mutation operations, and the combination of objective function and interaction with designers for getting fitness values to generate simple curves. The selected shapes are dealt with via 3D visualizing technology to form entities. These

LIU Hong; LI Yan

2006-01-01

202

Application of genetic algorithms in resource constrained network optimization  

Microsoft Academic Search

There are limited solution techniques available for resource constrained project scheduling problems with stochastic task durations. Due to computational complexity, scheduling heuristics have been found useful for large deterministic problems. In this paper, the authors demonstrate the use of a genetic algorithm to optimize over a linear combination of scheduling heuristics. A simulation model is used to evaluate the performance

J. Pet-Edwards; M. Mollaghasemi

1995-01-01

203

Genetic transformation of conifers and its application in forest biotechnology  

Microsoft Academic Search

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.

W. Tang; R. J. Newton

2003-01-01

204

On Application of the Local Search and the Genetic Algorithms ...  

E-print Network

genetic operators haven't been found yet or do not exists at all. In the remaining part of ... Both Optimal Binary Tree and Optimal Binary Search Tree problems can be ...... sample. In Robert E. Macho, editor, Information and Decision Processes,.

2010-04-29

205

Genetics  

NSDL National Science Digital Library

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.

Doherty, Jennifer; Waldron, Ingrid; Poethig, Scott

206

Reverse Genetics of Drosophila RNA Polymerase II: Identification and Characterization of Rpii140, the Genomic Locus for the Second-Largest Subunit  

PubMed Central

We have used a reverse genetics approach to isolate genes encoding two subunits of Drosophila melanogaster RNA polymerase II. RpII18 encodes the 18-kDa subunit and maps cytogenetically to polytene band region 83A. RpII140 encodes the 140-kDa subunit and maps to polytene band region 88A10:B1,2. Focusing on RpII140, we used in situ hybridization to map this gene to a small subinterval defined by the endpoints of a series of deficiencies impinging on the 88A/B region and showed that it does not represent a previously known genetic locus. Two recently defined complementation groups, A5 and Z6, reside in the same subinterval and thus were candidates for the RpII140 locus. Phenotypes of A5 mutants suggested that they affect RNA polymerase II, in that the lethal phase and the interaction with developmental loci such as Ubx resemble those of mutants in the gene for the largest subunit, RpII215. Indeed, we have achieved complete genetic rescue of representative recessive lethal mutations of A5 with a P-element construct containing a 9.1-kb genomic DNA fragment carrying RpII140. Interestingly, the initial construct also rescued lethal alleles in the neighboring complementation group, Z6, revealing that the 9.1-kb insert carries two genes. Deleting coding region sequences of RpII140, however, yielded a transformation vector that failed to rescue A5 alleles but continued to rescue Z6 alleles. These results strongly support the conclusion that the A5 complementation group is equivalent to the genomic RpII140 locus. PMID:8325487

Hamilton, B. J.; Mortin, M. A.; Greenleaf, A. L.

1993-01-01

207

Application of a recycle dialysis system in a reversed micellar reactor.  

PubMed

A recycle dialysis stirred cell has been successfully used for integrating the reaction and product recovery of the lipase-catalyzed hydrolysis of olive oil in bis(2-ethylhexyl) sodium sulfosuccinate (AOT)-iso-octane reversed micelles. The resistance of membrane to reversed micelles was monitored by the water content and found to be 95.9% rejection after 24 h and 93.4% rejection after 48 h. The resistance of the membrane to free surfactants, by monitoring the UV absorption, was found to be 98.5% rejection after 10 h and 97.3% rejection after 24 h. Mathematical formulations involving the enzymatic reaction coupled with mass transfer were developed for predicting the performance of a membrane reactor. Theoretical predictions in terms of time course of oleic acid concentrations were found to be in agreement with the experimental results. PMID:1368237

Chiang, C L; Tsai, S W

1992-01-01

208

Application of physicochemically modified silicon substrates as reverse-phase protein microarrays.  

PubMed

Physicochemically modified silicon substrates can provide a high quality alternative to nitrocellulose-coated glass slides for use in reverse-phase protein microarrays. Enhancement of protein microarray sensitivities is an important goal, especially because molecular targets within patient tissues exist in low abundance. The ideal array substrate has a high protein binding affinity and low intrinsic background signal. Silicon, which has low intrinsic autofluorescence, is being explored as a potential microarray surface. In a previous paper ( Nijdam , A. J. ; Cheng , M. M.-C. ; Fedele , R. ; Geho , D. H. ; Herrmann , P. ; Killian , K. ; Espina , V. ; Petricoin , E. F. ; Liotta , L. A. ; Ferrari , M. Physicochemically Modified Silicon as Substrate for Protein Microarrays . Biomaterials 2007 , 28 , 550 - 558 ), it is shown that physicochemical modification of silicon substrates increases the binding of protein to silicon to a level comparable with that of nitrocellulose. Here, we apply such substrates in a reverse-phase protein microarray setting in two model systems. PMID:19170514

Nijdam, A Jasper; Zianni, Michael R; Herderick, Edward E; Cheng, Mark M-C; Prosperi, Jenifer R; Robertson, Fredika A; Petricoin, Emanuel F; Liotta, Lance A; Ferrari, Mauro

2009-03-01

209

Quantitative Reverse Sample Genome Probing of Microbial Communities and Its Application to Oil Field Production Waters  

PubMed Central

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters. Images PMID:16349111

Voordouw, Gerrit; Shen, Yin; Harrington, Clare S.; Telang, Anita J.; Jack, Thomas R.; Westlake, Donald W. S.

1993-01-01

210

Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters  

SciTech Connect

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters.

Voordouw, G.; Shen, Y.; Harrington, C.S.; Teland, A.J. (Univ. of Calgary, Alberta (Canada)); Jack, T.R. (Novacor Research and Technology Corporation, Calgary, Alberta (Canada)); Westlake, W.S. (Univ. of Alberta (Canada))

1993-12-01

211

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

Microsoft Academic Search

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.

J. M. Schredder; T. Fujita

1984-01-01

212

REVERSED PHASE LIQUID CHROMATOGRAPHIC DETERMINATION OF VINPOCETINE IN HUMAN PLASMA AND ITS PHARMACOKINETIC APPLICATION  

Microsoft Academic Search

A simple, rapid specific and reliable high performance liquid chromatographic assay of vinpocetine in human plasma has been developed. Reversed phase chromatography was conducted using a mobile phase of methanol : water (80 : 20 v\\/v), containing 0.1% triethylamine, pH 7, adjusted with glacial acetic acid. The flow rate was 2 mL\\/min, UV detection at 274 nm. The drug after extraction from plasma was chromatographed using a C18

A. Abd Elbary; N. Foda; O. El-Gazayerly; M. El Khatib

2002-01-01

213

Development and application of a reverse Monte Carlo radiative transfer code for rocket plume base heating  

NASA Technical Reports Server (NTRS)

A reverse Monte Carlo radiative transfer code to predict rocket plume base heating is presented. In this technique rays representing the radiation propagation are traced backwards in time from the receiving surface to the point of emission in the plume. This increases the computational efficiency relative to the forward Monte Carlo technique when calculating the radiation reaching a specific point, as only the rays that strike the receiving point are considered.

Everson, John; Nelson, H. F.

1993-01-01

214

Application of the Integrated-Blanket-Coil concept to a compact reversed-field pinch reactor  

Microsoft Academic Search

The Integrated-Blanket-Coil (IBC) concept has been examined in the context of a compact reversed-field pinch (RFP) fusion reactor. The IBC approach is novel in that the functions of the blanket (tritium breeding and energy recovery) and the coil (magnetic field production) are fulfilled in a single component. This combination of functions is accomplished by using lithium metal as the coolant,

Duggan

1987-01-01

215

Cassava genetic transformation and its application in breeding.  

PubMed

As a major source of food, cassava (Manihot esculenta Crantz) is an important root crop in the tropics and subtropics of Africa and Latin America, and serves as raw material for the production of starches and bioethanol in tropical Asia. Cassava improvement through genetic engineering not only overcomes the high heterozygosity and serious trait separation that occurs in its traditional breeding, but also quickly achieves improved target traits. Since the first report on genetic transformation in cassava in 1996, the technology has gradually matured over almost 15 years of development and has overcome cassava genotype constraints, changing from mode cultivars to farmer-preferred ones. Significant progress has been made in terms of an increased resistance to pests and diseases, biofortification, and improved starch quality, building on the fundamental knowledge and technologies related to planting, nutrition, and the processing of this important food crop that has often been neglected. Therefore, cassava has great potential in food security and bioenergy development worldwide. PMID:21564542

Liu, Jia; Zheng, Qijie; Ma, Qiuxiang; Gadidasu, Kranthi Kumar; Zhang, Peng

2011-07-01

216

A reversal coarse-grained analysis with application to an altered functional circuit in depression  

PubMed Central

Introduction When studying brain function using functional magnetic resonance imaging (fMRI) data containing tens of thousands of voxels, a coarse-grained approach – dividing the whole brain into regions of interest – is applied frequently to investigate the organization of the functional network on a relatively coarse scale. However, a coarse-grained scheme may average out the fine details over small spatial scales, thus rendering it difficult to identify the exact locations of functional abnormalities. Methods A novel and general approach to reverse the coarse-grained approach by locating the exact sources of the functional abnormalities is proposed. Results Thirty-nine patients with major depressive disorder (MDD) and 37 matched healthy controls are studied. A circuit comprising the left superior frontal gyrus (SFGdor), right insula (INS), and right putamen (PUT) exhibit the greatest changes between the patients with MDD and controls. A reversal coarse-grained analysis is applied to this circuit to determine the exact location of functional abnormalities. Conclusions The voxel-wise time series extracted from the reversal coarse-grained analysis (source) had several advantages over the original coarse-grained approach: (1) presence of a larger and detectable amplitude of fluctuations, which indicates that neuronal activities in the source are more synchronized; (2) identification of more significant differences between patients and controls in terms of the functional connectivity associated with the sources; and (3) marked improvement in performing discrimination tasks. A software package for pattern classification between controls and patients is available in Supporting Information. PMID:24363967

Guo, Shuixia; Yu, Yun; Zhang, Jie; Feng, Jianfeng

2013-01-01

217

Application of genetic algorithms for optimization of tire pitch sequences  

Microsoft Academic Search

A simple genetic algorithms (GAs) has been applied to generate the optimum pitch sequence. Though a simple GAs worked properly,\\u000a there was the problem of the premature convergence. To solve this problem, we introduced the new operator named the growth\\u000a and combined it with a simple GAs. The growth operator, which is a kind of the hill-climbing technique, has the

Yukio Nakajima; Akihiko Abe

2000-01-01

218

Negative-Strand RNA Viruses: Genetic Engineering and Applications  

Microsoft Academic Search

The negative-strand RNA viruses are a broad group of animal viruses that comprise several important human pathogens, including influenza, measles, mumps, rabies, respiratory syncytial, Ebola, and hantaviruses. The development of new strategies to genetically manipulate the genomes of negative-strand RNA viruses has provided us with new tools to study the structure--function relationships of the viral components and their contributions to

Peter Palese; Hongyong Zheng; Othmar G. Engelhardt; Stephan Pleschka; Adolfo Garcia-Sastre

1996-01-01

219

Tools for genetic manipulations in Corynebacterium glutamicum and their applications  

Microsoft Academic Search

Corynebacterium glutamicum is an important industrial producer of various amino acids with great potential for the production of other metabolites.\\u000a The complete genome sequences of two C. glutamicum strains were determined and the use of genome-based approaches (transcriptomics, proteomics, metabolomics, and fluxomics)\\u000a provided large amounts of data on the metabolism of this bacterium and its regulation. Many tools for genetic

Jan Nešvera; Miroslav Pátek

2011-01-01

220

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

NASA Astrophysics Data System (ADS)

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

Sastry, Kumara Narasimha

221

Application of information-logical approach to studies of genetic systems  

SciTech Connect

A new information technology, the information-logical approach (ILA), which is based on information theory methods and the fuzzy sets theory, is considered. This method can be applied for the majority of biological and ecological studies, and in genetics. In breeding and genetic studies, ILA can be used as a basis for the development of methods that will allow one to take into account ecological, geographic, climatic, and other peculiarities of trait expression that influence productivity. Application of ILA also opens new prospects for analyzing results of genetic and ecological monitoring (e.g., post-Chernobyl` monitoring) to predict further behavior of the systems studied. This paper presents a general outline of information analysis, describes a block of one-factor analysis, which was implemented on a personal computer and has a user-friendly interface, and also presents several examples concerning application of ILA to specific genetic systems.

Dromashko, S.E.; Frenkel`, G.I.; Dubovskoi, B.O. [Institute of Genetics and Cytology, Minsk (Russian Federation)

1995-01-01

222

Next-generation sequencing technologies and applications for human genetic history and forensics  

PubMed Central

Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics. PMID:22115430

2011-01-01

223

Genetics  

NSDL National Science Digital Library

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.

National Science Teachers Association (NSTA)

2005-04-01

224

On thermodynamic and microscopic reversibility  

SciTech Connect

The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa.

Crooks, Gavin E.

2011-07-12

225

Application of genetic algorithms in nonlinear heat conduction problems.  

PubMed

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

Kadri, Muhammad Bilal; Khan, Waqar A

2014-01-01

226

[Application of population genetics in the field of medicine].  

PubMed

Human populations follow the same evolutionary principles as other organisms, although mixed with social and cultural elements, which can result in a high prevalence of certain diseases within specific ethnic groups. In this work, the Hardy-Weinberg principle is analyzed from a medical, social and biological viewpoint to understand the evolutionary processes of autosomal recessive diseases. It can be concluded that the incidence of these diseases is inversely related to the levels of genetic variability within populations, which depends on colonization, recolonization and migration events, as well as on social conventions such as racism, social stratification and segregation. PMID:24967923

Octavio-Aguilar, Pablo; Ramos-Frías, Josefina

2014-01-01

227

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

PubMed

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

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

2011-08-01

228

genetics  

NSDL National Science Digital Library

learning about our genetic make up We've been learning about DNA. Go to each web site, read and follow the instructions of the activities provided. On a piece of paper write your answers to the following questions and submit your work. Put the site for each of the questions you are answering. The first site is, ...

Curran, Carolyn

2011-12-05

229

Successful application of preimplantation genetic diagnosis for hypokalaemic periodic paralysis.  

PubMed

Hypokalaemic periodic paralysis is a rare dominant inherited disease where a person suffers sudden falls of circulating potassium concentrations, producing muscle weakness and sometimes severe paralysis. Attacks can occur as frequently as several times a day or once in a year. The age of onset is usually adolescence but symptoms can appear as early as 10 years of age. Muscle weakness can compromise vital functions such as breathing or swallowing and heart arrhythmias are also frequent during attacks. Preimplantation genetic diagnosis, an early form of prenatal diagnosis for couples at risk of transmitting inherited diseases, was used to prevent the transmission of this disease. Six polymorphic short tandem repeat or microsatellite markers (STR) closely linked to the CACNA1S gene were tested. Three fully informative markers were chosen to establish the disease-bearing haplotype in the family and to determine the genetic status of five embryos by multiplex fluorescent heminested PCR. Four of the five embryos tested were diagnosed as non-affected and one as affected. Two embryos were transferred resulting in a singleton pregnancy and the birth of a healthy girl. PMID:20541469

Alberola, Trinitat M; Vendrell, Xavier; Bautista-Llácer, Rosa; Vila, Maria; Calatayud, Carmen; Pérez-Alonso, Manuel

2010-08-01

230

Feature generation using genetic programming with application to fault classification.  

PubMed

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

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

2005-02-01

231

Application of Genetic Algorithm to Hexagon-Based Motion Estimation  

PubMed Central

With the improvement of science and technology, the development of the network, and the exploitation of the HDTV, the demands of audio and video become more and more important. Depending on the video coding technology would be the solution for achieving these requirements. Motion estimation, which removes the redundancy in video frames, plays an important role in the video coding. Therefore, many experts devote themselves to the issues. The existing fast algorithms rely on the assumption that the matching error decreases monotonically as the searched point moves closer to the global optimum. However, genetic algorithm is not fundamentally limited to this restriction. The character would help the proposed scheme to search the mean square error closer to the algorithm of full search than those fast algorithms. The aim of this paper is to propose a new technique which focuses on combing the hexagon-based search algorithm, which is faster than diamond search, and genetic algorithm. Experiments are performed to demonstrate the encoding speed and accuracy of hexagon-based search pattern method and proposed method. PMID:24592178

Cheng, Wan-Shu

2014-01-01

232

Application of physicochemically modified silicon substrates as reverse phase protein microarrays  

PubMed Central

Physicochemically modified silicon substrates can provide a high quality alternative to nitrocellulose-coated glass slides for use in reverse-phase protein microarrays. Enhancement of protein microarray sensitivities is an important goal, especially because molecular targets within patient tissues exist in low abundance. The ideal array substrate has a high protein binding affinity and low intrinsic background signal. Silicon, which has low intrinsic autofluorescence, is being explored as a potential microarray surface. In a previous paper (Nijdam, A.J., Cheng, M.M.C., Fedele, R., Geho, D.H., Herrmann, P., Killian, K., Espina, V., Petricoin, E.F., Liotta, L.A., Ferrari, M. (2007) Physicochemically Modified Silicon As Substrate For Protein Microarrays Biomater, 28, 550-558), it is shown that physicochemical modification of silicon substrates increases the binding of protein to silicon to a level comparable with that of nitrocellulose. Here, we apply such substrates in a reverse-phase protein microarray setting in two model systems. PMID:19170514

Jasper Nijdam, A.; Zianni, Michael R.; Herderick, Edward E.; Cheng, Mark M-C; Prosperi, Jenifer R.; Robertson, Fredika A.; Petricoin, Emanuel F.; Liotta, Lance A.; Ferrari, Mauro

2009-01-01

233

Prospects for applications of genetic engineering in pig breeding P. MULSANT, M. DALENS, Genevive ECHARD, J. GELLIN,  

E-print Network

Prospects for applications of genetic engineering in pig breeding P. MULSANT, M. DALENS, Geneviève, 31326 Castanet-Tolosan Cedex Genetic engineering provides an extremely high number of cloned mammalian DNA sequences. These sequences should be powerful tools for genetic analysis or improvement of the pig

Paris-Sud XI, Université de

234

Application of Silica-Based Hyper-Crosslinked Sulfonate-Modified Reversed Stationary Phases for Separating Highly Hydrophilic Basic Compounds  

PubMed Central

The separation and determination of hydrophilic basic compounds are of great importance in many fields including clinical and biological research, pharmaceutical development and forensic analysis. However, the most widely used analytical separation technique in these disciplines, reversed-phase liquid chromatography (RPLC), usually does not provide sufficient retention for several of the important classes of highly hydrophilic basic compounds including catecholamines, many drug metabolites and many drugs of abuse. Commonly eluents having little or no organic modifier and/or strong ion pairing agents must be used to achieve sufficient retention and separation. Use of highly aqueous eluents can lead to column failure by dewetting, resulting in poor retention, selectivity, reproducibility and slow recovery of performance. The use of a strong ion pairing agent to increase retention renders the separation incompatible with mass spectrometric detection and complicates preparative separations. This paper describes the successful applications of a novel type of silica-based, hyper-crosslinked, sulfonate-modified reversed stationary phase, denoted as ?SO3-HC-C8-L, for the separation of highly hydrophilic cations and related compounds by a hydrophobically assisted cation-exchange mechanism. Compared to conventional reversed-phases, the ?SO3-HC-C8-L phase showed significantly improved retention and separation selectivity. Concurrently, due to the presence of both cation-exchange and reversed-phase retention mechanisms and the high acid stability of hyper-crosslinked phases, the separation can be optimized by changing the type or concentration of ionic additive or organic modifier, and by varying the column temperature. In addition, gradients generated by programming the concentration of either the ionic additive or the organic modifier can be applied to reduce the analysis time without compromising resolution. Furthermore, remarkably different chromatographic selectivities, especially toward cationic solutes, were observed upon comparison of the ?SO3-HC-C8-L phase with conventional reversed-phases. We believe that the combination of these two types of stationary phases will be very useful in two-dimensional liquid chromatography. PMID:18617181

Luo, Hao; Ma, Lianjia; Paek, Changyub; Carr, Peter W.

2008-01-01

235

Application of Adjoint Methodology to Supersonic Aircraft Design Using Reversed Equivalent Areas  

NASA Technical Reports Server (NTRS)

This paper presents an approach to shape an aircraft to equivalent area based objectives using the discrete adjoint approach. Equivalent areas can be obtained either using reversed augmented Burgers equation or direct conversion of off-body pressures into equivalent area. Formal coupling with CFD allows computation of sensitivities of equivalent area objectives with respect to aircraft shape parameters. The exactness of the adjoint sensitivities is verified against derivatives obtained using the complex step approach. This methodology has the benefit of using designer-friendly equivalent areas in the shape design of low-boom aircraft. Shape optimization results with equivalent area cost functionals are discussed and further refined using ground loudness based objectives.

Rallabhandi, Sriram K.

2013-01-01

236

Applications of the Integrated-Blanket-Coil concept to the compact reversed-field pinch reactor  

SciTech Connect

A design of a compact fusion reactor is proposed based on the reversed field pinch and utilizing the ''Integrated-Blanket-Coil'' (IBC) concept. The IBC is applied to the toroidal field and divertor systems, with liquid metal used for cooling both the first wall and blanket. This simplifies the overall design by requiring only a single coolant cycle. In addition, safety is increased by eliminating any possible lithium-water interaction in the fusion power core. Finally, replacing conventional copper divertor coils with IBC components enhances tritium breeding and energy recovery. A generic problem with liquid metal coolants is their reduced heat transfer capabilities in magnetic fields. In this context, the use of liquid metal coolants may limit the allowable neutron wall loading to a value of 10 MW/m/sup 2/. Above this value it may be necessary to use water cooling for the first wall and divertor surfaces.

Duggan, W.P.; Steiner, D.; Embrechts, M.J.

1986-11-01

237

Non-Genetic Engineering Approaches for Isolating and Generating Novel Yeasts for Industrial Applications  

NASA Astrophysics Data System (ADS)

Generating novel yeast strains for industrial applications should be quite straightforward; after all, research into the genetics, biochemistry and physiology of Baker's Yeast, Saccharomyces cerevisiae, has paved the way for many advances in the modern biological sciences. We probably know more about this humble eukaryote than any other, and it is the most tractable of organisms for manipulation using modern genetic engineering approaches. In many countries, however, there are restrictions on the use of genetically-modified organisms (GMOs), particularly in foods and beverages, and the level of consumer acceptance of GMOs is, at best, variable. Thus, many researchers working with industrial yeasts use genetic engineering techniques primarily as research tools, and strain development continues to rely on non-GM technologies. This chapter explores the non-GM tools and strategies available to such researchers.

Chambers, P. J.; Bellon, J. R.; Schmidt, S. A.; Varela, C.; Pretorius, I. S.

238

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

PubMed

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

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

239

Generation by Reverse Genetics of an Effective, Stable, Live-Attenuated Newcastle Disease Virus Vaccine Based on a Currently Circulating, Highly Virulent Indonesian Strain  

PubMed Central

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

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

240

Molecular Identification and Genetic Analysis of Norovirus Genogroups I and II in Water Environments: Comparative Analysis of Different Reverse Transcription-PCR Assays?  

PubMed Central

Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses. PMID:17483265

La Rosa, G.; Fontana, S.; Di Grazia, A.; Iaconelli, M.; Pourshaban, M.; Muscillo, M.

2007-01-01

241

Genetic algorithms  

NASA Technical Reports Server (NTRS)

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.

Wang, Lui; Bayer, Steven E.

1991-01-01

242

A “Reverse-Schur” Approach to Optimization With Linear PDE Constraints: Application to Biomolecule Analysis and Design  

PubMed Central

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule’s electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts–in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method. PMID:23055839

Bardhan, Jaydeep P.; Altman, Michael D.

2009-01-01

243

Potassium channel openers increase aortic elastic fiber formation and reverse the genetically determined elastin deficit in the BN rat.  

PubMed

Hypertension is a cardiovascular disorder that appears in more than half of the patients with Williams-Beuren syndrome, hemizygous for the elastin gene among 26 to 28 other genes. It was shown that the antihypertensive drug minoxidil, an ATP-dependent potassium channel opener, enhances elastic fiber formation; however, no wide clinical application was developed because of its adverse side effects. The Brown Norway rat was used here as an arterial elastin-deficient model. We tested 3 different potassium channel openers, minoxidil, diazoxide, and pinacidil, and 1 potassium channel blocker, glibenclamide, on cultured smooth muscle cells from Brown Norway rat aorta. All tested potassium channel openers increased mRNAs encoding proteins and enzymes involved in elastic fiber formation, whereas glibenclamide had the opposite effect. The higher steady-state level of tropoelastin mRNA in minoxidil-treated cells was attributable to an increase in both transcription and mRNA stability. Treatment of Brown Norway rats for 10 weeks with minoxidil or diazoxide increased elastic fiber content and decreased cell number in the aortic media, without changing collagen content. The minoxidil-induced cardiac hypertrophy was reduced when animals simultaneously received irbesartan, an angiotensin II-receptor antagonist. This side effect of minoxidil was not observed in diazoxide-treated animals. In conclusion, diazoxide, causing less undesirable side effects than minoxidil, or coadministration of minoxidil and irbesartan, increases elastic fiber content, decreases cell number in the aorta and, thus, could be suitable for treating vascular pathologies characterized by diminished arterial elastin content and simultaneous hypertension. PMID:23918751

Slove, Séverin; Lannoy, Morgane; Behmoaras, Jacques; Pezet, Mylène; Sloboda, Natacha; Lacolley, Patrick; Escoubet, Brigitte; Buján, Julia; Jacob, Marie-Paule

2013-10-01

244

Orbit determination by genetic algorithm and application to GEO observation  

NASA Astrophysics Data System (ADS)

This paper demonstrates an initial orbit determination method that solves the problem by a genetic algorithm using two well-known solutions for the Lambert's problem: universal variable method and Battin method. This paper also suggests an intuitive error evaluation method in terms of rotational angle and orbit shape by separating orbit elements into two groups. As reference orbit, mean orbit elements (original two-lines elements) and osculating orbit elements considering the J2 effect are adopted and compared. Our proposed orbit determination method has been tested with actual optical observations of a geosynchronous spacecraft. It should be noted that this demonstration of the orbit determination is limited to one test case. This observation was conducted during approximately 70 min on 2013/05/15 UT. Our method was compared with the orbit elements propagated by SGP4 using the TLE of the spacecraft. The result indicates that our proposed method had a slightly better performance on estimating orbit shape than Gauss's methods and Escobal's method by 120 km. In addition, the result of the rotational angle is closer to the osculating orbit elements than the mean orbit elements by 0.02°, which supports that the estimated orbit is valid.

Hinagawa, Hideaki; Yamaoka, Hitoshi; Hanada, Toshiya

2014-02-01

245

Credit card fraud detection: An application of the gene expression messy genetic algorithm  

SciTech Connect

This paper describes an application of the recently introduced gene expression messy genetic algorithm (GEMGA) (Kargupta, 1996) for detecting fraudulent transactions of credit cards. It also explains the fundamental concepts underlying the GEMGA in the light of the SEARCH (Search Envisioned As Relation and Class Hierarchizing) (Kargupta, 1995) framework.

Kargupta, H.; Gattiker, J.R.; Buescher, K.

1996-05-01

246

Application of Fluorescence In Situ Hybridization (FISH) to Fish Genetics and Genome Mapping  

Microsoft Academic Search

The various applications of the technique of fluorescence in situ hybridization (FISH) to fish genetics will be reviewed for fishes being used as model organisms to study human disease, including those species for which major genome projects have been initiated. ``FISH on fish'' has been used to map highly repetitive sequences including centromere-specific sequences and sex-specific sequences, moderately repetitive sequences

Ruth B. Phillips

2001-01-01

247

Application of Genetic Algorithms in Colombian Interconnected Power System Operative Planning  

Microsoft Academic Search

Each interconnected electric system has to define its operating mode and how expansion and operation planning are made. This paper presents the first phase of the work of implementing a tool with application to Colombian power system operative planning. The tool uses genetic algorithms to optimize the cost functions that arise in which the elements of the system are the

Jaime A. Valencia; Walter M. Villa; Esteban Velilla; G. Marin A; José I. Gutiérrez; Mónica M. Montoya

2009-01-01

248

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

E-print Network

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

Paris-Sud XI, Université de

249

A Java collaborative interface for genetic programming applications: image analysis for scientific inquiry  

Microsoft Academic Search

Discusses several key issues involved in designing and using a Java collaborative interface for genetic programming applications over the World Wide Web. We present our implementation that has been used in a new system that assists scientists in classifying and extracting novel features in remotely sensed satellite imagery. This paper also identifies issues in developing a class library that facilitates

Tommaso F. Bersano-Begey; Jason M. Daida; John F. Vesecky; Frank L. Ludwig

1997-01-01

250

Applications of Differential-Display Reverse Transcription-PCR to Molecular Pathogenesis and Medical Mycology  

PubMed Central

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics. PMID:10885984

Sturtevant, Joy

2000-01-01

251

Control of nonlinear systems using periodic parametric perturbations with application to a reversed field pinch  

NASA Astrophysics Data System (ADS)

In this thesis, the possibility of controlling low- and high-dimensional chaotic systems by periodically driving an accessible system parameter is examined. This method has been carried out on several numerical systems and the MST Reversed Field Pinch. The numerical systems investigated include the logistic equation, the Lorenz equations, the Rossler equations, a coupled lattice of logistic equations, a coupled lattice of Lorenz equations, the Yoshida equations, which model tearing mode fluctuations in a plasma, and a neural net model for magnetic fluctuations on MST. This method was tested on the MST by sinusoidally driving a magnetic flux through the toroidal gap of the device. Numerically, periodic drives were found to be most effective at producing limit cycle behavior or significantly reducing the dimension of the system when the perturbation frequency was near natural frequencies of unstable periodic orbits embedded in the attractor of the unperturbed system. Several different unstable periodic orbits have been stabilized in this way for the low-dimensional numerical systems, sometimes with perturbation amplitudes that were less than 5% of the nominal value of the parameter being perturbed. In high- dimensional systems, limit cycle behavior and significant decreases in the system dimension were also achieved using perturbations with frequencies near the natural unstable periodic orbit frequencies. Results for the MST were not this encouraging, most likely because of an insufficient drive amplitude, the extremely high dimension of the plasma behavior, large amounts of noise, and a lack of stationarity in the transient plasma pulses.

Mirus, Kevin Andrew

252

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

NASA Astrophysics Data System (ADS)

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. Cost estimates are derived assuming the use of metal components and of advanced ceramics. (The latter reduces the costs by three- to five-fold). The process that led to the selection of the three reactions is described, and the effects of varying temperatures, pressures, and heat exchanger sizes are addressed. A state-of-the-art survey was performed as part of this study. As a result of this survey, it appears that formidable technical risks exist for any attempt to implement the systems analyzed in this study, especially in the area of reactor design and performance. The behavior of all components and complete systems under thermal energy transients is very poorly understood. This study indicates that thermochemical storage systems that store reactants as liquids have efficiencies below 60%, which is in agreement with the findings of earlier investigators.

Schredder, J. M.; Fujita, T.

1984-10-01

253

Bootstrap current in enhanced reversed shear tokamaks for volume neutron source applications  

SciTech Connect

The bootstrap current is evaluated for two reference tokamak designs for a Volume Neutron Source (VNS). One is a larger aspect ratio design using superconducting coils (VNS-SC) and the other is a small aspect ratio design using a solid core with normal conducting toroidal field coils (VNS-ST). The target plasma profiles are taken as representative of the recently observed enhanced reverse shear plasmas with hollow magnetic safety factor (q) profiles in the core and corresponding peaked density profiles. The higher q in the plasma center in combination with peaked density is shown to move the peak in the bootstrap current toward the plasma center. This reduces the current drive requirements to a very small axial seed current and a source localized around the location of the desired minimum in the q profile. Very high bootstrap current fractions can be attained in the VNS-SC design with normalized betas (defined in terms of the vacuum toroidal magnetic field at the geometric center of the plasma) of {beta}{sub N} {le} 3.5. The bootstrap current is lower in the VNS-ST design because of its lower aspect ratio; the highest bootstrap fraction found in these limited cases is 50% at {beta}{sub N} = 5.

Houlberg, W.A.

1995-12-31

254

Interactions of biomacromolecules with reverse hexagonal liquid crystals: Drug delivery and crystallization applications  

Microsoft Academic Search

Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications.The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products,

Dima Libster; Abraham Aserin; Nissim Garti

2011-01-01

255

Synthesis of anti-reverse cap analogs (ARCAs) and their applications in mRNA translation and stability.  

PubMed

Synthetic capped RNA transcripts produced by in vitro transcription in the presence of m(7)Gp(3)G have found a wide application in studying such processes as mRNA translation, pre-mRNA splicing, mRNA turnover, and intracellular transport of mRNA and snRNA. However, because of the presence of a 3'-OH on both m(7)Guo and Guo moieties of the cap structure, one-third to one-half of the mRNAs contain a cap incorporated in the reverse orientation. The reverse cap structures bind poorly to eIF4E, the cap binding protein, and reduce overall translational efficiency. We therefore replaced the conventional m(7)Gp(3)G cap by "anti-reverse" cap analogs (ARCAs) in which the 3'-OH of m(7)Guo moiety was substituted by 3'-deoxy or 3'-O-methyl groups, leading to m(7)3'dGp(3)G or m(2)(7,3'-O) Gp(3)G, respectively. The class of ARCAs was extended to analogs possessing an O-methyl group or deoxy group at C2' of m(7)Guo. We have also developed a series of ARCAs containing tetra- and pentaphosphates. mRNAs capped with various ARCAs were translated 1.1- to 2.6-fold more efficiently than their counterparts capped with m(7)Gp(3)G in both in vitro and in vivo systems. In a separate series, a methylene group was introduced between the alpha- and beta-, or beta- and gamma-phosphate moieties, leading to m(2)(7,3'-O)Gpp(CH2)pG and m(2)(7,3'-O)Gp(CH2)ppG. These analogs are resistant to cleavage by the decapping enzymes Dcp1/Dcp2 and DcpS, respectively. mRNA transcripts capped with m(2)(7,3'-O)Gpp(CH2)pG were more stable when introduced into cultured mammalian cells. In this chapter, we describe the synthesis of representative ARCAs and their biophysical and biochemical characterization, with emphasis on practical applications in mRNA translation. PMID:17923237

Grudzien-Nogalska, Ewa; Stepinski, Janusz; Jemielity, Jacek; Zuberek, Joanna; Stolarski, Ryszard; Rhoads, Robert E; Darzynkiewicz, Edward

2007-01-01

256

The Design and Application of Genetically Encodable Biosensors Based on Fluorescent Proteins  

PubMed Central

To track the activity of cellular signaling molecules within the endogenous cellular environment, researchers have developed a diverse set of genetically encodable fluorescent biosensors. These sensors, which can be targeted to specific subcellular regions to monitor specific pools of a given signaling molecule in real time, rely upon conformational changes in a sensor domain to alter the photophysical properties of green fluorescent protein (GFP) family members. In this introductory chapter, we first discuss the properties of GFP family members before turning our attention to the design and application of genetically encodable fluorescent biosensors to live cell imaging. PMID:24052376

Newman, Robert H.; Zhang, Jin

2014-01-01

257

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

Microsoft Academic Search

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

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

1980-01-01

258

Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice.  

PubMed

A variety of labdane-related diterpenoids, including phytocassanes, oryzalexins and momilactones, were identified as phytoalexins in rice (Oryza sativa L.). Momilactone B was also isolated as an allelochemical exuded from rice roots. The biosynthetic genes of these phytoalexins have been identified, including six labdane-related diterpene cyclase genes such as OsCPS2, OsCPS4, OsKSL4, OsKSL7, OsKSL8 and OsKSL10. Here we identified an OsCPS4 knockdown mutant, cps4-tos, by screening Tos17 mutant lines using polymerase chain reaction. OsCPS4 encodes a syn-copalyl diphosphate synthase responsible for momilactones and oryzalexin S biosynthesis. Because Tos17 was inserted into the third intron of OsCPS4, the mature OsCPS4 mRNA was detected in the cps4-tos mutant as well as the wild type. Nevertheless, mature OsCPS4 transcript levels in the cps4-tos mutant were about one sixth those in the wild type. The cps4-tos mutant was more susceptible to rice blast fungus than the wild type, possibly due to lower levels of momilactones and oryzalexin S in the mutant. Moreover, co-cultivation experiments suggested that the allelopathic effect of cps4-tos against some kinds of lowland weeds was significantly lower than that of the wild type, probably because of lower momilactone content exuded from cps4-tos roots. A reverse-genetic strategy using the cps4-tos mutant showed the possible roles of momilactones not only as phytoalexins but also as allelopathic substances. PMID:23621683

Toyomasu, Tomonobu; Usui, Masami; Sugawara, Chizu; Otomo, Kazuko; Hirose, Yuko; Miyao, Akio; Hirochika, Hirohiko; Okada, Kazunori; Shimizu, Takafumi; Koga, Jinichiro; Hasegawa, Morifumi; Chuba, Masaru; Kawana, Yoshiaki; Kuroda, Masaharu; Minami, Eiichi; Mitsuhashi, Wataru; Yamane, Hisakazu

2014-01-01

259

An Advanced Reverse Osmosis Technology For Application in Nuclear Desalination Facilities  

SciTech Connect

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)

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

2002-07-01

260

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

PubMed Central

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

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

2012-01-01

261

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

NASA Astrophysics Data System (ADS)

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)

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

1980-08-01

262

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

NASA Technical Reports Server (NTRS)

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)

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

1980-01-01

263

Reverse Osmosis Membrane.  

National Technical Information Service (NTIS)

The patent application describes the preparation of a reverse osmosis membrane by reaction of a film or layer of polyethylenimine with a polyfunctional reagent whose functional groups are capable of reacting with amine groups. The polyfunctional reagent i...

J. E. Cadotte

1975-01-01

264

Ultrasonic Time Reversal Mirrors  

NASA Astrophysics Data System (ADS)

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.

Fink, Mathias; Montaldo, Gabriel; Tanter, Mickael

2004-11-01

265

Application of Hierarchical Genetic Models to Raven and WAIS Subtests: A Dutch Twin Study  

Microsoft Academic Search

Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a genetic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard Progressive test score, collected in 194 18-year-old Dutch twin pairs. We investigated whether first-order group factors possess

Frühling V. Rijsdijk; P. A. Vernon; Dorret I. Boomsma

2002-01-01

266

Towards genetic improvement of commercially important microalga Haematococcus pluvialis for biotech applications  

Microsoft Academic Search

Haematococcus pluvialis is a unicellular green alga which produces a ketocarotenoid, astaxanthin which has pharmaceutical and nutraceutical applications\\u000a owing to its high antioxidant activity. Biotechnological approaches such as genetic transformation methods (Agrobacterium-mediated) and cloning strategies, are essential to improve\\/regulate this ketocarotenoid in Haematococcus. For this studies are necessary to improve Haematococcus through biotechnological means. In this connection, a suitable cocultivation

Shanmugam Kathiresan; Ravi Sarada

2009-01-01

267

Novel anthracene materials for applications in lithography and reversible photoswitching by light and air.  

PubMed

Herein we demonstrate how the photoreaction between anthracenes and singlet oxygen ((1)O(2)) is employed for applications either as photoswitch or as photoresist. Thin films of the diaryl-alkyl anthracene 1 and the analogous oligomeric species 2 were irradiated under photomasks to generate pattern structures composed of 1/1-O(2) and 2/2-O(2). Kelvin probe force microscopy (KPFM) provided a powerful and nondestructive method to image the pattern information. The following studies based on AFM, KPFM and contact angle measurements unfold that the two species 1 and 2 underwent different progressions after the imaging step. Degrading is observed for the monomeric compound 1 and the pattern eventually becomes recognizable in topography. In the oxidized state (1-O(2)) the monomeric species remains physically stable. In consequence, the unreacted portion is removable and the remaining oxygenated form 1-O(2) is sufficiently stable to protect an underlying substrate (e.g., silver) from etching. Thus, the system 1/1-O(2) operates as photoresist. On the other hand, both states of the oligomer 2 remain stable. The film is stable up to temperatures >120 degrees C required to erase the pattern within acceptable time by cycloreversion. Anthracene 2 therefore acts as erasable and rewritable photochromic switch. The different behavior between 1 and 2 is explained by phase transitions which cause crystallization and finally ablation. Such transitions affect only the monomeric system 1/1-O(2) and not the oligomeric system 2/2-O(2). In conclusion, we designed two very similar materials based on diarylanthracenes, which can act either as a photoresist or as a rewritable photochromic switch. PMID:20052984

Fudickar, Werner; Linker, Torsten

2010-03-16

268

Bonded stationary phases for reversed phase liquid chromatography with a water mobile phase: application to subcritical water extraction  

Microsoft Academic Search

Reversed phase high-performance liquid chromatography (RP-HPLC) is demonstrated for hydrophobic analytes such as aromatic hydrocarbons on a chemically bonded stationary phase and a mobile phase consisting of only water. Reversed phase liquid chromatography separations using a water-only mobile phase has been termed WRP-LC for water-only reversed phase LC. Reasonable capacity factors are achieved through the use of a non-porous silica

Toby E Young; Scott T Ecker; Robert E Synovec; Nathan T Hawley; Jonathan P Lomber; Chien M Wai

1998-01-01

269

Extracting directed information flow networks: an application to genetics and semantics.  

PubMed

We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge. PMID:21405885

Masucci, A P; Kalampokis, A; Eguíluz, V M; Hernández-García, E

2011-02-01

270

Salt solubility measurements in partially disulfonated poly(arylene ether sulfone) for reverse osmosis water purification applications.  

E-print Network

??Partially disulfonated poly(arylene ether sulfone) (BPS) membranes have shown great promise as robust, chlorine tolerant alternatives to the current polyamide materials as reverse osmosis desalination… (more)

Passaniti, Linda Kimberly

2010-01-01

271

Using reverse genetics to manipulate the NSs gene of the Rift Valley fever virus MP-12 strain to improve vaccine safety and efficacy.  

PubMed

Rift Valley fever virus (RVFV), which causes hemorrhagic fever, neurological disorders or blindness in humans, and a high rate abortion and fetal malformation in ruminants, 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 strain as well as wild-type RVFV strains, 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 RNA, 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 mRNA and promotes degradation of double-stranded RNA-dependent protein kinase (PKR) at the post-translational level. 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), 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 response. 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

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

2011-01-01

272

Engineering Applications of Artificial Intelligence 14 (2001) 114 Genetic adaptive control for an inverted wedge: experiments and  

E-print Network

Engineering Applications of Artificial Intelligence 14 (2001) 1­14 Genetic adaptive control. Passino* Department of Electrical Engineering, The Ohio State University, 2015 Neil Avenue, Columbus, OH and real-time implementation issues will be discussed and the genetic adaptive strategy will be compared

273

Gaining insights into the evolutionary behaviour in genetic algorithm calculations, with applications in structure solution from powder diffraction data  

Microsoft Academic Search

A general strategy is introduced for analysing the evolutionary events that occur during a genetic algorithm calculation, and the application of this approach is illustrated for the specific case of understanding the evolutionary trajectory leading to the correct structure solution in structure determination from powder diffraction data. Methods providing visual representations of the evolution of the population during a genetic

Scott Habershon; Kenneth D. M. Harris; Roy L. Johnston; Giles W. Turner; Jennifer M. Johnston

2002-01-01

274

IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS--PART C: APPLICATIONS AND REVIEWS, VOL. 40, NO. 2, MARCH 2010 121 A Survey on the Application of Genetic  

E-print Network

algorithms for training classifiers has been studied in the past few decades. Genetic programming (GP for the evolution of classi- fiers. This paper surveys existing literature about the application of genetic values) is employed to guide the learning process. Regression and classification are two types

Granada, Universidad de

275

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

PubMed Central

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

Anderson, Karen E

2013-01-01

276

On inferring and interpreting genetic population structure - applications to conservation, and the estimation of pairwise genetic relatedness.  

E-print Network

??The presence of population structure is ubiquitous in most wild populations of species. Detecting genetic population structure and understanding its consequences for the evolutionary trajectories… (more)

Sethuraman, Arun

2013-01-01

277

Genetic Instability at the Agouti Locus of the Mouse (Mus Musculus). I. Increased Reverse Mutation Frequency to the A(w) Allele in a/a Heterozygotes  

PubMed Central

We have compiled the reverse mutation rate data to the white bellied agouti (A(w)) allele in heterozygous A/a mice and shown it to be increased by a factor of at least 350 in comparison to the reverse mutation rate in homozygous a/a mice. Employing tightly linked flanking restriction fragment length polymorphism DNA markers, we have shown that reversion to A(w) is associated with crossing over in the vicinity of the agouti locus. The non-agouti (a) allele has been recently shown to contain an 11-kb insert within the first intron of the agouti gene. Together with our present results, these observations suggest possible mechanisms to explain the reversion events. PMID:7982562

Sandulache, R.; Neuhauser-Klaus, A.; Favor, J.

1994-01-01

278

Applications of Genetically Modified Tools to Safety Assessment in Drug Development  

PubMed Central

The process of new drug development consists of several stages; after identifying potential candidate compounds, preclinical studies using animal models link the laboratory and human clinical trials. Among many steps in preclinical studies, toxicology and safety assessments contribute to identify potential adverse events and provide rationale for setting the initial doses in clinical trials. Gene modulation is one of the important tools of modern biology, and is commonly employed to examine the function of genes of interest. Advances in new drug development have been achieved by exploding information on target selection and validation using genetically modified animal models as well as those of cells. In this review, a recent trend of genetically modified methods is discussed with reference to safety assessments, and the exemplary applications of gene-modulating tools to the tests in new drug development were summarized. PMID:24278499

Kay, Hee Yeon; Wu, Hongmin; Lee, Seo In

2010-01-01

279

Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture  

PubMed Central

Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs.

Martinez, Paulino; Vinas, Ana M.; Sanchez, Laura; Diaz, Noelia; Ribas, Laia; Piferrer, Francesc

2014-01-01

280

Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture.  

PubMed

Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs. PMID:25324858

Martínez, Paulino; Viñas, Ana M; Sánchez, Laura; Díaz, Noelia; Ribas, Laia; Piferrer, Francesc

2014-01-01

281

Gene genealogies for genetic association mapping, with application to Crohn's disease  

PubMed Central

A gene genealogy describes relationships among haplotypes sampled from a population. Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also has potential application in finding disease-predisposing genetic variants. As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies conditional on data at multiple genetic markers. We previously implemented an MCMC algorithm to sample from an approximation to the distribution of the gene genealogy conditional on haplotype data. Our approach samples ancestral trees, recombination and mutation rates at a genomic focal point. In this work, we describe how our sampler can be used to find disease-predisposing genetic variants in samples of cases and controls. We use a tree-based association statistic that quantifies the degree to which case haplotypes are more closely related to each other around the focal point than control haplotypes, without relying on a disease model. As the ancestral tree is a latent variable, so is the tree-based association statistic. We show how the sampler can be used to estimate the posterior distribution of the latent test statistic and corresponding latent p-values, which together comprise a fuzzy p-value. We illustrate the approach on a publicly-available dataset from a study of Crohn's disease that consists of genotypes at multiple SNP markers in a small genomic region. We estimate the posterior distribution of the tree-based association statistic and the recombination rate at multiple focal points in the region. Reassuringly, the posterior mean recombination rates estimated at the different focal points are consistent with previously published estimates. The tree-based association approach finds multiple sub-regions where the case haplotypes are more genetically related than the control haplotypes, and that there may be one or multiple disease-predisposing loci. PMID:24348515

Burkett, Kelly M.; Greenwood, Celia M. T.; McNeney, Brad; Graham, Jinko

2013-01-01

282

Gene genealogies for genetic association mapping, with application to Crohn's disease.  

PubMed

A gene genealogy describes relationships among haplotypes sampled from a population. Knowledge of the gene genealogy for a set of haplotypes is useful for estimation of population genetic parameters and it also has potential application in finding disease-predisposing genetic variants. As the true gene genealogy is unknown, Markov chain Monte Carlo (MCMC) approaches have been used to sample genealogies conditional on data at multiple genetic markers. We previously implemented an MCMC algorithm to sample from an approximation to the distribution of the gene genealogy conditional on haplotype data. Our approach samples ancestral trees, recombination and mutation rates at a genomic focal point. In this work, we describe how our sampler can be used to find disease-predisposing genetic variants in samples of cases and controls. We use a tree-based association statistic that quantifies the degree to which case haplotypes are more closely related to each other around the focal point than control haplotypes, without relying on a disease model. As the ancestral tree is a latent variable, so is the tree-based association statistic. We show how the sampler can be used to estimate the posterior distribution of the latent test statistic and corresponding latent p-values, which together comprise a fuzzy p-value. We illustrate the approach on a publicly-available dataset from a study of Crohn's disease that consists of genotypes at multiple SNP markers in a small genomic region. We estimate the posterior distribution of the tree-based association statistic and the recombination rate at multiple focal points in the region. Reassuringly, the posterior mean recombination rates estimated at the different focal points are consistent with previously published estimates. The tree-based association approach finds multiple sub-regions where the case haplotypes are more genetically related than the control haplotypes, and that there may be one or multiple disease-predisposing loci. PMID:24348515

Burkett, Kelly M; Greenwood, Celia M T; McNeney, Brad; Graham, Jinko

2013-01-01

283

Defect Band Luminescence Intensity Reversal as Related to Application of Anti-Reflection Coating on mc-Si PV Cells: Preprint  

SciTech Connect

Photoluminescence (PL) imaging is widely used to identify defective regions within mc-Si PV cells. Recent PL imaging investigations of defect band luminescence (DBL) in mc-Si have revealed a perplexing phenomenon. Namely, the reversal of the DBL intensity in various regions of mc-Si PV material upon the application of a SiNx:H anti-reflective coating (ARC). Regions with low DBL intensity before ARC application often exhibit high DBL intensity afterwards, and the converse is also true. PL imaging alone cannot explain this effect. We have used high resolution cathodoluminescence (CL) spectroscopy and electron beam induced current (EBIC) techniques to elucidate the origin of the DBL intensity reversal. Multiple sub-bandgap energy levels were identified that change in peak position and intensity upon the application of the ARC. Using this data, in addition to EBIC contrast information, we provide an explanation for the DBL intensity reversal based on the interaction of the detected energy levels with the SiNx:H ARC application. Multiple investigations have suggested that this is a global problem for mc-Si PV cells. Our results have the potential to provide mc-Si PV producers a pathway to increased efficiencies through defect mitigation strategies.

Guthrey, H.; Johnston, S.; Yan, F.; Gorman, B.; Al-Jassim, M.

2012-06-01

284

A Phosphate-Regulated Promoter for Fine-Tuned and Reversible Overexpression in Ostreococcus: Application to Circadian Clock Functional Analysis  

PubMed Central

Background The green picoalga Ostreococcus tauri (Prasinophyceae), which has been described as the smallest free-living eukaryotic organism, has minimal cellular ultra-structure and a very small genome. In recent years, O. tauri has emerged as a novel model organism for systems biology approaches that combine functional genomics and mathematical modeling, with a strong emphasis on light regulated processes and circadian clock. These approaches were made possible through the implementation of a minimal molecular toolbox for gene functional analysis including overexpression and knockdown strategies. We have previously shown that the promoter of the High Affinity Phosphate Transporter (HAPT) gene drives the expression of a luciferase reporter at high and constitutive levels under constant light. Methodology/Principal Findings Here we report, using a luciferase reporter construct, that the HAPT promoter can be finely and reversibly tuned by modulating the level and nature of phosphate in culture medium. This HAPT regulation was additionally used to analyze the circadian clock gene Time of Cab expression 1 (TOC1). The phenotype of a TOC1ox/CCA1:Luc line was reverted from arrhythmic to rhythmic simply by adding phosphate to the culture medium. Furthermore, since the time of phosphate injection had no effect on the phase of CCA1:Luc expression, this study suggests further that TOC1 is a central clock gene in Ostreococcus. Conclusions/Perspectives We have developed a phosphate-regulated expression system that allows fine gene function analysis in Ostreococcus. Recently, there has been a growing interest in microalgae as cell factories. This non-toxic phosphate-regulated system may prove useful in tuning protein expression levels quantitatively and temporally for biotechnological applications. PMID:22174815

Lozano, Jean-Claude; Bouget, François-Yves

2011-01-01

285

Genetic Counseling Program Information  

E-print Network

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, psychological, and familial implications of genetic contributions to disease. The process integrates

Berdichevsky, Victor

286

Reversible logic circuit synthesis  

Microsoft Academic Search

Reversible or information-lossless circuits have applications in digital signal processing, communication, computer graphics and cryptography. They are also a fundamental requirement in the emerging field of quantum computation. We investigate the synthesis of reversible circuits that employ a minimum number of gates and contain no redundant input-output line-pairs (temporary storage channels). We prove constructively that every even permutation can be

Vivek V. Shende; Aditya K. Prasad; I. L. Markov; J. P. Hayes

2002-01-01

287

Partial Reversible Gates(PRG) for Reversible BCD Arithmetic  

E-print Network

IEEE 754r is the ongoing revision to the IEEE 754 floating point standard and a major enhancement to the standard is the addition of decimal format. Furthermore, in the recent years reversible logic has emerged as a promising computing paradigm having its applications in low power CMOS, quantum computing, nanotechnology, and optical computing. The major goal in reversible logic is to minimize the number of reversible gates and garbage outputs. Thus, this paper proposes the novel concept of partial reversible gates that will satisfy the reversibility criteria for specific cases in BCD arithmetic. The partial reversible gate is proposed to minimize the number of reversible gates and garbage outputs, while designing the reversible BCD arithmetic circuits.

Thapliyal, Himanshu; Bajpai, Rajnish; Sharma, Kamal K

2007-01-01

288

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

PubMed

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

Groshong, Ashley M; Blevins, Jon S

2014-01-01

289

The Systems Genetics Resource: A Web Application to Mine Global Data for Complex Disease Traits  

PubMed Central

The Systems Genetics Resource (SGR) (http://systems.genetics.ucla.edu) is a new open-access web application and database that contains genotypes and clinical and intermediate phenotypes from both human and mouse studies. The mouse data include studies using crosses between specific inbred strains and studies using the Hybrid Mouse Diversity Panel. SGR is designed to assist researchers studying genes and pathways contributing to complex disease traits, including obesity, diabetes, atherosclerosis, heart failure, osteoporosis, and lipoprotein metabolism. Over the next few years, we hope to add data relevant to deafness, addiction, hepatic steatosis, toxin responses, and vascular injury. The intermediate phenotypes include expression array data for a variety of tissues and cultured cells, metabolite levels, and protein levels. Pre-computed tables of genetic loci controlling intermediate and clinical phenotypes, as well as phenotype correlations, are accessed via a user-friendly web interface. The web site includes detailed protocols for all of the studies. Data from published studies are freely available; unpublished studies have restricted access during their embargo period. PMID:23730305

van Nas, Atila; Pan, Calvin; Ingram-Drake, Leslie A.; Ghazalpour, Anatole; Drake, Thomas A.; Sobel, Eric M.; Papp, Jeanette C.; Lusis, Aldons J.

2013-01-01

290

Genetic Background Comparison Using Distance-based Regression, with Applications in Population Stratification Evaluation and Adjustment  

PubMed Central

Population stratification (PS) can lead to an inflated rate of false positive findings in genome-wide association studies (GWAS). A commonly used approach is to adjust for a fixed number of principal components (PCs) in GWAS but this approach could have a deleterious impact on power when the cases and controls are equally distributed along selected PCs, or if the adjustment of certain covariates, such as self-identified ethnicity or recruitment center, already included in the association analyses, correctly map to major axes of genetic heterogeneity. We propose a computationally efficient procedure, PC-Finder, to identify a minimal set of PCs while permitting an effective correction for PS. A general pseudo F statistic, derived from a non-parametric multivariate regression model, can be used to assess whether PS exists or has been adequately corrected by a set of selected PCs. Empirical data from two GWAS conducted as part of the Cancer Genetic Markers of Susceptibility (CGEMS) project demonstrate the application of the procedure. Furthermore, simulation studies show the power advantage of the proposed procedure in GWAS over currently used PS correction strategies, particularly when the PCs with substantial genetic variation are distributed similarly in cases and controls and therefore do not induce PS. PMID:19140130

Li, Qizhai; Wacholder, Sholom; Hunter, David J.; Hoover, Robert N.; Chanock, Stephen; Thomas, Gilles; Yu, Kai

2009-01-01

291

LABELING WHITE MATTER TRACTS IN HARDI BY FUSING MULTIPLE TRACT ATLASES WITH APPLICATIONS TO GENETICS  

PubMed Central

Accurate identification of white matter structures and segmentation of fibers into tracts is important in neuroimaging and has many potential applications. Even so, it is not trivial because whole brain tractography generates hundreds of thousands of streamlines that include many false positive fibers. We developed and tested an automatic tract labeling algorithm to segment anatomically meaningful tracts from diffusion weighted images. Our multi-atlas method incorporates information from multiple hand-labeled fiber tract atlases. In validations, we showed that the method outperformed the standard ROI-based labeling using a deformable, parcellated atlas. Finally, we show a high-throughput application of the method to genetic population studies. We use the sub-voxel diffusion information from fibers in the clustered tracts based on 105-gradient HARDI scans of 86 young normal twins. The whole workflow shows promise for larger population studies in the future.

Jin, Yan; Shi, Yonggang; Zhan, Liang; de Zubicaray, Greig I.; McMahon, Katie L.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.

2013-01-01

292

Update: Biochemistry of Genetic Manipulation.  

ERIC Educational Resources Information Center

Various topics on the biochemistry of genetic manipulation are discussed. These include genetic transformation and DNA; genetic expression; DNA replication, repair, and mutation; technology of genetic manipulation; and applications of genetic manipulation. Other techniques employed are also considered. (JN)

Barker, G. R.

1983-01-01

293

Reversible Sterilization  

ERIC Educational Resources Information Center

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)

Largey, Gale

1977-01-01

294

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

ERIC Educational Resources Information Center

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…

Gilman, Rich; Connor, Nancy; Haney, Michelle

2005-01-01

295

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

ERIC Educational Resources Information Center

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…

Lorié, William A.

2013-01-01

296

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

Microsoft Academic Search

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

Kumara Narasimha Sastry

2007-01-01

297

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...

298

Reverse genetic analysis of the glutathione metabolic pathway suggests a novel role of PHGPX and URE2 genes in aluminum resistance in Saccharomyces cerevisiae  

Microsoft Academic Search

We have taken a systematic genetic approach to study the potential role of glutathione metabolism in aluminum (Al) toxicity and resistance, using disruption mutants available in Saccharomyces cerevisiae. Yeast disruption mutants defective in phospholipid hydroperoxide glutathione peroxidases (PHGPX; phgpx1 ?, phgpx2 ?, and phgpx3?), were tested for their sensitivity to Al. The triple mutant, phgpx1 ? \\/2? \\/3?, was more

U. Basu; J. L. Southron; J. L. Stephens; G. J. Taylor

2004-01-01

299

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

PubMed

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

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

2014-10-01

300

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

PubMed Central

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

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

2014-01-01

301

Likelihood ratio testing for admixture models with application to genetic linkage analysis.  

PubMed

We consider likelihood ratio tests (LRT) and their modifications for homogeneity in admixture models. The admixture model is a two-component mixture model, where one component is indexed by an unknown parameter while the parameter value for the other component is known. This model is widely used in genetic linkage analysis under heterogeneity in which the kernel distribution is binomial. For such models, it is long recognized that testing for homogeneity is nonstandard, and the LRT statistic does not converge to a conventional??(2) ?distribution. In this article, we investigate the asymptotic behavior of the LRT for general admixture models and show that its limiting distribution is equivalent to the supremum of a squared Gaussian process. We also discuss the connection and comparison between LRT and alternative approaches such as modifications of LRT and score tests, including the modified LRT (Fu, Chen, and Kalbfleisch, 2006,?Statistica Sinica?16, 805-823). The LRT is an omnibus test that is powerful to detect general alternative hypotheses. In contrast, alternative approaches may be slightly more powerful to detect certain type of alternatives, but much less powerful for others. Our results are illustrated by simulation studies and an application to a genetic linkage study of schizophrenia. PMID:21385166

Di, Chong-Zhi; Liang, Kung-Yee

2011-12-01

302

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

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

2013-01-01

303

An adaptive reanalysis method for genetic algorithm with application to fast truss optimization  

NASA Astrophysics Data System (ADS)

Although the genetic algorithm (GA) for structural optimization is very robust, it is very computationally intensive and hence slower than optimality criteria and mathematical programming methods. To speed up the design process, the authors present an adaptive reanalysis method for GA and its applications in the optimal design of trusses. This reanalysis technique is primarily derived from the Kirsch’s combined approximations method. An iteration scheme is adopted to adaptively determine the number of basis vectors at every generation. In order to illustrate this method, three classical examples of optimal truss design are used to validate the proposed reanalysis-based design procedure. The presented numerical results demonstrate that the adaptive reanalysis technique affects very slightly the accuracy of the optimal solutions and does accelerate the design process, especially for large-scale structures.

Xu, Tao; Zuo, Wenjie; Xu, Tianshuang; Song, Guangcai; Li, Ruichuan

2010-05-01

304

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

NASA Astrophysics Data System (ADS)

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.

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

305

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

Microsoft Academic Search

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

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

1984-01-01

306

First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize.  

PubMed

An innovative covalent microsphere immunoassay, based on the usage of fluorescent beads coupled to a specific antibody, was developed for the quantification of the endotoxin Cry1Ab present in MON810 and Bt11 genetically modified (GM) maize lines. In particular, a specific protocol was developed to assess the presence of Cry1Ab in a very broad range of GM maize concentrations, from 0.1 to 100% [weight of genetically modified organism (GMO)/weight]. Test linearity was achieved in the range of values from 0.1 to 3%, whereas fluorescence signal increased following a nonlinear model, reaching a plateau at 25%. The limits of detection and quantification were equal to 0.018 and 0.054%, respectively. The present study describes the first application of quantitative high-throughput immunoassays in GMO analysis. PMID:17300145

Fantozzi, Anna; Ermolli, Monica; Marini, Massimiliano; Scotti, Domenico; Balla, Branko; Querci, Maddalena; Langrell, Stephen R H; Van den Eede, Guy

2007-02-21

307

Reverse Logistics.  

National Technical Information Service (NTIS)

The Army has a serious problem with materiel in the supply chain that is moving in the reverse direction. The supply chain is a series of inter- related processes and activities that move supplies and services from the suppliers to the ultimate end users....

J. L. Walden

2001-01-01

308

AUTOMATIC CREATION OF A GENETIC NETWORK FOR THE lac OPERON FROM OBSERVED DATA BY MEANS OF GENETIC PROGRAMMING  

E-print Network

to automatically create (reverse engineer) a computer program representing the logic underlying the genetic network "reverse engineer" the logic underlying a genetic network. This reverse engineering entails creating bothAUTOMATIC CREATION OF A GENETIC NETWORK FOR THE lac OPERON FROM OBSERVED DATA BY MEANS OF GENETIC

Fernandez, Thomas

309

Application of molecular markers to assess genetic relationships among accessions of wild oat, Avena sterilis  

Microsoft Academic Search

The Avena sterilis collection in the National Small Grains Collection (NSGC) is an invaluable source of genetic variation to be exploited by oat breeding programs. Prior knowledge of the structure and distribution of genetic variation within the A. sterilis collection would be useful to efficiently screen the collection for valuable traits. To determine genetic structure within a subset of the

J. C. Goffreda; W. B. Burnquist; S. C. Beer; S. D. Tanksley; M. E. Sorrells

1992-01-01

310

A simultaneous parameter adaptation scheme for genetic algorithms with application to phased array synthesis  

Microsoft Academic Search

Genetic algorithms are commonly used to solve many optimization and synthesis problems. An important issue facing the user is the selection of genetic algorithm parameters, such as mutation rate, mutation range, and number of crossovers. This paper demonstrates a real-valued genetic algorithm that simultaneously adapts several such parameters during the optimization process. This adaptive algorithm is shown to outperform its

Daniel W. Boeringer; Douglas H. Werner; David W. Machuga

2005-01-01

311

GENETIC ACTIVITY PROFILES--APPLICATION IN ASSESSING POTENTIAL CARCINOGENICITY OF COMPLEX ENVIRONMENTAL MIXTURES  

EPA Science Inventory

Some knowledge of the potential genetic activity of a complex environmental mixture may be gained from an assessment of the genetic activity of its component chemicals. he expanded Genetic Activity Profile (GAP) data base provides a computer generated graphic representation of ge...

312

Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies.  

PubMed

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

Abdul-Muneer, P M

2014-01-01

313

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

PubMed Central

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

Abdul-Muneer, P. M.

2014-01-01

314

Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis.  

PubMed

Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR. PMID:23734951

Lou, Xinhui; Zhang, Ying

2013-07-10

315

Repeatability in column preparation of a reversed-phase C18 monolith and its application to separation of tocopherol homologues.  

PubMed

This work investigated the repeatability of column preparation for a reversed-phase C18 monolith, namely stearyl methacrylate-co-ethylene glycol dimethacrylate (SMA-EDMA). The columns were thermally polymerised using three commonly available heating devices (GC oven, hot air oven and water bath) and their chromatographic performance evaluated using micro-liquid chromatography for separation of five test compounds. Precision in terms of %RSD of retention times were 9.0, 6.5, and 12.5 using GC oven, hot air oven and water bath, respectively. Between-batch precision for the hot air oven (n=3 days) was less than 10.4% for retention time. The SMA-EDMA monolith was applied to the separation of tocopherol homologues by capillary electrochromatography. Usually tocopherol homologues cannot be completely separated by conventional reversed-phase C8- or C18-packed bed or C18-silica based monolithic columns. Polymer monolith has been shown to give remarkable selectivity towards the tocopherols compared to the conventional microparticulate phase and silica based monolith. Successful separation of the tocopherol isomers was achieved on the SMA-EDMA monolith without any column modification. PMID:21641454

Kositarat, Sirichai; Smith, Norman William; Nacapricha, Duangjai; Wilairat, Prapin; Chaisuwan, Patcharin

2011-06-15

316

Reversible concentric ring microfluidic interconnects  

E-print Network

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 ...

Thompson, Mary Kathryn, 1980-

2004-01-01

317

Reverse osmosis reverses conventional wisdom with Superfund cleanup success  

SciTech Connect

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.

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

1994-09-01

318

Extended Fixed Attribute Dynamics Method and an Illustrative Application in Bio-demographic-genetic Analysis on Longevity  

PubMed Central

This chapter presents and discuss the extended Fixed Attributes Dynamics (FAD) method to estimate the independent effect of a genetic variant (or other fixed attribute) in the absence of another relevant genetic variant (or another relevant fixed attribute), the joint effects when both are present and the effects of interactions between them. We present an illustrative application of the extended FAD method for estimating the general, independent and joint effects of the FOXO genotypes on longevity, based on the genotypic data of 760 centenarians from the Chinese Longitudinal Healthy Longevity Survey, and the 1,060 middle-age controls. We also discuss the strengths and limitations of the FAD method.

Zeng, Yi

2014-01-01

319

Simultaneous feature selection and classification based on genetic algorithms: an application to colonic polyp detection  

NASA Astrophysics Data System (ADS)

Selecting a set of relevant features is a crucial step in the process of building robust classifiers. Searching all possible subsets of features is computationally impractical for large number of features. Generally, classifiers are used for the evaluation of the separability of a certain feature subset. The performance of these classifiers depends on some predefined parameters. However, the choice of these parameters for a given classifier is influenced by the given feature subset and vice versa. The computational cost for feature selection would be largely increased by including the selection of optimal parameters for the classifier (for each subset). This paper attempts to tackle the problem by introducing genetic algorithms (GAs) to combine the processes. The proposed approach can choose the most relevant features from a feature set whilst simultaneously optimising the parameters of the classifier. Its performance was tested on a colon polyp database from a cohort study using a weighted support vector machine (SVM) classifier. As a general approach, other classifiers such as artificial neural networks (ANN) and decision trees could be used. This approach could also be applied to other classification problems such as other computer aided detection/diagnosis applications.

Zheng, Yalin; Yang, Xiaoyun; Siddique, Musib; Beddoe, Gareth

2008-03-01

320

Genetic interaction analysis of point mutations enables interrogation of gene function at a residue-level resolution: exploring the applications of high-resolution genetic interaction mapping of point mutations.  

PubMed

We have achieved a residue-level resolution of genetic interaction mapping - a technique that measures how the function of one gene is affected by the alteration of a second gene - by analyzing point mutations. Here, we describe how to interpret point mutant genetic interactions, and outline key applications for the approach, including interrogation of protein interaction interfaces and active sites, and examination of post-translational modifications. Genetic interaction analysis has proven effective for characterizing cellular processes; however, to date, systematic high-throughput genetic interaction screens have relied on gene deletions or knockdowns, which limits the resolution of gene function analysis and poses problems for multifunctional genes. Our point mutant approach addresses these issues, and further provides a tool for in vivo structure-function analysis that complements traditional biophysical methods. We also discuss the potential for genetic interaction mapping of point mutations in human cells and its application to personalized medicine. PMID:24842270

Braberg, Hannes; Moehle, Erica A; Shales, Michael; Guthrie, Christine; Krogan, Nevan J

2014-07-01

321

Pragmatic Language in autism and fragile X syndrome: Genetic and clinical applications  

PubMed Central

Evidence suggests a strong genetic basis to autism. Our research program focuses on identifying genetically meaningful phenotypes in autism, through family-genetic and cross-population methods, with a particular focus on language and social phenotypes that have been shown to aggregate in families of individuals with autism. In this article, we discuss recent findings from family study research implicating particular language and personality features as markers for genetic liability to autism and fragile X syndrome and FMR1-related variation in relatives. We conclude with consideration of the clinical implications of such findings. PMID:24660047

Losh, Molly; Martin, Gary E.; Klusek, Jessica; Hogan-Brown, Abigail L.

2013-01-01

322

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

SciTech Connect

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.

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

2012-03-31

323

Judaism, Genetic Screening and Genetic Therapy  

Microsoft Academic Search

Genetic screening, gene therapy and other applications of genetic engineering are permissible in Judaism when used for the treatment, cure, or prevention of disease. Such genetic manipulation is not considered to be a violation of God's natural law, but a legitimate implementation of the biblical mandate to heal. If Tay-Sachs disease, diabetes, hemophilia, cystic fibrosis, Huntington's disease or other genetic

FRED ROSNER

324

Implementing leagility in reverse logistics channels  

Microsoft Academic Search

The importance of the topic of reverse logistics has increased gradually over the past few years. This paper primarily focuses on one facet of reverse logistics, which involves the return of damaged products to be repaired by a manufacturer. The application of the ‘leagile’ paradigm in the reverse logistics process and its expected outcome, in terms of costs and lead-time

R. Banomyong; V. Veerakachen; N. Supatn

2008-01-01

325

Bidimensional reversed-phase high-pressure liquid chromatography analysis of cultured cell neuropeptides: application to atrial natriuretic factor.  

PubMed

We report here a one-step procedure for extraction and analysis of neuropeptides in chromaffin cell culture media and acid extracts using reversed-phase HPLC. The bidimensional HPLC system consists of a precolumn connected to a six-port switching valve which is on-line with an analytical column. The direct injection of the biological samples onto the precolumn previously equilibrated with 15% acetonitrile allows the elimination of interfering substances. The samples purified on the precolumn can then be eluted onto the analytical column via the switching valve for neuropeptide separation. This trace-enrichment system allows a minimum of sample handling, both saving time and reducing possibilities of loss and contamination. This method has been applied to monitor the precursor and mature forms of atrial natriuretic factor from chromaffin cell secretion media and cell content extracts. The recovery of atrial natriuretic factor is in the range of 80-100%. This procedure could be applied to the study of the precursor-product relationship of any neuropeptide, e.g., from radiolabeled extracts of pulse-chase experiments performed on cultured chromaffin cells. PMID:2527010

Nguyen, T T; De Léan, A; Ong, H

1989-05-15

326

Improvement of influenza A/Fujian/411/02 (H3N2) virus growth in embryonated chicken eggs by balancing the hemagglutinin and neuraminidase activities, using reverse genetics.  

PubMed

The H3N2 influenza A/Fujian/411/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A/Fujian/411/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A/Fujian/411/02 virus was examined in this study by the reverse genetics technology. Two antigenically related strains that replicated well in embryonated chicken eggs, A/Sendai-H/F4962/02 and A/Wyoming/03/03, were compared with the prototype A/Fujian/411/02 virus. A/Sendai differed from A/Fujian by three amino acids in the neuraminidase (NA), whereas A/Wyoming differed from A/Fujian by five amino acids in the hemagglutinin (HA). The HA and NA segments of these three viruses were reassorted with cold-adapted A/Ann Arbor/6/60, the master donor virus for the live attenuated type A influenza vaccines (FluMist). The HA and NA residues differed between these three H3N2 viruses evaluated for their impact on virus replication in MDCK cells and in embryonated chicken eggs. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. Thus, the balance between the HA and NA activities is critical for influenza virus replication in a different host system. The HA or NA changes that increased A/Fujian/411/02 virus replication in embryonated chicken eggs were found to have no significant impact on antigenicity of these recombinant viruses. This study demonstrated that the reverse genetics technology could be used to improve the manufacture of the influenza vaccines. PMID:15890915

Lu, Bin; Zhou, Helen; Ye, Dan; Kemble, George; Jin, Hong

2005-06-01

327

Teaching Applied Genetics and Molecular Biology to Agriculture Engineers. Application of the European Credit Transfer System  

ERIC Educational Resources Information Center

We have been teaching applied molecular genetics to engineers and adapted the teaching methodology to the European Credit Transfer System. We teach core principles of genetics that are universal and form the conceptual basis of most molecular technologies. The course then teaches widely used techniques and finally shows how different techniques…

Weiss, J.; Egea-Cortines, M.

2008-01-01

328

Black-and-white spots in the application of genetics to dairy cattle breeding  

Microsoft Academic Search

We have (briefly) discussed the various statistical and genetic assumptions underlying the evaluation and analysis of data on production and functional traits, with the emphasis that researchers should at least be aware of those assumptions. However, it is right to ask what impact violations or ignorance of these assumptions have on genetic progress. Most likely, the answer is \\

William G. Hill; Peter M. Visscher; Susan Brotherstone

329

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

Microsoft Academic Search

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

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

330

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

Microsoft Academic Search

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

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

2007-01-01

331

A SURVEY OF GENETIC ALGORITHMS APPLICATIONS FOR IMAGE ENHANCEMENT AND SEGMENTATION  

Microsoft Academic Search

It was proved that genetic algorithms are the most powerful unbiased optimization techniques for sampling a large solution space. Because of unbiased stochastic sampling, they were quickly adapted in image processing. They were applied for the image enhancement, segmentation, feature extraction and classification as well as the image generation. This article gives a brief overview of the canonical genetic algorithm

Mantas Paulinas

2007-01-01

332

Application of information-logical approach to studies of genetic systems  

Microsoft Academic Search

A new information technology, the information-logical approach (ILA), which is based on information theory methods and the fuzzy sets theory, is considered. This method can be applied for the majority of biological and ecological studies, and in genetics. In breeding and genetic studies, ILA can be used as a basis for the development of methods that will allow one to

S. E. Dromashko; B. O. Dubovskoi

1995-01-01

333

Applications of DNA genetic markers to the study of plant growth and development  

Microsoft Academic Search

DNA genetic markers, such as restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNA markers (RAPDs), are powerful tools for studying the genetics of plant growth and development. DNA markers are defined sequences of DNA that can be used in traditional linkage mapping. Using DNA marker technology, scientists can uncover relationships between cloned cDNA sequences and classically characterized genes.

Nevin Dale Young

1993-01-01

334

High capacity, reversible alloying reactions in SnSb/C nanocomposites for Na-ion battery applications  

SciTech Connect

A new SnSb/C nanocomposite based on Na alloying reactions is demonstrated as anode for Na-ion battery applications. The electrode can achieve an exceptionally high capacity (544 mA h g?1, almost double that of intercalation carbon materials), good rate capacity and cyclability (80% capacity retention over 50 cycles) for Na-ion storage.

Xiao, Lifen; Cao, Yuliang; Xiao, Jie; Wang, Wei; Kovarik, Libor; Nie, Zimin; Liu, Jun

2012-04-04

335

An Experimental Study of Jets With Reversing Buoyancy With Application to the Partial Collapse Regime of Explosive Volcanic Eruptions  

NASA Astrophysics Data System (ADS)

Tephra from explosive eruptions exhibit two characteristic kinds of deposits because mechanical processes in the volcanic column can have two highly contrasting outcomes. Pumice airfall deposits are created by sedimentation from umbrella clouds that spread in the atmosphere from high buoyant plumes, whereas ignimbrites are emplaced by pyroclastic flows generated when the column collapses above the vent. Physical models use a powerful "top-hat" formalism to explain this phenomenology. Field data and observations of historical eruptions nevertheless indicate the existence of an important intermediate regime where the column partially collapses. This transitional regime occurs for a given range of source parameters which are not well constrained because the top-hat models are only able to predict a sharp limit between the extreme regimes. The behavior of the volcanic mixture depends crucially on the rate of entrainment of atmospheric air into the jet, on the dynamics of the pyroclasts and on the rate of heat exchange between gas and pyroclasts. The complex dynamics generated by the particle load and their heating makes it difficult to study by theoretically other than sophisticated numerical computations. To develop an alternative approach to study the role of particules in the volcanic jet close to the transition we have built a new laboratory apparatus in which a 2- phase jet of hot air laden with small hot particules is ejected into a large chamber of cold air. Scaling analyses are first necessary to achieve dynamic similarity with volcanic plumes in laboratory. Our apparatus is able to reproduce jets of reversing buoyancy and hence attain the three regimes observed in the field according by manipulating initial conditions. We investigate the transitional regime by varying the control parameters which are the initial jet radius, the fraction of particles, the ejection velocity and the initial temperature of the mixture. The jet partially collapses for a range of initial conditions larger than that estimated from single-phase experiments. We quantify partitioning of mass between convecting and collapsing parts of the jet.

Tait, S.; Carazzo, G.; Kaminski, E.

2006-12-01

336

Network Reverse Engineering Approach in Synthetic Biology  

NASA Astrophysics Data System (ADS)

Synthetic biology is a new branch of interdisciplinary science that has been developed in recent years. The main purpose of synthetic biology is to apply successful principles that have been developed in electronic and chemical engineering to develop basic biological functional modules, and through rational design, develop man-made biological systems that have predicted useful functions. Here, we discuss an important principle in rational design of functional biological circuits: the reverse engineering design. We will use a research project that was conducted at Peking University for the International Genetic Engineering Machine Competition (iGEM) to illustrate the principle: synthesis a cell which has a semi-log dose-response to the environment. Through this work we try to demonstrate the potential application of network engineering in synthetic biology.

Zhang, Haoqian; Liu, Ao; Lu, Yuheng; Sheng, Ying; Wu, Qianzhu; Yin, Zhenzhen; Chen, Yiwei; Liu, Zairan; Pan, Heng; Ouyang, Qi

2013-12-01

337

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

NASA Astrophysics Data System (ADS)

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

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

338

Genetic algorithms optimization approach supported by the first-order derivative and Newton-Raphson methods: Application to fluorescence spectroscopy  

NASA Astrophysics Data System (ADS)

The application of genetic algorithms (GA) optimization approach supported by the first-order derivative (FOD) and Newton-Raphson (NR) methods to time-resolved polarized fluorescence spectroscopy, is discussed. It is demonstrated that the application of both methods to ?2 function reduces the number of adjustable model parameters. The combination of GA-optimizer with the FOD and NR methods improves considerably the efficiency of global analysis of kinetic and polarized fluorescence decays for solutions and organized media, including the case of excited-state processes.

Fisz, J. J.; Buczkowski, M.; Budzi?ski, M. P.; Kolenderski, P.

2005-05-01

339

Optimization of reversible sequential circuits  

E-print Network

In recent years reversible logic has been considered as an important issue for designing low power digital circuits. It has voluminous applications in the present rising nanotechnology such as DNA computing, Quantum Computing, low power VLSI and quantum dot automata. In this paper we have proposed optimized design of reversible sequential circuits in terms of number of gates, delay and hardware complexity. We have designed the latches with a new reversible gate and reduced the required number of gates, garbage outputs, and delay and hardware complexity. As the number of gates and garbage outputs increase the complexity of reversible circuits, this design will significantly enhance the performance. We have proposed reversible D-latch and JK latch which are better than the existing designs available in literature.

Sayem, Abu Sadat Md

2010-01-01

340

Molecular Aspects of Ischemic Heart Disease: Ischemia\\/Reperfusion-Induced Genetic Changes and Potential Applications of Gene and RNA Interference Therapy  

Microsoft Academic Search

Molecular biologic techniques have a variety of applications in the study of ischemic heart disease, including roles in elucidating cardiac genetic changes resulting from ischemia as well as in developing therapeutic interventions to treat ischemic heart disease. This review describes recent studies documenting genetic changes associated with myocardial ischemia and infarction as well as those investigating the safety and effectiveness

Margaret A. Nordlie; Loren E. Wold; Boris Z. Simkhovich; Casilde Sesti; Robert A. Kloner

341

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

in software development and object­oriented program­ ming, have prompted a need to reverse engineer and re methods in software development and object­oriented programming, there is a strong motivation to reverse 1993 A Two­Phase Approach to Reverse Engineering Using Formal Methods Gerald C. Gannod and Betty H. C

Cheng, Betty H.C.

342

Optimized reversible BCD adder using new reversible logic gates  

E-print Network

Reversible logic has received great attention in the recent years due to their ability to reduce the power dissipation which is the main requirement in low power digital design. It has wide applications advanced computing, low power CMOS design, Optical information processing, DNA computing, bio information, quantum computation and nanotechnology. This paper presents an optimized reversible BCD adder using a new reversible gate. A comparative result is presented which shows that the proposed design is more optimized in terms of number of gates, number of garbage outputs and quantum cost than the existing designs.

Bhagyalakshmi, H R

2010-01-01

343

Application of long-range and binding reverse transcription-quantitative PCR to indicate the viral integrities of noroviruses.  

PubMed

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

Li, Dan; De Keuckelaere, Ann; Uyttendaele, Mieke

2014-10-15

344

Control of Wettability of Carbon Nanotube Array by Reversible Dry Oxidation for Superhydrophobic Coating and Supercapacitor Applications  

NASA Astrophysics Data System (ADS)

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.)

Aria, Adrianus Indrat

345

An Application of Computer Simulation to the Teaching of Genetics in the Upper Secondary School  

ERIC Educational Resources Information Center

Describes an exercise in which senior high school biology students used a computer to simulate genetic mapping. The exercise was designed to enhance the students' grasp of the concepts of linkage and crossing-over. (JR)

Dean, P. G.; Murphy, P. J.

1973-01-01

346

Genetic Regulation of Platelet Receptor Expression and Function: Application in Clinical Practice and Drug Development  

PubMed Central

Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering 1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, 2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and 3) the role of platelet function/genetic testing in guiding antiplatelet therapy. PMID:21084706

Williams, Marlene S.; Weiss, Ethan J.; Sabatine, Marc S.; Bray, Paul F.; Simon, Daniel I.; Bahou, Wadie F.; Becker, Lewis C.; Parise, Leslie V.; Dauerman, Harold L.; French, Patricia A.; Becker, Richard C.; Smyth, Susan S.

2014-01-01

347

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

PubMed Central

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

Sun, Xue; Yu, Weihui; Hu, Cheng

2014-01-01

348

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity.  

PubMed

Current studies of phenotype diversity by genome-wide association studies (GWAS) are mainly focused on identifying genetic variants that influence level changes of individual traits without considering additional alterations at the system-level. However, in addition to level alterations of single phenotypes, differences in association between phenotype levels are observed across different physiological states. Such differences in molecular correlations between states can potentially reveal information about the system state beyond that reported by changes in mean levels alone. In this study, we describe a novel methodological approach, which we refer to as genome metabolome integrated network analysis (GEMINi) consisting of a combination of correlation network analysis and genome-wide correlation study. The proposed methodology exploits differences in molecular associations to uncover genetic variants involved in phenotype variation. We test the performance of the GEMINi approach in a simulation study and illustrate its use in the context of obesity and detailed quantitative metabolomics data on systemic metabolism. Application of GEMINi revealed a set of metabolic associations which differ between normal and obese individuals. While no significant associations were found between genetic variants and body mass index using a standard GWAS approach, further investigation of the identified differences in metabolic association revealed a number of loci, several of which have been previously implicated with obesity-related processes. This study highlights the advantage of using molecular associations as an alternative phenotype when studying the genetic basis of complex traits and diseases. PMID:24573330

Valcárcel, Beatriz; Ebbels, Timothy M D; Kangas, Antti J; Soininen, Pasi; Elliot, Paul; Ala-Korpela, Mika; Järvelin, Marjo-Riitta; de Iorio, Maria

2014-05-01

349

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

PubMed Central

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

Holtgrawe, Daniela; Sorensen, Thomas Rosleff; Viehover, Prisca; Schneider, Jessica; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, Bernd

2014-01-01

350

Genome metabolome integrated network analysis to uncover connections between genetic variants and complex traits: an application to obesity  

PubMed Central

Current studies of phenotype diversity by genome-wide association studies (GWAS) are mainly focused on identifying genetic variants that influence level changes of individual traits without considering additional alterations at the system-level. However, in addition to level alterations of single phenotypes, differences in association between phenotype levels are observed across different physiological states. Such differences in molecular correlations between states can potentially reveal information about the system state beyond that reported by changes in mean levels alone. In this study, we describe a novel methodological approach, which we refer to as genome metabolome integrated network analysis (GEMINi) consisting of a combination of correlation network analysis and genome-wide correlation study. The proposed methodology exploits differences in molecular associations to uncover genetic variants involved in phenotype variation. We test the performance of the GEMINi approach in a simulation study and illustrate its use in the context of obesity and detailed quantitative metabolomics data on systemic metabolism. Application of GEMINi revealed a set of metabolic associations which differ between normal and obese individuals. While no significant associations were found between genetic variants and body mass index using a standard GWAS approach, further investigation of the identified differences in metabolic association revealed a number of loci, several of which have been previously implicated with obesity-related processes. This study highlights the advantage of using molecular associations as an alternative phenotype when studying the genetic basis of complex traits and diseases. PMID:24573330

Valcarcel, Beatriz; Ebbels, Timothy M. D.; Kangas, Antti J.; Soininen, Pasi; Elliot, Paul; Ala-Korpela, Mika; Jarvelin, Marjo-Riitta; de Iorio, Maria

2014-01-01

351

Local and global ancestry inference and applications to genetic association analysis for admixed populations.  

PubMed

Genetic association studies in recently admixed populations offer exciting opportunities to identify novel variants underlying phenotypic diversity. At the same time, genetic heterogeneity resulting from population admixture has to be accounted for to ensure validity of association tests. The whole-genome sequence data and the genome-wide single-nucleotide polymorphism chip data for Mexican American individuals provided by Genetic Analysis Workshop 18 (GAW18) presents a unique opportunity to evaluate and compare methods for the statistical analysis of admixed genetic data. We summarize here the five contributions from the GAW18 working group on admixture mapping and adjusting for admixture. Although group members considered a variety of research topics, the general theme was inference and consideration of ancestry admixture in genetic analyses. The topics considered can be grouped into three categories: (1) global and local ancestry inference and estimation, (2) association and admixture mapping, and (3) genotype imputation in admixed samples. We describe the approaches that were used and the most relevant findings from each contribution. We also provide insight into the strengths and limitations of the state-of-the-art methods considered for genetic analyses in admixed populations. PMID:25112189

Thornton, Timothy A; Bermejo, Justo Lorenzo

2014-09-01

352

Design of a Printed Quadrifilar-Helical Antenna on a Dielectric Cylinder by Means of a Genetic Algorithm [Antenna Applications Corner  

Microsoft Academic Search

This paper presents the application of a genetic algorithm (GA) to the optimization of an S-band quadrifilar-helical antenna, which is printed on a dielectric cylinder. This antenna was designed for LEO satellite applications. Its saddle-shaped pattern should compensate for free-space loss variations in the satellite's footprint. The steady-state genetic algorithm was used for this optimization and an elitist strategy was

Elham Sharifi Moghaddam; Jay Kralovec

2011-01-01

353

Applications  

NASA Astrophysics Data System (ADS)

Economic incentives have spurred numerous applications of genetically engineered organisms in manufacture of pharmaceuticals and industrial chemicals. These successes, involving a variety of methods of genetic manipulation, have dispelled early fears that genetic engineering could not be handled safely, even in the laboratory. Consequently, the potential for applications in the wider environment without physical containment is being considered for agriculture, mining, pollution control, and pest control. These proposed applications range from modest extensions of current plant breeding techniques for new disease-resistant species to radical combinations of organisms (for example, nitrogen-fixing corn plants). These applications raise concerns about potential ecological impacts (see chapter 5), largely because of adverse experiences with both deliberate and inadvertent introductions of nonindigenous species.

Stern, Arthur M.

1986-07-01

354

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

PubMed Central

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

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

2014-01-01

355

Novel Design for Reversible Arithmetic Logic Unit  

NASA Astrophysics Data System (ADS)

Reversible logic circuits are of high interests to calculate with minimum energy consumption having applications in low-power CMOS design, optical computing and nanotechnology, especially in quantum computer. Quantum computer requires quantum arithmetic. A new design of a reversible arithmetic logic unit (reversible ALU) for quantum arithmetic has been proposed in this article. As we known, ALU is an important part of central processing unit (CPU) as the execution unit. So this article provides explicit construction of reversible ALU effecting basic arithmetic operations. By provided the corresponding control unit, the proposed reversible ALU can combine the classical arithmetic and logic operation in a reversible integrated system. This article provides a new more powerful ALU which contains more functions and it will make contribute to the realization of reversible Programmable Logic Device (RPLD) in future using reversible ALU.

Zhou, Rigui; Li, Yancheng; Zhang, Manqun; Hu, BenQiong

2014-07-01

356

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

PubMed Central

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

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

2013-01-01

357

Ion-pair reversed-phase chromatography of short double-stranded deoxyribonucleic acid in silicon micro-pillar array columns: retention model and applications.  

PubMed

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

Zhang, Lei; Majeed, Bivragh; Lagae, Liesbet; Peumans, Peter; Van Hoof, Chris; De Malsche, Wim

2013-06-14

358

Clinical genetic testing for male factor infertility: current applications and future directions.  

PubMed

Spermatogenesis involves the aggregated action of up to 2300 genes, any of which, could, potentially, provide targets for diagnostic tests of male factor infertility. Contrary to the previously proposed common variant hypothesis for common diseases such as male infertility, genome-wide association studies and targeted gene sequencing in cohorts of infertile men have identified only a few gene polymorphisms that are associated with male infertility. Unfortunately, the search for genetic variants associated with male infertility is further hampered by the lack of viable animal models of human spermatogenesis, difficulty in robustly phenotyping infertile men and the complexity of pedigree studies in male factor infertility. In this review, we describe basic genetic principles involved in understanding the genetic basis of male infertility and examine the utility and proper clinical use of the proven genetic assays of male factor infertility, specifically Y chromosome microdeletions, chromosomal translocations, karyotype, cystic fibrosis transmembrane conductance regulator mutation analysis and sperm genetic tests. Unfortunately, these tests are only able to diagnose the cause of about 20% of male factor infertility. The remainder of the review will be devoted to examining novel tests and diagnostic tools that have the potential to explain the other 80% of male factor infertility that is currently classified as idiopathic. Those tests include epigenetic analysis of the spermatozoa and the evaluation of rare genetic variants and copy number variations in patients. Success in advancing to the implementation of such areas is not only dependent on technological advances in the laboratory, but also improved phenotyping in the clinic. PMID:24711280

Hotaling, J; Carrell, D T

2014-05-01

359

Characterization of reverse genetics-derived cold-adapted master donor virus A/Leningrad/134/17/57 (H2N2) and reassortants with H5N1 surface genes in a mouse model.  

PubMed

Live attenuated influenza vaccines (LAIV) offer significant advantages over subunit or split inactivated vaccines to mitigate an eventual influenza pandemic, including simpler manufacturing processes and more cross-protective immune responses. Using an established reverse genetics (rg) system for wild-type (wt) A/Leningrad/134/1957 and cold-adapted (ca) A/Leningrad/134/17/1957 (Len17) master donor virus (MDV), we produced and characterized three rg H5N1 reassortant viruses carrying modified HA and intact NA genes from either A/Vietnam/1203/2004 (H5N1, VN1203, clade 1) or A/Egypt/321/2007 (H5N1, EG321, clade 2) virus. A mouse model of infection was used to determine the infectivity and tissue tropism of the parental wt viruses compared to the ca master donor viruses as well as the H5N1 reassortants. All ca viruses showed reduced replication in lungs and enhanced replication in nasal epithelium. In addition, the H5N1 HA and NA enhanced replication in lungs unless it was restricted by the internal genes of the ca MDV. Mice inoculated twice 4 weeks apart with the H5N1 reassortant LAIV candidate viruses developed serum hemagglutination inhibition HI and IgA antibody titers to the homologous and heterologous viruses consistent with protective immunity. These animals remained healthy after challenge inoculation with a lethal dose with homologous or heterologous wt H5N1 highly pathogenic avian influenza (HPAI) viruses. The profiles of viral replication in respiratory tissues and the immunogenicity and protective efficacy characteristics of the two ca H5N1 candidate LAIV viruses warrant further development into a vaccine for human use. PMID:24648485

Isakova-Sivak, Irina; Chen, Li-Mei; Bourgeois, Melissa; Matsuoka, Yumiko; Voeten, J Theo M; Heldens, Jacco G M; van den Bosch, Han; Klimov, Alexander; Rudenko, Larisa; Cox, Nancy J; Donis, Ruben O

2014-05-01

360

Utility of a multiplex reverse transcriptase-polymerase chain reaction assay (HemaVision) in the evaluation of genetic abnormalities in Korean children with acute leukemia: a single institution study  

PubMed Central

Purpose In children with acute leukemia, bone marrow genetic abnormalities (GA) have prognostic significance, and may be the basis for minimal residual disease monitoring. Since April 2007, we have used a multiplex reverse transcriptase-polymerase chain reaction tool (HemaVision) to detect of GA. Methods In this study, we reviewed the results of HemaVision screening in 270 children with acute leukemia, newly diagnosed at The Catholic University of Korea from April 2007 to December 2011, and compared the results with those of fluorescence in situ hybridization (FISH), and G-band karyotyping. Results Among the 270 children (153 males, 117 females), 187 acute lymphoblastic leukemia and 74 acute myeloid leukemia patients were identified. Overall, GA was detected in 230 patients (85.2%). HemaVision, FISH, and G-band karyotyping identified GA in 125 (46.3%), 126 (46.7%), and 215 patients (79.6%), respectively. TEL-AML1 (20.9%, 39/187) and AML1-ETO (27%, 20/74) were the most common GA in ALL and AML, respectively. Overall sensitivity of HemaVision was 98.4%, with false-negative results in 2 instances: 1 each for TEL-AML1 and MLL-AF4. An aggregate of diseasesspecific FISH showed 100% sensitivity in detection of GA covered by HemaVision for actual probes utilized. G-band karyotype revealed GA other than those covered by HemaVison screening in 133 patients (49.3%). Except for hyperdiplody and hypodiploidy, recurrent GA as defined by the World Health Organizationthat were not screened by HemaVision, were absent in the karyotype. Conclusion HemaVision, supported by an aggregate of FISH tests for important translocations, may allow for accurate diagnosis of GA in Korean children with acute leukemia. PMID:23807891

Kim, Hye-Jin; Oh, Hyun Jin; Jang, Pil-Sang; Chung, Nack-Gyun; Kim, Myungshin; Lim, Jihyang; Cho, Bin; Kim, Hack-Ki

2013-01-01

361

Application of genetic algorithm to optimize burnable poison placement in pressurized water reactors  

Microsoft Academic Search

An efficient and a practical genetic algorithm tool was developed and applied successfully to Burnable Poisons (BPs) placement optimization problem in the reference Three Mile Island-1 (TMI-1) core. Core BP optimization problem means developing a BP loading map for a given core loading configuration that minimizes the total Gadolinium (Gd) amount in the core without violating any design constraints. The

Serkan Yilmaz; Kostadin Ivanov; Samuel Levine

2005-01-01

362

An application of genetic algorithms to lot-streaming flow shop scheduling  

Microsoft Academic Search

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

SUK-HUN YOON; JOSE A. VENTURA

2002-01-01

363

The Application of Genetically Engineered Herpes Simplex Viruses to the Treatment of Experimental Brain Tumors  

Microsoft Academic Search

Due to lack of effective therapy, primary brain tumors are the focus of intense investigation of novel experimental approaches that use vectors and recombinant viruses. Therapeutic approaches have been both indirect, whereby vectors are used, or direct to allow for direct cell killing by the introduced virus. Genetically engineered herpes simplex viruses are currently being evaluated as an experimental approach

Samita S. Andreansky; Bin He; G. Yancey Gillespie; Liliana Soroceanu; James Markert; Joany Chou; Bernard Roizman; Richard J. Whitley

1996-01-01

364

The Application of the Genetic Algorithm to Two-Dimensional Strings: The Source Apportionment Problem  

Microsoft Academic Search

This paper outlines the use of the Genetic Algorithm to manipulate two-dimensional strings. Mutation and reproduction operators can be applied to these strings in the normal way, but simple two-point crossover, crossing a single block between strings, samples the matrix elements in a two-dimensional string very unevenly. An unbiased crossover operator - UNBLOX - which corresponds to wraparound crossover in

Hugh M. Cartwright; Stephen P. Harris

1993-01-01

365

The application of genetics approaches to the study of exceptional longevity in humans: potential and limitations  

PubMed Central

The average life-span of the population of industrialized countries has improved enormously over the last decades. Despite evidence pointing to the role of food intake in modulating life-span, exceptional longevity is still considered primarily an inheritable trait, as pointed out by the description of families with centenarian clusters and by the elevated relative probability of siblings of centenarians to become centenarians themselves. However, rather than being two separate concepts, the genetic origin of exceptional longevity and the more recently observed environment-driven increase in the average age of the population could possibly be explained by the same genetic variants and environmentally modulated mechanisms (caloric restriction, specific nutrients). In support of this hypothesis, polymorphisms selected for in the centenarian population as a consequence of demographic pressure have been found to modulate cellular signals controlled also by caloric restriction. Here, we give an overview of the recent findings in the field of the genetics of human exceptional longevity, of how some of the identified polymorphisms modulate signals also influenced by food intake and caloric restriction, of what in our view have been the limitations of the approaches used over the past years to study genetics (sib-pair-, candidate gene association-, and genome-wide association-studies), and briefly of the limitations and the potential of the new, high-throughput, next-generation sequencing techniques applied to exceptional longevity. PMID:22524405

2012-01-01

366

Application of genetic algorithm (GA) technique on demand estimation of fossil fuels in Turkey  

Microsoft Academic Search

The main objective is to investigate Turkey's fossil fuels demand, projection and supplies by using the structure of the Turkish industry and economic conditions. This study develops scenarios to analyze fossil fuels consumption and makes future projections based on a genetic algorithm (GA). The models developed in the nonlinear form are applied to the coal, oil and natural gas demand

Olcay Ersel Canyurt; Harun Kemal Ozturk

2008-01-01

367

Application of genetic algorithms to fault diagnosis in nuclear power plants  

Microsoft Academic Search

A nuclear power plant (NPP) is a complex and highly reliable special system. Without expert knowledge, fault confirmation in the NPP can be prevented by illusive and real-time signals. A new method of fault diagnosis, based on genetic algorithms (GAs) has been developed to resolve this problem. This NPP fault diagnosis method combines GAs and classical probability with an expert

Zhou Yangping; Zhao Bingquan; Wu DongXin

2000-01-01

368

On the application of genetic algorithms for optimising composites against impact loading  

Microsoft Academic Search

A genetic algorithm (GA) was adopted to optimise the response of a composite laminate subject to impact. Two different impact scenarios are presented: low-velocity impact of a slender laminated strip and high-velocity impact of a rectangular plate by a spherical impactor. In these cases, the GA's objective was to, respectively, minimise the peak deflection and minimise penetration by varying the

M. Yong; B. G. Falzon; L. Iannucci

2008-01-01

369

Polymorphic Simple Sequence Repeat Regions in Chloroplast Genomes: Applications to the Population Genetics of Pines  

Microsoft Academic Search

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

W. Powell; M. Morgante; R. McDevitt; G. G. Vendramin; J. A. Rafalski

1995-01-01

370

Toward the application of genetic algorithms to real world resource constrained project scheduling problems  

Microsoft Academic Search

Much research has been invested in the optimisation of the Resource Constrained Project Scheduling Problem (RCPSP) using genetic algorithms. Reviews of this work can be found in Lancaster and Ozbayrak (1) and Kolisch and Hartmann (2). This research however doesn't extend to the solution of real world RCPSP. As part of ongoing research the authors describe a practical implementation of

J. Lancaster; K. Chenga

371

Application of vector optimization employing modified genetic algorithm to permanent magnet motor design  

Microsoft Academic Search

This paper presents a method to solve the vector optimization problem that determines both the noninferior solution set and the best compromise solution employing a modified genetic algorithm. The algorithm differs from the conventional one in the definition of fitness value and convergence criterion. Some parameters of the algorithm are adjusted to the vector optimization. The algorithm also contains the

Dong-Joon Sim; Hyun-Kyo Jung; Song-Yop Hahn; Jong-Soo Won

1997-01-01

372

Application of the Protection Motivation Theory to Genetic Testing for Breast Cancer Risk  

Microsoft Academic Search

Background. Many women, even women at low risk, are interested in genetic testing for breast cancer risk. However, the test has little to offer for women at low to moderate risk. We applied the Protection Motivation Theory (PMT) to investigate predictors of women's motivation to obtain such a test.Methods. Women at low to moderate risk (n = 330) were recruited

Almut W. Helmes

2002-01-01

373

A genetic linkage map of the mouse: Current applications and future prospects  

Microsoft Academic Search

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.

Neal G. Copeland; Nancy A. Jenkins; Debra J. Gilbert; Janan T. Eppig; L. J. Maltais; J. H. Nadeau; J. C. Miller; W. F. Dietrich; A. Weaver; S. E. Lincoln; R. G. Steen; L. D. Steing; Eric S. Lander

1993-01-01

374

The Use of Prior Distributions to Learn Genetic Olivier Gevaert1  

E-print Network

of a struc- ture prior for reverse-engineering genetic networks with Bayesian network models can improve more reliable models of genetic networks. 1 Introduction Reverse engineering genetic networks has been and extensions of Bayesian networks are popular models for reverse engineering genetic networks ([5, 15, 9, 10

375

Design of a compact reversible binary coded decimal adder circuit  

Microsoft Academic Search

Reversible logic is an emerging research area and getting remarkable interests over the past few years. Interest is sparked in reversible logic by its applications in several technologies, such as quantum, optical, thermodynamics and adiabatic CMOS. This paper represents a synthesis method to realize reversible binary coded decimal adder circuit. Firstly, a reversible full-adder circuit has been proposed that shows

Ahsan Raja Chowdhury

2006-01-01

376

Cost-effectiveness of MODY genetic testing: translating genomic advances into practical health applications.  

PubMed

OBJECTIVE To evaluate the cost-effectiveness of a genetic testing policy for HNF1A-, HNF4A-, and GCK-MODY in a hypothetical cohort of type 2 diabetic patients 25-40 years old with a MODY prevalence of 2%. RESEARCH DESIGN AND METHODS We used a simulation model of type 2 diabetes complications based on UK Prospective Diabetes Study data, modified to account for the natural history of disease by genetic subtype to compare a policy of genetic testing at diabetes diagnosis versus a policy of no testing. Under the screening policy, successful sulfonylurea treatment of HNF1A-MODY and HNF4A-MODY was modeled to produce a glycosylated hemoglobin reduction of -1.5% compared with usual care. GCK-MODY received no therapy. Main outcome measures were costs and quality-adjusted life years (QALYs) based on lifetime risk of complications and treatments, expressed as the incremental cost-effectiveness ratio (ICER) (USD/QALY). RESULTS The testing policy yielded an average gain of 0.012 QALYs and resulted in an ICER of 205,000 USD. Sensitivity analysis showed that if the MODY prevalence was 6%, the ICER would be ~50,000 USD. If MODY prevalence was >30%, the testing policy was cost saving. Reducing genetic testing costs to 700 USD also resulted in an ICER of ~50,000 USD. CONCLUSIONS Our simulated model suggests that a policy of testing for MODY in selected populations is cost-effective for the U.S. based on contemporary ICER thresholds. Higher prevalence of MODY in the tested population or decreased testing costs would enhance cost-effectiveness. Our results make a compelling argument for routine coverage of genetic testing in patients with high clinical suspicion of MODY. PMID:24026547

Naylor, Rochelle N; John, Priya M; Winn, Aaron N; Carmody, David; Greeley, Siri Atma W; Philipson, Louis H; Bell, Graeme I; Huang, Elbert S

2014-01-01

377

Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components  

PubMed Central

An electrochemical biosensor for the detection of genetically modified food components is presented. The biosensor was based on 21-mer single-stranded oligonucleotide (ssDNA probe) specific to either 35S promoter or nos terminator, which are frequently present in transgenic DNA cassettes. ssDNA probe was covalently attached by 5?-phosphate end to amino group of cysteamine self-assembled monolayer (SAM) on gold electrode surface with the use of activating reagents – water soluble 1-ethyl-3(3?-dimethylaminopropyl)-carbodiimide (EDC) and N-hydroxy-sulfosuccinimide (NHS). The hybridization reaction on the electrode surface was detected via methylene blue (MB) presenting higher affinity to ssDNA probe than to DNA duplex. The electrode modification procedure was optimized using 19-mer oligoG and oligoC nucleotides. The biosensor enabled distinction between DNA samples isolated from soybean RoundupReady® (RR soybean) and non-genetically modified soybean. The frequent introduction of investigated DNA sequences in other genetically modified organisms (GMOs) give a broad perspectives for analytical application of the biosensor.

Tichoniuk, Mariusz; Ligaj, Marta; Filipiak, Marian

2008-01-01

378

Reverse Genetic Approaches to Cloning Deafness Genes  

Microsoft Academic Search

Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints

S. D. M. Brown; K. A. Brown; M. J. Sutcliffe; J. S. Cavanna; A. J. Greenfield; K. P. Steel

1991-01-01

379

Reversible phosphorylation in mitochondria.  

E-print Network

??Mitochondria represent an underappreciated site of regulation by reversible phosphorylation. Our work has focused on the identification of proteins involved in regulating mitochondria by reversible… (more)

Rardin, Matthew James

2008-01-01

380

A fast fine-grained genetic algorithm for spectrum fitting: An application to X-ray spectra  

NASA Astrophysics Data System (ADS)

Often the result of the interaction of radiation with matter is represented by a spectrum. Regardless of the type of radiation used, a spectrum consists of peaks superimposed on a background. The important information is contained in the peak, so the derivation of the peaks parameters is fundamental. However, in most cases the fitting of the spectrum is an ill-posed problem, because of the presence of superimposed peaks. In this case the algorithms reported in the literature sometimes fail. For these reasons a genetic algorithm approach has been developed and is described here. Its novelty for this kind of application is represented by the use of a fine-grained strategy that makes it considerably faster than other implementations of this class of algorithms. Some results of its application to X-ray spectra are presented and discussed.

Brunetti, Antonio

2013-03-01

381

Genetic variation and its maintenance  

SciTech Connect

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.

Roberts, D.F.; De Stefano, G.F.

1986-01-01

382

Sustainable Development and Norwegian Genetic Engineering Regulations: Applications, Impacts, and Challenges  

Microsoft Academic Search

The main purpose of The NorwegianGene Technology Act (1993) is to enforcecontainment of genetically modified organisms(GMOs) and control of GMO releases.Furthermore, the Act intends to ensure that``production and use of GMOs should take placein an ethically and socially justifiable way,in accordance with the principle of sustainabledevelopment and without detrimental effects tohealth and the environment.'' Hence it isobvious that, for the

Anne Ingeborg Myhr; Terje Traavik

2003-01-01

383

A review of the current applications of genetic algorithms in assembly line balancing  

Microsoft Academic Search

Most of the problems involving the design and plan of manufacturing systems are combinatorial and NP-hard. A well-known manufacturing\\u000a optimization problem is the assembly line balancing problem (ALBP). Due to the complexity of the problem, in recent years,\\u000a a growing number of researchers have employed genetic algorithms. In this article, a survey has been conducted from the recent\\u000a published literature

Seren Ozmehmet Tasan; Semra Tunali

2008-01-01

384

Application of a Genetic Algorithm for the Optimization of a Complex Reservoir System in Tunisia  

Microsoft Academic Search

A genetic algorithm (GA) model is developed and used for optimizing the allocation of water resources within a complex multiple\\u000a reservoir system located in Tunisia. The GA model considers two objectives: the water allocation to demand centers and the\\u000a salinity level of the water supply to end users. These two objectives are combined into a single objective function using\\u000a a

Mohamed Hedi Louati; Sihem Benabdallah; Fethi Lebdi; Darko Milutin

2011-01-01

385

Forest-tree biotechnology: genetic transformation and its application to future forests  

Microsoft Academic Search

The wide use of forest-tree products and the progressive deterioration of natural forests mean that foresters can no longer rely on the exploitation of existing forests. Extensive accelerated-breeding programs are needed for reforestation and to improve existing forest-tree species. Plant genetic-transformation techniques and gene isolation and characterization are no longer serious problems; forest-tree species should be a major target for

Tzvi Tzfira; Amir Zuker; Arie Altman

1998-01-01

386

A genetically informed, group FMRI connectivity modeling approach: application to schizophrenia.  

PubMed

While neuroimaging data can provide valuable phenotypic information to inform genetic studies, the opposite is also true: known genotypes can be used to inform brain connectivity patterns from fMRI data. Here, we propose a framework for genetically informed group brain connectivity modeling. Subjects are first stratified according to their genotypes, and then a group regularized regression model is employed for brain connectivity modeling utilizing the time courses from a priori specified regions of interest (ROIs). With such an approach, each ROI time course is in turn predicted from all other ROI time courses at zero lag using a group regression framework which also incorporates a penalty based on genotypic similarity. Simulations supported such an approach when, as previously studies have indicated to be the case, genetic influences impart connectivity differences across subjects. The proposed method was applied to resting state fMRI data from Schizophrenia and normal control subjects. Genotypes were based on D-amino acid oxidase activator (DAOA) single-nucleotide polymorphisms (SNPs) information. With DAOA SNPs information integrated, the proposed approach was able to more accurately model the diversity in connectivity patterns. Specifically, connectivity with the left putamen, right posterior cingulate, and left middle frontal gyri were found to be jointly modulated by DAOA genotypes and the presence of Schizophrenia. We conclude that the proposed framework represents a multimodal analysis approach for incorporating genotypic variability into brain connectivity analysis directly. PMID:24557696

Liu, Aiping; Chen, Xiaohui; Wang, Z Jane; Xu, Qi; Appel-Cresswell, Silke; McKeown, Martin J

2014-03-01

387

Optimization of fuels from waste composition with application of genetic algorithm.  

PubMed

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

Ma?gorzata, Wzorek

2014-05-01

388

Improving Reversal Median Computation Using Commuting Reversals and Cycle Information  

PubMed Central

Abstract In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all existing solvers are extremely slow when the genomes are distant. In this paper, we present a new reversal median heuristic for unichromosomal genomes. The new method works by applying sets of reversals in a batch where all such reversals both commute and do not break the cycle of any other. Our testing using simulated datasets shows that this method is much faster than the leading solver for difficult datasets with only a slight accuracy penalty, yet retains better accuracy than other heuristics with comparable speed, and provides the additional option of searching for multiple medians. This method dramatically increases the speed of current direct optimization methods and enables us to extend the range of their applicability to organellar and small nuclear genomes with more than 50 reversals along each edge. PMID:18774904

Arndt, William

2008-01-01

389

Reverse logistics - a framework  

Microsoft Academic Search

In this paper we define and compare Reverse Logistics definitions. We start by giving an understanding framework of Reverse Logistics: the why-what-how. By this means, we put in context the driving forces for Reverse Logistics, a typology of return reasons, a classification of products, processes and actors. In addition we provide a decision framework for Reverse Logistics and we present

Marisa P. de Brito; Rommert Dekker

2002-01-01

390

Molecular Studies in Horses with SRY-Positive XY Sex Reversal  

E-print Network

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...

Fang, Erica

2012-02-14

391

Application of Massively Parallel Sequencing to Genetic Diagnosis in Multiplex Families with Idiopathic Sensorineural Hearing Impairment  

PubMed Central

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

Wu, Chen-Chi; Lin, Yin-Hung; Lu, Ying-Chang; Chen, Pei-Jer; Yang, Wei-Shiung; Hsu, Chuan-Jen; Chen, Pei-Lung

2013-01-01

392

Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.  

PubMed

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

Wu, Chen-Chi; Lin, Yin-Hung; Lu, Ying-Chang; Chen, Pei-Jer; Yang, Wei-Shiung; Hsu, Chuan-Jen; Chen, Pei-Lung

2013-01-01

393

Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.  

PubMed

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

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

394

Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus).  

PubMed

In this study, the cross-amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross-amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2-4, 0.086-0.629 and 0.288-0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison. PMID:17177698

Roth, T; Pfeiffer, I; Weising, K; Brenig, B

2006-12-01

395

Genetic algorithm based adaptive neural network ensemble and its application in predicting carbon flux  

USGS Publications Warehouse

To improve the accuracy in prediction, Genetic Algorithm based Adaptive Neural Network Ensemble (GA-ANNE) is presented. Intersections are allowed between different training sets based on the fuzzy clustering analysis, which ensures the diversity as well as the accuracy of individual Neural Networks (NNs). Moreover, to improve the accuracy of the adaptive weights of individual NNs, GA is used to optimize the cluster centers. Empirical results in predicting carbon flux of Duke Forest reveal that GA-ANNE can predict the carbon flux more accurately than Radial Basis Function Neural Network (RBFNN), Bagging NN ensemble, and ANNE. ?? 2007 IEEE.

Xue, Y.; Liu, S.; Hu, Y.; Yang, J.; Chen, Q.

2007-01-01

396

Gene isolation by complementation in Candida albicans and applications to physical and genetic mapping.  

PubMed Central

We have isolated three genes, ARG57, SER57, and LYS1, on the basis of their function in Candida albicans. A C. albicans transformation vector containing the C. albicans URA3 gene, a Candida ARS sequence, and a portion of the Saccharomyces cerevisiae 2 microns circle containing the replication origin was constructed. Clones from genomic libraries in this vector were isolated by direct complementation of the auxotrophies in strain 1006 (arg57 ser57 lys1 ura3 MPA1). Transformants typically contain two to four plasmids in a mixed tandem multimer. A scheme to resolve mixed multimers into monomers in vivo by transformation of S. cerevisiae with Candida transformant DNA selecting Ura+ transformants was devised. Monomeric plasmids were then isolated by transformation of Escherichia coli with the S. cerevisiae transformant DNA. These were retested by transformation of strain 1006 to identify the specific plasmid that complemented the auxotrophy. The chromosomal locations of the genes were determined by hybridization to C. albicans chromosomes separated on contour-clamped homogenous electric field gels. We used these locations to assess the stability of individual C. albicans chromosomes in parasexual genetic analysis. The Lys(+)-complementing clone was shown to be LYS1 by complementation of S. cerevisiae lys1 mutants. These cloned genes help to align the Candida physical and genetic maps and provide additional markers for the transformation system. Images PMID:1541560

Goshorn, A K; Grindle, S M; Scherer, S

1992-01-01

397

[Application of DNA extraction kit, 'GM quicker' for detection of genetically modified soybeans].  

PubMed

Several DNA extraction methods have been officially introduced to detect genetically modified soybeans, but the choice of DNA extraction kits depend on the nature of the samples, such as grains or processed foods. To overcome this disadvantage, we examined whether the GM quicker kit is available for both grains and processed foods. We compared GM quicker with four approved DNA extraction kits in respect of DNA purity, copy numbers of lectin gene, and working time. We found that the DNA quality of GM quicker was superior to that of the other kits for grains, and the procedure was faster. However, in the case of processed foods, GM quicker was not superior to the other kits. We therefore investigated an unapproved GM quicker 3 kit, which is available for DNA extraction from processed foods, such as tofu and boiled soybeans. The GM quicker 3 kit provided good DNA quality from both grains and processed foods, so we made a minor modification of the GM quicker-based protocol that was suitable for processed foods, using GM quicker and its reagents. The modified method enhanced the performance of GM quicker with processed foods. We believe that GM quicker with the modified protocol is an excellent tool to obtain high-quality DNA from grains and processed foods for detection of genetically modified soybeans. PMID:22450668

Sato, Noriko; Sugiura, Yoshitsugu; Tanaka, Toshitsugu

2012-01-01

398

Genetic effects of vinylcyclohexene diepoxide in yeast.  

PubMed

Using D7 strain of S. cerevisiae where we can consider three genetic effects such as mitotic gene conversion, mitotic cross over and reverse mutation we tested vinylcyclohexene diepoxide "in vitro" without metabolic activation. In this condition VCD is very toxic and induces both three genetic effects namely mitotic gene conversion, mitotic cross over and reverse mutation. PMID:7016138

Bronzetti, G; Bauer, C; Corsi, C; Leporini, C; Nieri, R

1980-09-30

399

Intertransaction Class Association Rule Mining Based on Genetic Network Programming and Its Application to Stock Market Prediction  

NASA Astrophysics Data System (ADS)

Intertransaction association rules have been reported to be useful in many fields such as stock market prediction, but still there are not so many efficient methods to dig them out from large data sets. Furthermore, how to use and measure these more complex rules should be considered carefully. In this paper, we propose a new intertransaction class association rule mining method based on Genetic Network Programming (GNP), which has the ability to overcome some shortages of Apriori-like based intertransaction association methods. Moreover, a general classifier model for intertransaction rules is also introduced. In experiments on the real world application of stock market prediction, the method shows its efficiency and ability to obtain good results and can bring more benefits with a suitable classifier considering larger interval span.

Yang, Yuchen; Mabu, Shingo; Shimada, Kaoru; Hirasawa, Kotaro

400

Application of Genetic and Gradient Descent Algorithms to Wavefront Compensation for the Deep-Space Optical Communications Receiver  

NASA Astrophysics Data System (ADS)

Present adaptive optics systems use a wavefront sensor to detect phase errors in the incoming wavefront. Knowledge of these phase errors then is used to correct the incoming wavefront, reducing image distortion. However, these systems require that a portion of the incoming light be diverted to the wavefront sensor and away from the main receiver's focal plane, which results in a loss of signal power in the receiver in optical communication applications. Accordingly, it is desirable to develop a system that relies entirely on the focal-plane intensity distribution as opposed to a separate wavefront sensor in order to detect and correct wavefront errors. Two common stochastic optimization techniques -- genetic algorithms and gradient descent algorithms -- are evaluated in this article. Although these algorithms are promising, further work is necessary to enable them to be used in practical adaptive optics systems due to their slow convergence speeds relative to the rate of change in the atmosphere.

Mukai, R.; Wilson, K.; Vilnrotter, V.

2005-05-01

401

Binary Classification using Decision Tree based Genetic Programming and Its Application to Analysis of Bio-mass Data  

NASA Astrophysics Data System (ADS)

In machine learning, pattern recognition may be the most popular task. ``Similar'' patterns identification is also very important in biology because first, it is useful for prediction of patterns associated with disease, for example cancer tissue (normal or tumor) second, similarity or dissimilarity of the kinetic patterns is used to identify coordinately controlled genes or proteins involved in the same regulatory process. Third, similar genes (proteins) share similar functions. In this paper, we present an algorithm which uses genetic programming to create decision tree for binary classification problem. The application of the algorithm was implemented on five real biological databases. Base on the results of comparisons with well-known methods, we see that the algorithm is outstanding in most of cases.

To, Cuong; Pham, Tuan D.

2010-01-01

402

Securing a mobile adhoc network from routing attacks through the application of genetic algorithm  

E-print Network

In recent years, the static shortest path (SP) problem has been well addressed using intelligent optimization techniques, e.g., artificial neural networks, genetic algorithms (GAs), particle swarm optimization, etc. However, with the advancement in wireless communications, more and more mobile wireless networks appear, e.g., mobile networks [mobile ad hoc networks (MANETs)], wireless sensor networks, etc. One of the most important characteristics in mobile wireless networks is the topology dynamics, i.e., the network topology changes over time due to energy conservation or node mobility. Therefore, the SP routing problem in MANETs turns out to be a dynamic optimization problem. GA's are able to find, if not the shortest, at least an optimal path between source and destination in mobile ad-hoc network nodes. And we obtain the alternative path or backup path to avoid reroute discovery in the case of link failure or node failure.

Nikhil, Kumar; Sharma, Pankaj

2012-01-01

403

Application of carrier testing to genetic counseling for X-linked agammaglobulinemia  

SciTech Connect

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

Allen, R.C.; Nachtman, R.G.; Belmont, J.W.; Rosenblatt, H.M.

1994-01-01

404

Calibration of neural networks using genetic algorithms, with application to optimal path planning  

NASA Technical Reports Server (NTRS)

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.

Smith, Terence R.; Pitney, Gilbert A.; Greenwood, Daniel

1987-01-01

405

Analysis of a stochastic predator-prey model with applications to intrahost HIV genetic diversity.  

PubMed

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 between the visible and invisible HIV variants can reach steady states in which either a single variant exists or in which coexistence occurs depending on the parameter regime. We show that in some parameter regimes the end state of the system is stochastic. From a genetics perspective, we study the impact of the population dynamics on the lineages of an HIV sample taken after an escape mutation occurs. We show that the lineages go through severe bottlenecks and that in certain parameter regimes the lineage distribution can be characterized by a Kingman coalescent. Our results depend on methods from diffusion theory and coalescent theory. PMID:22139471

Leviyang, Sivan

2012-12-01

406

HIV-1 Reverse Transcription  

PubMed Central

Reverse transcription and integration are the defining features of the Retroviridae; the common name “retrovirus” derives from the fact that these viruses use a virally encoded enzyme, reverse transcriptase (RT), to convert their RNA genomes into DNA. Reverse transcription is an essential step in retroviral replication. This article presents an overview of reverse transcription, briefly describes the structure and function of RT, provides an introduction to some of the cellular and viral factors that can affect reverse transcription, and discusses fidelity and recombination, two processes in which reverse transcription plays an important role. In keeping with the theme of the collection, the emphasis is on HIV-1 and HIV-1 RT. PMID:23028129

Hu, Wei-Shau; Hughes, Stephen H.

2012-01-01

407

Properly apply reverse osmosis  

SciTech Connect

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.

Kucera, J.

1997-02-01

408

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...

409

Genetic Counseling Program Information  

E-print Network

Genetic Counseling Program Information for Potential Applicants #12;Page 2 of 12 8.24.11 Program Overview "Genetic counseling is the process of helping people understand and adapt to the medical, psychological, and familial implications of genetic contributions to disease. The process integrates

Finley Jr., Russell L.

410

Review article Genetic transformation  

E-print Network

Review article Genetic transformation: a short review of methods and their applications, results of phenotypic traits has been examined. Agrobacterium I biotechnology I forest tree I genetic transformation Biotechnology includes tissue culture, mo- lecular biology and genetic transformation. This field of research

Paris-Sud XI, Université de

411

Addressing Genetics Delivering Health  

E-print Network

Addressing Genetics Delivering Health A strategy for advancing the dissemination and application of genetics knowledge throughout our health professions Funded by Hilary Burton September 2003 Executive Summary #12;Summary of Recommendations Establishment of a national Steering Group for Genetics Education q

Rambaut, Andrew

412

Reversion of flowering  

Microsoft Academic Search

Reversion from floral to vegetative growth is under environmental control in many plant species. However the factors regulating\\u000a floral reversion, and the events at the shoot apex that take place when it occurs, have received less attention than those\\u000a associated with the transition to flowering.\\u000a \\u000a Reversions may be categorized as flower reversion, in which the flower meristem resumes leaf production,

N. H. Battey; R. F. Lyndon

1990-01-01

413

Biological laser printing of genetically modified Escherichia coli for biosensor applications.  

PubMed

One of the primary requirements of cell- or tissue-based sensors is the placement of cells and cellular material at or near the sensing elements of the device. The ability to achieve precise, reproducible and rapid placement of cells is the focus of this study. We have developed a technique, biological laser printing or BioLP, which satisfies these requirements and has advantages over current technologies. BioLP is capable of rapidly depositing patterns of active biomolecules and living cells onto a variety of material surfaces. Unlike ink jet or manual spotting techniques, this process delivers small volume (nl to fl) aliquots of biomaterials without the use of an orifice, thus eliminating potential clogging issues and enabling diverse classes of biomaterials to be deposited. This report describes the use of this laser-based printing method to transfer genetically-modified bacteria capable of responding to various chemical stressors onto agar-coated slides and into microtiter plates. The BioLP technology enables smaller spot sizes, increased resolution, and improved reproducibility compared to related technologies. PMID:15308228

Barron, J A; Rosen, R; Jones-Meehan, J; Spargo, B J; Belkin, S; Ringeisen, B R

2004-09-15

414

Applications of information theory, genetic algorithms, and neural models to predict oil flow  

NASA Astrophysics Data System (ADS)

This work introduces a new information-theoretic methodology for choosing variables and their time lags in a prediction setting, particularly when neural networks are used in non-linear modeling. The first contribution of this work is the Cross Entropy Function (XEF) proposed to select input variables and their lags in order to compose the input vector of black-box prediction models. The proposed XEF method is more appropriate than the usually applied Cross Correlation Function (XCF) when the relationship among the input and output signals comes from a non-linear dynamic system. The second contribution is a method that minimizes the Joint Conditional Entropy (JCE) between the input and output variables by means of a Genetic Algorithm (GA). The aim is to take into account the dependence among the input variables when selecting the most appropriate set of inputs for a prediction problem. In short, theses methods can be used to assist the selection of input training data that have the necessary information to predict the target data. The proposed methods are applied to a petroleum engineering problem; predicting oil production. Experimental results obtained with a real-world dataset are presented demonstrating the feasibility and effectiveness of the method.

Ludwig, Oswaldo; Nunes, Urbano; Araújo, Rui; Schnitman, Leizer; Lepikson, Herman Augusto

2009-07-01

415

Time reversal matched field  

Microsoft Academic Search

Time reversal techniques obtain increased resolution by exploiting scattering and multipath in propagation through inhomogeneous channels. Fink and collaborators has used time reversal to achieve super-resolution focusing in acoustics with controlled ultrasonic experiments in water tanks. More recently large-scale acoustics experiments in the ocean have confirmed the resolution ability of time reversal. In this paper, matched field detection with time

J. Moura

2004-01-01

416

Genetically Engineered Tetravalent Single-Chain Fv of the Pancarcinoma Monoclonal Antibody CC49: Improved Biodistribution and Potential for Therapeutic Application1  

Microsoft Academic Search

Failure of radiolabeled monoclonal antibodies (MAbs) in the treatment of solid tumors, for the most part, is a result of undesirable pharmacoki- netics that lead to significant radiation exposure of normal tissues and an inadequate delivery of radiation doses to tumors. Using genetic engineer- ing, antitumor MAbs can be optimized for desirable clinical applications. In the present study, we report

Apollina Goel; David Colcher; Janina Baranowska-Kortylewicz; Sam Augustine; Barbara J. M. Booth; Gabriela Pavlinkova; Surinder K. Batra

2000-01-01

417

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

E-print Network

. The second problem considered here is the job shop scheduling problem where the objective is to minimize the makespan. Local search techniques which have been applied to this problem are discussed with the emphasis being on genetic algorithms. A genetic...

Graves, Gregory Howard

2012-06-07

418

Application of hierarchical genetic models to Raven and WAIS subtests: a Dutch twin study  

Microsoft Academic Search

Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a ge- netic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard Progressive test score, collected in 194 18-year-old Dutch twin pairs. We in- vestigated whether first-order group

Frühling V. Rijsdijk; P. A. Vernon; Dorret I. Boomsma

2002-01-01

419

Genetic application in a facility location problem with random demand within queuing framework  

Microsoft Academic Search

In many service and industrial applications of the facility location problem, the number of required facilities along with\\u000a allocation of the customers to the facilities are the two major questions that need to be answered. In this paper, a facility\\u000a location problem with stochastic customer demand and immobile servers is studied. Two objectives considered in this problem\\u000a are: (1) minimizing

Seyed Hamid Reza Pasandideh; Seyed Taghi Akhavan Niaki

420

Application of siRNA Library in High-Throughput Genetic Screens of Mammalian Cells  

Microsoft Academic Search

Small interfering (si)RNA directs gene-specific silencing in both model organisms and mammalian cells through RNA interference. The discovery of this phenomenon has provided a valuable tool to study loss-of-function phenotype of gene. The most recent breakthrough in the generation of large-scale mammalian siRNA libraries fur- ther moves forward the application of RNA interference, providing a powerful plat- form to carry

Li-Na Zhao; Ting-Ting Li; Yang-Lin Pan; Han-Bing Ning; Zhi-Guo Liu; Dai-Ming Fan

2005-01-01

421

Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping  

Microsoft Academic Search

BACKGROUND: The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the

Joy Nakitandwe; Friederike Trognitz; Bodo Trognitz

2007-01-01

422

SURFACE FLUID REGISTRATION OF CONFORMAL REPRESENTATION: APPLICATION TO DETECT DISEASE BURDEN AND GENETIC INFLUENCE ON HIPPOCAMPUS  

PubMed Central

In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistentsurface 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 morphometrydifference between diagnostic groups. Experimental results show that the new system has better performance than two publically available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E ?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 workprovides a new MRI analysis tool that may help presymptomatic AD research. PMID:23587689

Shi, Jie; Thompson, Paul M.; Gutman, Boris; Wang, Yalin

2013-01-01

423

Surface fluid registration of conformal representation: application to detect disease burden and genetic influence on hippocampus.  

PubMed

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

Shi, Jie; Thompson, Paul M; Gutman, Boris; Wang, Yalin

2013-09-01

424

Reversible Friedel-Crafts acylations of 3-alkyl-1-(phenylsulfonyl)pyrroles: Application to the synthesis of an ant trail pheromone  

Microsoft Academic Search

Friedel-Crafts acylations of 3-alkyl-1-(phenylsulfonyl)pyrroles appear to be kinetically favored at the adjacent C-2 position but rearrangement to the C-5 position can occur after prolonged reaction times. This reversible Friedel-Crafts methodology has been employed for the synthesis of the ant trail pheromone, methyl 4-methylpyrrole-2-carboxylate.

Dong Xiao; Jeffrey A. Schreier; James H. Cook; Paul G. Seybold; Daniel M. Ketcha

1996-01-01

425

Genetic network analysis in light of massively parallel biological data acquisition.  

PubMed

Complementary DNA microarray and high density oligonucleotide arrays opened the opportunity for massively parallel biological data acquisition. Application of these technologies will shift the emphasis in biological research from primary data generation to complex quantitative data analysis. Reverse engineering of time-dependent gene-expression matrices is amongst the first complex tools to be developed. The success of reverse engineering will depend on the quantitative features of the genetic networks and the quality of information we can obtain from biological systems. This paper reviews how the (1) stochastic nature, (2) the effective size, and (3) the compartmentalization of genetic networks as well as (4) the information content of gene expression matrices will influence our ability to perform successful reverse engineering. PMID:10380181

Szallasi, Z

1999-01-01

426

A New Look at Reversible Logic Implementation of Decimal Adder  

Microsoft Academic Search

Reversibility plays a fundamental role when computations with minimal energy dissipation are considered. In recent years, reversible logic has emerged as one of the most important approaches for power optimization with its application in low power CMOS, quantum computing and nanotechnology. This research proposes a new implementation of Binary Coded Decimal (BCD) adder in reversible logic. The design reduces the

R. K. James; T. K. Shahana; K. P. Jacob; S. Sasi

2007-01-01

427

Quality control in the application of flow cytometry to studies of environmentally-induced genetic damage  

SciTech Connect

Flow cytometry (FCM) has been used to demonstrate altered DNA content in fish, reptiles, birds and mammals exposed to radionuclides, PAHs and other contaminants. However, artifacts resulting from sample preparation, handling, variations in instrument parameters or other factors may confound such measurements. Some artifacts resemble genotoxic responses and so could lead to erroneous positive conclusions. As part of ongoing studies of effects of various pollutants on DNA content in fishes, the authors tested sample handling and preparation methods for the induction of artifacts. The authors describe QA/QC methods, including control of staining, conditions, doublet discrimination by comparison of peak versus integral fluorescence, internal DNA standards, and the use of time versus fluorescence plots. Consistent application of these practices is essential to obtain valid measurements of DNA content in environmental samples, and neglect of these can result in poor quality data and the acceptance of incorrect hypotheses.

McCreedy, C.D.; Robinson, J.P.; Dallas, C.E.; Jagoe, C.H.

1999-07-01

428

Reverse breeding: a novel breeding approach based on engineered meiosis  

PubMed Central

Reverse breeding (RB) is a novel plant breeding technique designed to directly produce parental lines for any heterozygous plant, one of the most sought after goals in plant breeding. RB generates perfectly complementing homozygous parental lines through engineered meiosis. The method is based on reducing genetic recombination in the selected heterozygote by eliminating meiotic crossing over. Male or female spores obtained from such plants contain combinations of non-recombinant parental chromosomes which can be cultured in vitro to generate homozygous doubled haploid plants (DHs). From these DHs, complementary parents can be selected and used to reconstitute the heterozygote in perpetuity. Since the fixation of unknown heterozygous genotypes is impossible in traditional plant breeding, RB could fundamentally change future plant breeding. In this review, we discuss various other applications of RB, including breeding per chromosome. PMID:19811618

Dirks, Rob; van Dun, Kees; de Snoo, C Bastiaan; van den Berg, Mark; Lelivelt, Cilia L C; Voermans, William; Woudenberg, Leo; de Wit, Jack P C; Reinink, Kees; Schut, Johan W; van der Zeeuw, Eveline; Vogelaar, Aat; Freymark, Gerald; Gutteling, Evert W; Keppel, Marina N; van Drongelen, Paul; Kieny, Matthieu; Ellul, Philippe; Touraev, Alisher; Ma, Hong; de Jong, Hans; Wijnker, Erik

2009-01-01

429

Robustness in Regulatory Interaction Networks. A Generic Approach with Applications at Different Levels: Physiologic, Metabolic and Genetic  

PubMed Central

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

Demongeot, Jacques; Ben Amor, Hedi; Elena, Adrien; Gillois, Pierre; Noual, Mathilde; Sene, Sylvain

2009-01-01

430

Synthesis of Fault Tolerant Reversible Logic Circuits  

E-print Network

Reversible logic is emerging as an important research area having its application in diverse fields such as low power CMOS design, digital signal processing, cryptography, quantum computing and optical information processing. This paper presents a new 4*4 universal reversible logic gate, IG. It is a parity preserving reversible logic gate, that is, the parity of the inputs matches the parity of the outputs. The proposed parity preserving reversible gate can be used to synthesize any arbitrary Boolean function. It allows any fault that affects no more than a single signal readily detectable at the circuit's primary outputs. Finally, it is shown how a fault tolerant reversible full adder circuit can be realized using only two IGs. It has also been demonstrated that the proposed design offers less hardware complexity and is efficient in terms of gate count, garbage outputs and constant inputs than the existing counterparts.

Islam, Md Saiful; Begum, Zerina; Hafiz, Mohd Zulfiquar; Mahmud, Abdullah Al; 10.1109/CAS-ICTD.2009.4960883

2010-01-01

431

Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways  

Microsoft Academic Search

The chemical-genetic profile can be defined as quantitative values of deletion strains' growth defects under exposure to chemicals. In yeast, the compendium of chemical-genetic profiles of genomewide deletion strains under many different chemicals has been used for identifying direct target proteins and a common mode-of-action of those chemicals. In the previous study, valuable biological information such as protein–protein and genetic

Sangjo Han; Dongsup Kim; Christos A. Ouzounis

2008-01-01

432

Lesson 46: Reversives  

E-print Network

] [resurrect] [abort] [praise] [reprimand] B). Utanzu wa kufanya au kulinyambua neon [reversed meaning nguo. [Mother is arranging the clothes.] Mama anapangua nguo. [Mother is disarranging the clothes.] 3

433

Forward chemical genetic screening.  

PubMed

Chemical genetics utilizes small molecules to perturb biological processes. Unlike conventional genetics methods, which involve the alteration of genetic information mostly with lasting effects, chemical genetics allows temporary and reversible alterations of biological processes. Furthermore, it enables the alteration of biological processes in a dose-dependent manner, providing an advantage over conventional genetics. In the present chapter, the general procedures of forward chemical genetic screening are described. Forward chemical genetic screening can be performed in three steps. The first step involves the identification of small molecules that induce phenotypic or physiological changes in a biological system from a chemical library. In the second step, cellular targets that interact with the isolated chemical, which are mostly proteins, are identified. Although several methods can be applied in the second step, the most common one is affinity pull-down assay using a target protein that binds to the isolated compound. However, affinity pull-down of a target protein is a formidable barrier in forward chemical genetics. We introduced a tagged chemical library approach that significantly facilitates the identification of target proteins. The third step consists of the validation of the target protein, which should include the assessment of target specificity. This step is critical because small molecules often show pleiotropic effects due to low specificity. The specificity test may include a competition assay using cold competitors and a genetic study using mutants or transgenic lines modified for the cellular target. PMID:24057378

Choi, Hyunmo; Kim, Jun-Young; Chang, Young Tae; Nam, Hong Gil

2014-01-01

434

The efficiency of reverse engineering in the design of the ORCA XI autonomous underwater vehicle by Rachel E. Sharples.  

E-print Network

??Reverse engineering is the process of determining how a system works to aid duplication, maintenance, or redesign. Applications of reverse engineering include mechanical, electrical, software,… (more)

Sharples, Rachel E

2010-01-01

435

Time reversal acoustics for small targets using decomposition of the time reversal operator  

NASA Astrophysics Data System (ADS)

The method of time reversal acoustics has been the focus of considerable interest over the last twenty years. Time reversal imaging methods have made consistent progress as effective methods for signal processing since the initial demonstration that physical time reversal methods can be used to form convergent wave fields on a localized target, even under conditions of severe multipathing. Computational time reversal methods rely on the properties of the so-called 'time reversal operator' in order to extract information about the target medium. Applications for which time reversal imaging have previously been explored include medical imaging, non-destructive evaluation, and mine detection. Emphasis in this paper will fall on two topics within the general field of computational time reversal imaging. First, we will examine previous work on developing a time reversal imaging algorithm based on the MUltiple SIgnal Classificat