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Sample records for chemical genetic approach

  1. A Chemical Genetic Approach To The Study Of Cellular Transport

    NARCIS (Netherlands)

    Nieland, T.J.F.

    2005-01-01

    The focus of this thesis is the use of chemical genetics to study two different aspects of membrane biology, (a) the mechanisms underlying cellular lipid transport and (b) the intersection between endocytic and exocytic traffic. The broad goals of chemical genetics are to find novel chemical tool

  2. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches

    DEFF Research Database (Denmark)

    Ugelvig, Line; Drijfhout, Falko; Kronauer, Daniel;

    2008-01-01

    BACKGROUND: The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14...... populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of...... independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations. RESULTS: Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression...

  3. The introduction history of invasive garden ants in Europe: Integrating genetic, chemical and behavioural approaches

    OpenAIRE

    Boomsma Jacobus J; Kronauer Daniel JC; Drijfhout Falko P; Ugelvig Line V; Pedersen Jes S; Cremer Sylvia

    2008-01-01

    Abstract Background The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We eva...

  4. The introduction history of invasive garden ants in Europe: Integrating genetic, chemical and behavioural approaches

    Directory of Open Access Journals (Sweden)

    Boomsma Jacobus J

    2008-02-01

    Full Text Available Abstract Background The invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations. Results Three clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants. Conclusion The three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport.

  5. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    Energy Technology Data Exchange (ETDEWEB)

    Han, Sangjo [Bioinformatics Lab, Healthcare Group, SK Telecom, 9-1, Sunae-dong, Pundang-gu, Sungnam-si, Kyunggi-do 463-784 (Korea, Republic of); Lee, Minho [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Chang, Hyeshik [Department of Biological Science, Seoul National University, 599 Gwanakro, Gwanak-gu, Seoul 151-747 (Korea, Republic of); Nam, Miyoung [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Park, Han-Oh [Bioneer Corp., 8-11 Munpyeongseo-ro, Daedeok-gu, Daejeon 306-220 (Korea, Republic of); Kwak, Youn-Sig [Department of Applied Biology, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam 660-701 (Korea, Republic of); Ha, Hye-jeong [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of); Kim, Dongsup [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Hwang, Sung-Ook [Department of Obstetrics and Gynecology, Inha University Hospital, 7-206 Sinheung-dong, Jung-gu, Incheon 400-711 (Korea, Republic of); Hoe, Kwang-Lae [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Kim, Dong-Uk [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of)

    2013-07-12

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defect measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)

  6. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    International Nuclear Information System (INIS)

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defect measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)

  7. Genetic k-Means Clustering Approach for Mapping Human Vulnerability to Chemical Hazards in the Industrialized City: A Case Study of Shanghai, China

    Directory of Open Access Journals (Sweden)

    Weihua Zeng

    2013-06-01

    Full Text Available Reducing human vulnerability to chemical hazards in the industrialized city is a matter of great urgency. Vulnerability mapping is an alternative approach for providing vulnerability-reducing interventions in a region. This study presents a method for mapping human vulnerability to chemical hazards by using clustering analysis for effective vulnerability reduction. Taking the city of Shanghai as the study area, we measure human exposure to chemical hazards by using the proximity model with additionally considering the toxicity of hazardous substances, and capture the sensitivity and coping capacity with corresponding indicators. We perform an improved k-means clustering approach on the basis of genetic algorithm by using a 500 m × 500 m geographical grid as basic spatial unit. The sum of squared errors and silhouette coefficient are combined to measure the quality of clustering and to determine the optimal clustering number. Clustering result reveals a set of six typical human vulnerability patterns that show distinct vulnerability dimension combinations. The vulnerability mapping of the study area reflects cluster-specific vulnerability characteristics and their spatial distribution. Finally, we suggest specific points that can provide new insights in rationally allocating the limited funds for the vulnerability reduction of each cluster.

  8. Genetic approaches to somatosensation.

    OpenAIRE

    Abrahamsen, B.

    2008-01-01

    Three approaches to understanding peripheral pain pathways are described in this thesis. Cre-loxP technology has been used to delete genes specifically in specialised sensory neurons that respond to tissue damage (nociceptors). The sodium channel selective Nav1.8 promoter is used to drive Cre expression. I used a mouse expressing diphtheria toxin A-chain downstream of a floxed stop signal, crossed with the Nayl.8Cre mouse to delete all cells expressing this channel. This lead to massive cell ...

  9. Genetic Recombination as a Chemical Reaction Network

    OpenAIRE

    Müller, Stefan; Hofbauer, Josef

    2015-01-01

    The process of genetic recombination can be seen as a chemical reaction network with mass-action kinetics. We review the known results on existence, uniqueness, and global stability of an equilibrium in every compatibility class and for all rate constants, from both the population genetics and the reaction networks point of view.

  10. Quantitative genetic activity graphical profiles for use in chemical evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Waters, M.D. [Environmental Protection Agency, Washington, DC (United States); Stack, H.F.; Garrett, N.E.; Jackson, M.A. [Environmental Health Research and Testing, Inc., Research Triangle Park, NC (United States)

    1990-12-31

    A graphic approach, terms a Genetic Activity Profile (GAP), was developed to display a matrix of data on the genetic and related effects of selected chemical agents. The profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each chemical. Either the lowest effective dose or highest ineffective dose is recorded for each agent and bioassay. Up to 200 different test systems are represented across the GAP. Bioassay systems are organized according to the phylogeny of the test organisms and the end points of genetic activity. The methodology for producing and evaluating genetic activity profile was developed in collaboration with the International Agency for Research on Cancer (IARC). Data on individual chemicals were compiles by IARC and by the US Environmental Protection Agency (EPA). Data are available on 343 compounds selected from volumes 1-53 of the IARC Monographs and on 115 compounds identified as Superfund Priority Substances. Software to display the GAPs on an IBM-compatible personal computer is available from the authors. Structurally similar compounds frequently display qualitatively and quantitatively similar profiles of genetic activity. Through examination of the patterns of GAPs of pairs and groups of chemicals, it is possible to make more informed decisions regarding the selection of test batteries to be used in evaluation of chemical analogs. GAPs provided useful data for development of weight-of-evidence hazard ranking schemes. Also, some knowledge of the potential genetic activity of complex environmental mixtures may be gained from an assessment of the genetic activity profiles of component chemicals. The fundamental techniques and computer programs devised for the GAP database may be used to develop similar databases in other disciplines. 36 refs., 2 figs.

  11. Genomic and functional approaches to genetic adaptation

    OpenAIRE

    Carnero-Montoro, Elena

    2013-01-01

    The genetic basis of phenotypes that have contributed to the adaptation of species and organisms to new environments is a central question in evolutionary genetics. The recent accumulation of genetic variability data has allowed a genome-wide search for different signatures of positive selection which has led to the discovery of hundreds of putative candidate genes that may have played a role in adaptation. However, such hypothesis-free approaches do not reveal either causal va...

  12. Chemical Genetics: Budding Yeast as a Platform for Drug Discovery and Mapping of Genetic Pathways

    Directory of Open Access Journals (Sweden)

    Jorrit M. Enserink

    2012-08-01

    Full Text Available The budding yeast Saccharomyces cerevisiae is a widely used model organism, and yeast genetic methods are powerful tools for discovery of novel functions of genes. Recent advancements in chemical-genetics and chemical-genomics have opened new avenues for development of clinically relevant drug treatments. Systematic mapping of genetic networks by high-throughput chemical-genetic screens have given extensive insight in connections between genetic pathways. Here, I review some of the recent developments in chemical-genetic techniques in budding yeast.

  13. Neurobiological approaches in human behavior genetics.

    Science.gov (United States)

    Vogel, F

    1981-03-01

    An attempt should be made to base analysis of problems in human behavior genetics on existing knowledge of human biochemical genetics and neurobiology. Examples for this approach are studies showing HY antigen patterns of the opposite sex in transsexuality, slight psychological deviations in heterozygotes of recessive metabolic diseases such as phenylketonuria and lipid storage diseases, and psychological studies in healthy individuals with various genetic variants of the normal human electroencephalogram (EEG). Results of such studies will help gradually to replace emotional controversy by rational assessment of facts. PMID:7271684

  14. The calculus a genetic approach

    CERN Document Server

    Toeplitz, Otto

    2007-01-01

    When first published posthumously in 1963, this book presented a radically different approach to the teaching of calculus.  In sharp contrast to the methods of his time, Otto Toeplitz did not teach calculus as a static system of techniques and facts to be memorized. Instead, he drew on his knowledge of the history of mathematics and presented calculus as an organic evolution of ideas beginning with the discoveries of Greek scholars, such as Archimedes, Pythagoras, and Euclid, and developing through the centuries in the work of Kepler, Galileo, Fermat, Newton, and Leibniz. Through this unique a

  15. Genetic Algorithm Approaches for Actuator Placement

    Science.gov (United States)

    Crossley, William A.

    2000-01-01

    This research investigated genetic algorithm approaches for smart actuator placement to provide aircraft maneuverability without requiring hinged flaps or other control surfaces. The effort supported goals of the Multidisciplinary Design Optimization focus efforts in NASA's Aircraft au program. This work helped to properly identify various aspects of the genetic algorithm operators and parameters that allow for placement of discrete control actuators/effectors. An improved problem definition, including better definition of the objective function and constraints, resulted from this research effort. The work conducted for this research used a geometrically simple wing model; however, an increasing number of potential actuator placement locations were incorporated to illustrate the ability of the GA to determine promising actuator placement arrangements. This effort's major result is a useful genetic algorithm-based approach to assist in the discrete actuator/effector placement problem.

  16. Genetic approaches in comparative and evolutionary physiology.

    Science.gov (United States)

    Storz, Jay F; Bridgham, Jamie T; Kelly, Scott A; Garland, Theodore

    2015-08-01

    Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology. PMID:26041111

  17. Genetic susceptibility factors for multiple chemical sensitivity revisited

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Linneberg, Allan; Andersen, Charlotte Brasch; Fenger, Mogens; Dirksen, Asger; Vesterhauge, Søren; Werge, Thomas; Elberling, Jesper; Berg, Nikolaj Drimer

    2010-01-01

    study was to investigate genetic susceptibility factors for MCS and self-reported chemical sensitivity in a population sample. Ninety six MCS patients and 1,207 controls from a general population divided into four severity groups of chemical sensitivity were genotyped for variants in the genes encoding...

  18. Reverse Genetics Approaches to Control Arenavirus.

    Science.gov (United States)

    Martínez-Sobrido, Luis; Cheng, Benson Yee Hin; de la Torre, Juan Carlos

    2016-01-01

    Several arenavirus cause hemorrhagic fever disease in humans and pose a significant public health problem in their endemic regions. To date, no licensed vaccines are available to combat human arenavirus infections, and anti-arenaviral drug therapy is limited to an off-label use of ribavirin that is only partially effective. The development of arenavirus reverse genetics approaches provides investigators with a novel and powerful approach for the investigation of the arenavirus molecular and cell biology. The use of cell-based minigenome systems has allowed examining the cis- and trans-acting factors involved in arenavirus replication and transcription and the identification of novel anti-arenaviral drug targets without requiring the use of live forms of arenaviruses. Likewise, it is now feasible to rescue infectious arenaviruses entirely from cloned cDNAs containing predetermined mutations in their genomes to investigate virus-host interactions and mechanisms of pathogenesis, as well as to facilitate screens to identify anti-arenaviral drugs and development of novel live-attenuated arenavirus vaccines. Recently, reverse genetics have also allowed the generation of tri-segmented arenaviruses expressing foreign genes, facilitating virus detection and opening the possibility of implementing live-attenuated arenavirus-based vaccine vector approaches. Likewise, the development of single-cycle infectious, reporter-expressing, arenaviruses has provided a new experimental method to study some aspects of the biology of highly pathogenic arenaviruses without the requirement of high-security biocontainment required to study HF-causing arenaviruses. In this chapter we summarize the current knowledge on arenavirus reverse genetics and the implementation of plasmid-based reverse genetics techniques for the development of arenavirus vaccines and vaccine vectors. PMID:27076139

  19. Genetic susceptibility factors for multiple chemical sensitivity revisited

    DEFF Research Database (Denmark)

    Berg, Nikolaj Drimer; Berg Rasmussen, Henrik; Linneberg, Allan; Brasch-Andersen, Charlotte; Fenger, Mogens; Dirksen, Asger; Vesterhauge, Søren; Werge, Thomas; Elberling, Jesper

    2010-01-01

    study was to investigate genetic susceptibility factors for MCS and self-reported chemical sensitivity in a population sample. Ninety six MCS patients and 1,207 controls from a general population divided into four severity groups of chemical sensitivity were genotyped for variants in the genes encoding...... compared in post hoc analyses with all individuals from the population sample (p=0.02). Genetic variants in paraoxonase 1 and methylene tetrahydrofolate reductase were not associated with MSC or with self-reported chemical sensitivity in the population sample. Our results suggest that variants in the genes...

  20. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map

    OpenAIRE

    Maria M. Martins; Zhou, Alicia Y.; Corella, Alexandra; Horiuchi, Dai; Yau, Christina; Rakshandehroo, Taha; Gordan, John D; Levin, Rebecca S.; Johnson, Jeff; Jascur, John; Shales, Mike; Sorrentino, Antonio; Cheah, Jaime; Clemons, Paul A.; Shamji, Alykhan F.

    2014-01-01

    There is an urgent need in oncology to link molecular aberrations in tumors with therapeutics that can be administered in a personalized fashion. One approach identifies synthetic-lethal genetic interactions or dependencies that cancer cells acquire in the presence of specific mutations. Using engineered isogenic cells, we generated a systematic and quantitative chemical-genetic interaction map that charts the influence of 51 aberrant cancer genes on 90 drug responses. The dataset strongly pr...

  1. Genetic Neural Approach for Heart Disease Prediction

    Directory of Open Access Journals (Sweden)

    Nilakshi P. Waghulde

    2014-09-01

    Full Text Available Data mining techniques are used to explore, analyze and extract data using complex algorithms in order to discover unknown patterns in the process of knowledge discovery. Heart disease is a major life threatening disease that cause to death and it has a serious long term disability. The time taken to recover from heart disease depends on patient’s severity. Heart disease diagnosis is complex task which requires much experience and knowledge. Nowadays, health care industry contain huge amount of health care data, which contain hidden information. Advanced data mining techniques along with computer generated information are used for appropriate results. Neural Network is widely used tool for predicting heart diseases diagnosis. A Heart Disease Prediction System is developed using Neural Network and Genetic Algorithm. This system calculates the number of hidden nodes for neural network which train the network with proper selection of neural network architecture and uses the global optimization of genetic algorithm for initialization of neural network. For prediction, the system uses 12 parameters such as sex, age, blood cholesterol etc. From the result, it is found that genetic neural approach predicts the heart disease upto 98% accuracy.

  2. Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling

    Science.gov (United States)

    Lohn, Jason; Colombano, Silvano

    1997-01-01

    We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

  3. Different approaches to tailoring chemical pulp fibres

    OpenAIRE

    El-Sharkawy, Khalil

    2008-01-01

    The objective of this thesis work was to examine different approaches to tailor chemical fibres of different raw materials. The focus in searching for new approaches was on pressure screen fractionation, selective treatment of each fraction, mechanical pre-treatment before refining, refiner loadability and its link to fibre properties and filling design, and on-line quality control of fibre properties. The evaluation is based on the impacts on fibre properties, filtration, refining and the re...

  4. Chemical Genetics of Acetyl-CoA Carboxylases

    Directory of Open Access Journals (Sweden)

    Xuyu Zu

    2013-01-01

    Full Text Available Chemical genetic studies on acetyl-CoA carboxylases (ACCs, rate-limiting enzymes in long chain fatty acid biosynthesis, have greatly advanced the understanding of their biochemistry and molecular biology and promoted the use of ACCs as targets for herbicides in agriculture and for development of drugs for diabetes, obesity and cancers. In mammals, ACCs have both biotin carboxylase (BC and carboxyltransferase (CT activity, catalyzing carboxylation of acetyl-CoA to malonyl-CoA. Several classes of small chemicals modulate ACC activity, including cellular metabolites, natural compounds, and chemically synthesized products. This article reviews chemical genetic studies of ACCs and the use of ACCs for targeted therapy of cancers.

  5. Prediction of Synergism from Chemical-Genetic Interactions by Machine Learning.

    Science.gov (United States)

    Wildenhain, Jan; Spitzer, Michaela; Dolma, Sonam; Jarvik, Nick; White, Rachel; Roy, Marcia; Griffiths, Emma; Bellows, David S; Wright, Gerard D; Tyers, Mike

    2015-12-23

    The structure of genetic interaction networks predicts that, analogous to synthetic lethal interactions between non-essential genes, combinations of compounds with latent activities may exhibit potent synergism. To test this hypothesis, we generated a chemical-genetic matrix of 195 diverse yeast deletion strains treated with 4,915 compounds. This approach uncovered 1,221 genotype-specific inhibitors, which we termed cryptagens. Synergism between 8,128 structurally disparate cryptagen pairs was assessed experimentally and used to benchmark predictive algorithms. A model based on the chemical-genetic matrix and the genetic interaction network failed to accurately predict synergism. However, a combined random forest and Naive Bayesian learner that associated chemical structural features with genotype-specific growth inhibition had strong predictive power. This approach identified previously unknown compound combinations that exhibited species-selective toxicity toward human fungal pathogens. This work demonstrates that machine learning methods trained on unbiased chemical-genetic interaction data may be widely applicable for the discovery of synergistic combinations in different species. PMID:27136353

  6. Bringing Genetics into the Classroom: A Practice-based Approach.

    Science.gov (United States)

    Lea, Dale Halsey; Thomas-Lawson, Marjorie

    2001-01-01

    Case studies illustrating baccalaureate and advanced practice nursing roles in genetic health care form the basis of an integrated approach to genetics education in nursing curricula. Use of such case studies involves nurses in obtaining informed consent from clients. (SK)

  7. Identifying Novel Cancer Therapies Using Chemical Genetics and Zebrafish.

    Science.gov (United States)

    Dang, Michelle; Fogley, Rachel; Zon, Leonard I

    2016-01-01

    Chemical genetics is the use of small molecules to perturb biological pathways. This technique is a powerful tool for implicating genes and pathways in developmental programs and disease, and simultaneously provides a platform for the discovery of novel therapeutics. The zebrafish is an advantageous model for in vivo high-throughput small molecule screening due to translational appeal, high fecundity, and a unique set of developmental characteristics that support genetic manipulation, chemical treatment, and phenotype detection. Chemical genetic screens in zebrafish can identify hit compounds that target oncogenic processes-including cancer initiation and maintenance, metastasis, and angiogenesis-and may serve as cancer therapies. Notably, by combining drug discovery and animal testing, in vivo screening of small molecules in zebrafish has enabled rapid translation of hit anti-cancer compounds to the clinic, especially through the repurposing of FDA-approved drugs. Future technological advancements in automation and high-powered imaging, as well as the development and characterization of new mutant and transgenic lines, will expand the scope of chemical genetics in zebrafish. PMID:27165351

  8. Engineering electrical properties of graphene: chemical approaches

    Science.gov (United States)

    Kim, Yong-Jin; Kim, Yuna; Novoselov, Konstantin; Hong, Byung Hee

    2015-12-01

    To ensure the high performance of graphene-based devices, it is necessary to engineer the electrical properties of graphene with enhanced conductivity, controlled work function, opened or closed bandgaps, etc. This can be performed by various non-covalent chemical approaches, including molecular adsorption, substrate-induced doping, polymerization on graphene, deposition of metallic thin films or nanoparticles, etc. In addition, covalent approaches such as the substitution of carbon atoms with boron or nitrogen and the functionalization with hydrogen or fluorine are useful to tune the bandgaps more efficiently, with better uniformity and stability. In this review, representative examples of chemically engineered graphene and its device applications will be reviewed, and remaining challenges will be discussed.

  9. An Integrated Approach to Crop Genetic Improvement

    Institute of Scientific and Technical Information of China (English)

    Martin A. J. Parry; Malcolm J. Hawkesford

    2012-01-01

    The balance between the supply and demand of the major food crops is fragile,fueling concerns for long-term global food security.The rising population,increasing wealth and a proliferation of nonfood uses (e.g.bioenergy) has led to growing demands on agriculture,while increased production is limited by greater urbanization,and the degradation of land.Furthermore,global climate change with increasing temperatures and lower,more erratic rainfall is projected to decrease agricultural yields.There is a predicted need to increase food production by at least 70% by 2050 and therefore an urgent need to develop novel and integrated approaches,incorporating high-throughput phenotyping that will both increase production per unit area and simultaneously improve the resource use efficiency of crops.Yield potential,yield stability,nutrient and water use are all complex multigenic traits and while there is genetic variability,their complexity makes such traits difficult to breed for directly.Nevertheless molecular plant breeding has the potential to deliver substantial improvements,once the component traits and the genes underlying these traits have been identified.In addition,interactions between the individual traits must also be taken into account,a demand that is difficult to fulfill with traditional screening approaches.Identified traits will be incorporated into new cultivars using conventional or biotechnological tools.In order to better understand the relationship between genotype,component traits,and environment over time,a multidisciplinary approach must be adopted to both understand the underlying processes and identify candidate genes,QTLs and traits that can be used to develop improved crops.

  10. An integrated approach to crop genetic improvement.

    Science.gov (United States)

    Parry, Martin A J; Hawkesford, Malcolm J

    2012-04-01

    The balance between the supply and demand of the major food crops is fragile, fueling concerns for long-term global food security. The rising population, increasing wealth and a proliferation of non-food uses (e.g. bioenergy) has led to growing demands on agriculture, while increased production is limited by greater urbanization, and the degradation of land. Furthermore, global climate change with increasing temperatures and lower, more erratic rainfall is projected to decrease agricultural yields. There is a predicted need to increase food production by at least 70% by 2050 and therefore an urgent need to develop novel and integrated approaches, incorporating high-throughput phenotyping that will both increase production per unit area and simultaneously improve the resource use efficiency of crops. Yield potential, yield stability, nutrient and water use are all complex multigenic traits and while there is genetic variability, their complexity makes such traits difficult to breed for directly. Nevertheless molecular plant breeding has the potential to deliver substantial improvements, once the component traits and the genes underlying these traits have been identified. In addition, interactions between the individual traits must also be taken into account, a demand that is difficult to fulfill with traditional screening approaches. Identified traits will be incorporated into new cultivars using conventional or biotechnological tools. In order to better understand the relationship between genotype, component traits, and environment over time, a multidisciplinary approach must be adopted to both understand the underlying processes and identify candidate genes, QTLs and traits that can be used to develop improved crops. PMID:22348899

  11. Bio-inspired Silicification of Silica-binding Peptide-Silk Protein Chimeras: Comparison of Chemically and Genetically Produced Proteins

    OpenAIRE

    Canabady-Rochelle, Laetitia L.S.; Belton, David J.; Deschaume, Olivier; Currie, Heather A.; Kaplan, David L; Perry, Carole C.

    2012-01-01

    Novel protein chimeras constituted of ‘silk’ and a silica-binding peptide (KSLSRHDHIHHH) were synthesized by genetic or chemical approaches and their influence on silica-silk based chimera composite formation evaluated. Genetic chimeras were constructed from 6 or 15 repeats of the 32 amino acid consensus sequence of Nephila clavipes spider silk ([SGRGGLGGQG AGAAAAAGGA GQGGYGGLGSQG]n) to which one silica binding peptide was fused at the N terminus. For the chemical chimera, 25 equivalents of t...

  12. Genetic Approaches to Develop Salt Tolerant Germplasm

    KAUST Repository

    Tester, Mark A.

    2015-08-19

    Forty percent of the world\\'s food is produced under irrigation, and this is directly threatened by over-exploitation and changes in the global environment. One way to address this threat is to develop systems for increasing our ability to use lower quality water, in particular saline water. Low cost partial desalination of brackish water, use of saline water for cooling and increases in the salinity tolerance of crops can all contribute to the development of this new agricultural system. In this talk, the focus will be on the use of forward genetic approaches for discovery of genes related to salinity tolerance in barley and tomatoes. Rather than studying salinity tolerance as a trait in itself, we dissect salinity tolerance into a series of components that are hypothesised to contribute to overall salinity tolerance (following the paradigm of Munns & Tester, 2008). For example, one significant component of tolerance of most crop plants to moderate soil salinity is due to the ability to maintain low concentrations of Na+ in the leaves, and much analysis of this aspect has been done (e.g. Roy et al., 2013, 2014). A major site for the control of shoot Na+ accumulation is at the plasma membrane of the mature stele of the root. Alleles of HKT, a major gene underlying this transport process have been characterized and, in work led by Dr Rana Munns (CSIRO), have now been introgressed into commercial durum wheat and led to significantly increased yields in saline field conditions (Munns et al., 2012). The genotyping of mapping populations is now highly efficient. However, the ability to quantitatively phenotype these populations is now commonly limiting forward progress in plant science. The increasing power of digital imaging and computational technologies offers the opportunity to relieve this phenotyping bottleneck. The Plant Accelerator is a 4500m2 growth facility that provides non-destructive phenotyping of large populations of plants (http

  13. Chemical approaches to studying stem cell biology

    Institute of Scientific and Technical Information of China (English)

    Wenlin Li; Kai Jiang; Wanguo Wei; Yan Shi; Sheng Ding

    2013-01-01

    Stem cells,including both pluripotent stem cells and multipotent somatic stem cells,hold great potential for interrogating the mechanisms of tissue development,homeostasis and pathology,and for treating numerous devastating diseases.Establishment of in vitro platforms to faithfully maintain and precisely manipulate stem cell fates is essential to understand the basic mechanisms of stem cell biology,and to translate stem cells into regenerative medicine.Chemical approaches have recently provided a number of small molecules that can be used to control cell selfrenewal,lineage differentiation,reprogramming and regeneration.These chemical modulators have been proven to be versatile tools for probing stem cell biology and manipulating cell fates toward desired outcomes.Ultimately,this strategy is promising to be a new frontier for drug development aimed at endogenous stem cell modulation.

  14. Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae.

    Science.gov (United States)

    Suresh, Sundari; Schlecht, Ulrich; Xu, Weihong; Bray, Walter; Miranda, Molly; Davis, Ronald W; Nislow, Corey; Giaever, Guri; Lokey, R Scott; St Onge, Robert P

    2016-01-01

    Chemical-genetic interactions (CGIs) describe a phenomenon where the effects of a chemical compound (i.e., a small molecule) on cell growth are dependent on a particular gene. CGIs can reveal important functional information about genes and can also be powerful indicators of a compound's mechanism of action. Mapping CGIs can lead to the discovery of new chemical probes, which, in contrast to genetic perturbations, operate at the level of the gene product (or pathway) and can be fast-acting, tunable, and reversible. The simple culture conditions required for yeast and its rapid growth, as well as the availability of a complete set of barcoded gene deletion strains, facilitate systematic mapping of CGIs in this organism. This process involves two basic steps: first, screening chemical libraries to identify bioactive compounds affecting growth and, second, measuring the effects of these compounds on genome-wide collections of mutant strains. Here, we introduce protocols for both steps that have great potential for the discovery and development of new small-molecule tools and medicines. PMID:27587783

  15. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  16. Genetics and the clinical approach to paragangliomas.

    Science.gov (United States)

    Schulte, K-M; Talat, N; Galata, G; Aylwin, S; Izatt, L; Eisenhofer, G; Barthel, A; Bornstein, S R

    2014-12-01

    This study analyses new information on gene mutations in paragangliomas and puts them into a clinical context. A suspicion of malignancy is critical to determine the workup and surgical approach in adrenal (A-PGL) and extra-adrenal (E-PGL) paragangliomas (PGLs). Malignancy rates vary with location, family history, and gene tests results. Currently there is no algorithm incorporating the above information for clinical use. A sum of 1,821 articles were retrieved from PubMed using the search terms "paraganglioma genetics". Thirty-seven articles were selected of which 9 were analyzed. It was found that 599/2,487 (24%) patients affected with paragangliomas had a germline mutation. Of these 30.2% were mutations in SDHB, 25% VHL, 19.4% RET, 18.4% SDHD, 5.0% NF1, and 2.0% SDHC genes. A family history was positive in 18.1-64.3% of patients. Adrenal PGLs accounted for 55.1% in mutation (+) and 81.0% in mutation (-) patients (RR 1.2, p < 0.0001). Bilateral A-PGLs accounted for 56.4% in mutation (+) and 3.2% in mutation (-) patients (RR 8.7, p < 0.0001). E-PGL were found in 33.6% of mut+ and 17.3% of mut- (RR 1.7, p < 0.0001). In mutation (+) patients PGLs malignancy varied with location, adrenal (6.4%) thoraco-abdominal E-PGL (38%), H & N E-PGL (10%). Malignancy rates were 8.2% in mutation (-) and lower in mutation (+) PGLs except for SDHB 36.5% and SDHC 8.3%. Exclusion of a mutation lowered the probability of malignancy significantly in E-PGL (RR 0.03 (95% CI 0.1-0.6); p < 0.001). Mutation analysis provides valuable preoperative information to assess the risk of malignancy in A-PG and E-PGLs and should be considered in the work up of all E-PGL lesions. PMID:25014332

  17. Genetic Algorithms for the Optimization of Catalysts in Chemical Engineering

    Czech Academy of Sciences Publication Activity Database

    Holeňa, Martin

    Hong Kong : Newswood Limited, 2008, s. 969-974. ISBN 978-988-98671-0-2. - (Lecture Notes in Engineering and Computer Science). [WCECS 2008. World Congress on Engineering and Computer Science. San Francisco (US), 22.10.2008-24.10.2008] R&D Projects: GA ČR GA201/08/0802; GA ČR GEICC/08/E018 Institutional research plan: CEZ:AV0Z10300504 Keywords : genetic algorithms * chemical engineering * constrained optimization * mixed optimization * program generator Subject RIV: IN - Informatics, Computer Science

  18. Chemical bond approach to metals and alloys

    International Nuclear Information System (INIS)

    The BCS theory of superconductivity was extended to the transition elements and their alloys by a chemical bond approach based on the electronic configurations of the Engel-- Brewer theory of alloys. The net attractive potential between electrons in Cooper pairs, V/sub BCS/, for the late transition series elements and alloys is shown to arise mainly from a generalized electron--electron interaction related to bonding of electrons on the d level alone, the phonon-induced attraction being nearly zero. A mechanism is proposed in which a scattering of superconducting d electrons into nonsuperconducting s and p states is responsible for a predictable reduction in V/sub BCS/. The electron-per-atom ratio and a new chemical parameter, the average atomic radius for coordination twelve, were applied successfully to the prediction of the maximum energy product of multiphase commercial permanent magnets. The correlations developed for the maximum energy product with these two parameters can be applied to optimize the compositions of existing permanent magnets or suggest hypothetical alloy mixtures of possibly better magnetic properties. Heats of reaction of the

  19. The Evolution of Adenoviral Vectors through Genetic and Chemical Surface Modifications

    Directory of Open Access Journals (Sweden)

    Cristian Capasso

    2014-02-01

    Full Text Available A long time has passed since the first clinical trial with adenoviral (Ad vectors. Despite being very promising, Ad vectors soon revealed their limitations in human clinical trials. The pre-existing immunity, the marked liver tropism and the high toxicity of first generation Ad (FG-Ad vectors have been the main challenges for the development of new approaches. Significant effort toward the development of genetically and chemically modified adenoviral vectors has enabled researchers to create more sophisticated vectors for gene therapy, with an improved safety profile and a higher transduction ability of different tissues. In this review, we will describe the latest findings in the high-speed, evolving field of genetic and chemical modifications of adenoviral vectors, a field in which different disciplines, such as biomaterial research, virology and immunology, co-operate synergistically to create better gene therapy tools for modern challenges.

  20. The evolution of adenoviral vectors through genetic and chemical surface modifications.

    Science.gov (United States)

    Capasso, Cristian; Garofalo, Mariangela; Hirvinen, Mari; Cerullo, Vincenzo

    2014-02-01

    A long time has passed since the first clinical trial with adenoviral (Ad) vectors. Despite being very promising, Ad vectors soon revealed their limitations in human clinical trials. The pre-existing immunity, the marked liver tropism and the high toxicity of first generation Ad (FG-Ad) vectors have been the main challenges for the development of new approaches. Significant effort toward the development of genetically and chemically modified adenoviral vectors has enabled researchers to create more sophisticated vectors for gene therapy, with an improved safety profile and a higher transduction ability of different tissues. In this review, we will describe the latest findings in the high-speed, evolving field of genetic and chemical modifications of adenoviral vectors, a field in which different disciplines, such as biomaterial research, virology and immunology, co-operate synergistically to create better gene therapy tools for modern challenges. PMID:24549268

  1. A novel genetic programming approach for epileptic seizure detection.

    Science.gov (United States)

    Bhardwaj, Arpit; Tiwari, Aruna; Krishna, Ramesh; Varma, Vishaal

    2016-02-01

    The human brain is a delicate mix of neurons (brain cells), electrical impulses and chemicals, known as neurotransmitters. Any damage has the potential to disrupt the workings of the brain and cause seizures. These epileptic seizures are the manifestations of epilepsy. The electroencephalograph (EEG) signals register average neuronal activity from the cerebral cortex and label changes in activity over large areas. A detailed analysis of these electroencephalograph (EEG) signals provides valuable insights into the mechanisms instigating epileptic disorders. Moreover, the detection of interictal spikes and epileptic seizures in an EEG signal plays an important role in the diagnosis of epilepsy. Automatic seizure detection methods are required, as these epileptic seizures are volatile and unpredictable. This paper deals with an automated detection of epileptic seizures in EEG signals using empirical mode decomposition (EMD) for feature extraction and proposes a novel genetic programming (GP) approach for classifying the EEG signals. Improvements in the standard GP approach are made using a Constructive Genetic Programming (CGP) in which constructive crossover and constructive subtree mutation operators are introduced. A hill climbing search is integrated in crossover and mutation operators to remove the destructive nature of these operators. A new concept of selecting the Globally Prime offspring is also presented to select the best fitness offspring generated during crossover. To decrease the time complexity of GP, a new dynamic fitness value computation (DFVC) is employed to increase the computational speed. We conducted five different sets of experiments to evaluate the performance of the proposed model in the classification of different mixtures of normal, interictal and ictal signals, and the accuracies achieved are outstandingly high. The experimental results are compared with the existing methods on same datasets, and these results affirm the potential use of

  2. Somatic cell genetic approaches to Down's syndrome.

    Science.gov (United States)

    Patterson, D; Jones, C; Scoggin, C; Miller, Y E; Graw, S

    1982-01-01

    Somatic cell genetic analysis of mutants of Chinese hamster ovary cells with deficient purine synthesis and of hybrids between these mutants and human cells is described. Data are presented substantiating that two genes for enzymes of purine synthesis, AdeC and AdeG, can be coordinately regulated in mammalian cells. Analysis of a human-hamster hybrid cell, Ade C/21, which contains a normal complement of hamster chromosomes and human chromosome 21 as its only human genetic component recognizable by electrophoretic and immunogenetic techniques demonstrates that genes associated with the presence of human chromosome 21 and required for the synthesis of specific polypeptides and specific human lethal cell surface antigens can be detected in these hybrids. PMID:6217778

  3. Stego-audio Using Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    V. Santhi

    2014-06-01

    Full Text Available With the rapid development of digital multimedia applications, the secure data transmission becomes the main issue in data communication system. So the multimedia data hiding techniques have been developed to ensure the secured data transfer. Steganography is an art of hiding a secret message within an image/audio/video file in such a way that the secret message cannot be perceived by hacker/intruder. In this study, we use RSA encryption algorithm to encrypt the message and Genetic Algorithm (GA to encode the message in the audio file. This study presents a method to access the negative audio bytes and includes the negative audio bytes in the message encoding and position embedding process. This increases the capacity of encoding message in the audio file. The use of GA operators in Genetic Algorithm reduces the noise distortions.

  4. Genomic and Genetic Approaches to Solvent Tolerance

    Energy Technology Data Exchange (ETDEWEB)

    Eleftherios T. Papoutsakis

    2005-06-10

    The proposed research is to understand and exploit the molecular basis that determines tolerance of the industrially important anaerobic clostridia to solvents. Furthermore, we aim to develop general genomic and metabolic engineering strategies for understanding the molecular basis of tolerance to chemicals and for developing tolerant strains. Our hypothesis is that the molecular basis of what makes bacterial cells able to withstand high solvent concentrations can be used to metabolically engineer cells so that they can tolerate higher concentrations of solvents and related chemicals.

  5. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge

    Directory of Open Access Journals (Sweden)

    Joana Martins

    2015-11-01

    Full Text Available Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

  6. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

    Science.gov (United States)

    Martins, Joana; Vasconcelos, Vitor

    2015-11-01

    Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential. PMID:26580631

  7. Bioinspired silicification of silica-binding peptide-silk protein chimeras: comparison of chemically and genetically produced proteins.

    Science.gov (United States)

    Canabady-Rochelle, Laetitia L S; Belton, David J; Deschaume, Olivier; Currie, Heather A; Kaplan, David L; Perry, Carole C

    2012-03-12

    Novel protein chimeras constituted of "silk" and a silica-binding peptide (KSLSRHDHIHHH) were synthesized by genetic or chemical approaches and their influence on silica-silk based chimera composite formation evaluated. Genetic chimeras were constructed from 6 or 15 repeats of the 32 amino acid consensus sequence of Nephila clavipes spider silk ([SGRGGLGGQG AGAAAAAGGA GQGGYGGLGSQG](n)) to which one silica binding peptide was fused at the N terminus. For the chemical chimera, 28 equiv of the silica binding peptide were chemically coupled to natural Bombyx mori silk after modification of tyrosine groups by diazonium coupling and EDC/NHS activation of all acid groups. After silica formation under mild, biomaterial-compatible conditions, the effect of peptide addition on the properties of the silk and chimeric silk-silica composite materials was explored. The composite biomaterial properties could be related to the extent of silica condensation and to the higher number of silica binding sites in the chemical chimera as compared with the genetically derived variants. In all cases, the structure of the protein/chimera in solution dictated the type of composite structure that formed with the silica deposition process having little effect on the secondary structural composition of the silk-based materials. Similarly to our study of genetic silk based chimeras containing the R5 peptide (SSKKSGSYSGSKGSKRRIL), the role of the chimeras (genetic and chemical) used in the present study resided more in aggregation and scaffolding than in the catalysis of condensation. The variables of peptide identity, silk construct (number of consensus repeats or silk source), and approach to synthesis (genetic or chemical) can be used to "tune" the properties of the composite materials formed and is a general approach that can be used to prepare a range of materials for biomedical and sensor-based applications. PMID:22229696

  8. Genetic Programming Approach for Predicting Surface Subsidence Induced by Mining

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The surface subsidence induced by mining is a complex problem, which is related with many complex and uncertain factors.Genetic programming (GP) has a good ability to deal with complex and nonlinear problems, therefore genetic programming approach is proposed to predict mining induced surface subsidence in this article.First genetic programming technique is introduced, second, surface subsidence genetic programming model is set up by selecting its main affective factors and training relating to practical engineering data, and finally, predictions are made by the testing of data, whose results show that the relative error is approximately less than 10%, which can meet the engineering needs, and therefore, this proposed approach is valid and applicable in predicting mining induced surface subsidence.The model offers a novel method to predict surface subsidence in mining.

  9. Integrating Genetic Algorithm, Tabu Search Approach for Job Shop Scheduling

    CERN Document Server

    Thamilselvan, R

    2009-01-01

    This paper presents a new algorithm based on integrating Genetic Algorithms and Tabu Search methods to solve the Job Shop Scheduling problem. The idea of the proposed algorithm is derived from Genetic Algorithms. Most of the scheduling problems require either exponential time or space to generate an optimal answer. Job Shop scheduling (JSS) is the general scheduling problem and it is a NP-complete problem, but it is difficult to find the optimal solution. This paper applies Genetic Algorithms and Tabu Search for Job Shop Scheduling problem and compares the results obtained by each. With the implementation of our approach the JSS problems reaches optimal solution and minimize the makespan.

  10. Multiple Comparisons in Genetic Association Studies: A Hierarchical Modeling Approach

    Science.gov (United States)

    Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel

    2016-01-01

    Multiple comparisons or multiple testing has been viewed as a thorny issue in genetic association studies aiming to detect disease-associated genetic variants from a large number of genotyped variants. We alleviate the problem of multiple comparisons by proposing a hierarchical modeling approach that is fundamentally different from the existing methods. The proposed hierarchical models simultaneously fit as many variables as possible and shrink unimportant effects towards zero. Thus, the hierarchical models yield more efficient estimates of parameters than the traditional methods that analyze genetic variants separately, and also coherently address the multiple comparisons problem due to largely reducing the effective number of genetic effects and the number of statistically ‘significant’ effects. We develop a method for computing the effective number of genetic effects in hierarchical generalized linear models, and propose a new adjustment for multiple comparisons, the hierarchical Bonferroni correction, based on the effective number of genetic effects. Our approach not only increases the power to detect disease-associated variants but also controls the Type I error. We illustrate and evaluate our method with real and simulated data sets from genetic association studies. The method has been implemented in our freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/). PMID:24259248

  11. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

    Science.gov (United States)

    Kanthaswamy, S

    2015-10-01

    This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

  12. A genetic and computational approach to structurally classify neuronal types

    OpenAIRE

    Sümbül, Uygar; Song, Sen; McCulloch, Kyle; Becker, Michael; Lin, Bin; Sanes, Joshua R.; Masland, Richard H.; Seung, H. Sebastian

    2014-01-01

    The importance of cell types in understanding brain function is widely appreciated but only a tiny fraction of neuronal diversity has been catalogued. Here, we exploit recent progress in genetic definition of cell types in an objective structural approach to neuronal classification. The approach is based on highly accurate quantification of dendritic arbor position relative to neurites of other cells. We test the method on a population of 363 mouse retinal ganglion cells. For each cell, we de...

  13. Understanding the Science-Learning Environment: A Genetically Sensitive Approach

    Science.gov (United States)

    Haworth, Claire M. A.; Davis, Oliver S. P.; Hanscombe, Ken B.; Kovas, Yulia; Dale, Philip S.; Plomin, Robert

    2013-01-01

    Previous studies have shown that environmental influences on school science performance increase in importance from primary to secondary school. Here we assess for the first time the relationship between the science-learning environment and science performance using a genetically sensitive approach to investigate the aetiology of this link. 3000…

  14. Chemical Genetics Uncovers Novel Inhibitors of Lignification, Including p-Iodobenzoic Acid Targeting CINNAMATE-4-HYDROXYLASE.

    Science.gov (United States)

    Van de Wouwer, Dorien; Vanholme, Ruben; Decou, Raphaël; Goeminne, Geert; Audenaert, Dominique; Nguyen, Long; Höfer, René; Pesquet, Edouard; Vanholme, Bartel; Boerjan, Wout

    2016-09-01

    Plant secondary-thickened cell walls are characterized by the presence of lignin, a recalcitrant and hydrophobic polymer that provides mechanical strength and ensures long-distance water transport. Exactly the recalcitrance and hydrophobicity of lignin put a burden on the industrial processing efficiency of lignocellulosic biomass. Both forward and reverse genetic strategies have been used intensively to unravel the molecular mechanism of lignin deposition. As an alternative strategy, we introduce here a forward chemical genetic approach to find candidate inhibitors of lignification. A high-throughput assay to assess lignification in Arabidopsis (Arabidopsis thaliana) seedlings was developed and used to screen a 10-k library of structurally diverse, synthetic molecules. Of the 73 compounds that reduced lignin deposition, 39 that had a major impact were retained and classified into five clusters based on the shift they induced in the phenolic profile of Arabidopsis seedlings. One representative compound of each cluster was selected for further lignin-specific assays, leading to the identification of an aromatic compound that is processed in the plant into two fragments, both having inhibitory activity against lignification. One fragment, p-iodobenzoic acid, was further characterized as a new inhibitor of CINNAMATE 4-HYDROXYLASE, a key enzyme of the phenylpropanoid pathway synthesizing the building blocks of the lignin polymer. As such, we provide proof of concept of this chemical biology approach to screen for inhibitors of lignification and present a broad array of putative inhibitors of lignin deposition for further characterization. PMID:27485881

  15. An imaging genetics approach to understanding social influence

    Directory of Open Access Journals (Sweden)

    Emily eFalk

    2012-06-01

    Full Text Available Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain’s reward system. We next review neuroimaging evidence linking social punishment (exclusion to brain systems involved in the experience of pain, as well as evidence linking exclusion to conformity. We suggest that genetic variants that increase sensitivity to social cues may predispose individuals to be more sensitive to either social rewards or punishments (or potentially both, which in turn increases conformity and susceptibility to normative social influences more broadly. To this end, we review evidence for genetic moderators of neurochemical responses in the brain, and suggest ways in which genes and pharmacology may modulate sensitivity to social influences. We conclude by proposing an integrative imaging genetics approach to the study of brain mediators and genetic modulators of a variety of social influences on human attitudes, beliefs, and actions.

  16. Chemical toxicity approach for emergency response

    International Nuclear Information System (INIS)

    In the event of an airborne release of chemical agent or toxic industrial chemical by accidental or intentional means, emergency responders must have a reasonable estimate of the location and size of the resulting hazard area. Emergency responders are responsible for warning persons downwind of the hazard to evacuate or shelter-in-place and must know where to look for casualties after the hazard has passed or dissipated. Given the same source characterization, modern hazard assessment models provide comparable concentration versus location and time estimates. Even urban hazard assessment models often provide similar predictions. There is a major shortcoming, though, in applying model output to estimating human toxicity effects. There exist a variety of toxicity values for non-lethal effects ranging from short-term to occupational to lifetime exposures. For health and safety purposes, these estimates are all safe-sided in converting animal data to human effects and in addressing the most sensitive subset of the population. In addition, these values are usually based on an assumed 1 hour exposure duration at constant concentration and do not reflect either a passing clouds concentration profile or duration. Emergency responders need expected value toxicity parameters rather than the existing safe-sided ones. This presentation will specify the types of toxicity values needed to provide appropriate chemical hazard estimates to emergency responders and will demonstrate how dramatically their use changes the hazard area.(author)

  17. Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

    OpenAIRE

    Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

    2013-01-01

    Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Che...

  18. WONOEP appraisal: new genetic approaches to study epilepsy.

    Science.gov (United States)

    Rossignol, Elsa; Kobow, Katja; Simonato, Michele; Loeb, Jeffrey A; Grisar, Thierry; Gilby, Krista L; Vinet, Jonathan; Kadam, Shilpa D; Becker, Albert J

    2014-08-01

    New genetic investigation techniques, including next-generation sequencing, epigenetic profiling, cell lineage mapping, targeted genetic manipulation of specific neuronal cell types, stem cell reprogramming, and optogenetic manipulations within epileptic networks are progressively unraveling the mysteries of epileptogenesis and ictogenesis. These techniques have opened new avenues to discover the molecular basis of epileptogenesis and to study the physiologic effects of mutations in epilepsy-associated genes on a multilayer level, from cells to circuits. This manuscript reviews recently published applications of these new genetic technologies in the study of epilepsy, as well as work presented by the authors at the genetic session of the XII Workshop on the Neurobiology of Epilepsy (WONOEP 2013) in Quebec, Canada. Next-generation sequencing is providing investigators with an unbiased means to assess the molecular causes of sporadic forms of epilepsy and has revealed the complexity and genetic heterogeneity of sporadic epilepsy disorders. To assess the functional impact of mutations in these newly identified genes on specific neuronal cell types during brain development, new modeling strategies in animals, including conditional genetics in mice and in utero knock-down approaches, are enabling functional validation with exquisite cell-type and temporal specificity. In addition, optogenetics, using cell-type-specific Cre recombinase driver lines, is enabling investigators to dissect networks involved in epilepsy. In addition, genetically encoded cell-type labeling is providing new means to assess the role of the nonneuronal components of epileptic networks such as glial cells. Furthermore, beyond its role in revealing coding variants involved in epileptogenesis, next-generation sequencing can be used to assess the epigenetic modifications that lead to sustained network hyperexcitability in epilepsy, including methylation changes in gene promoters and noncoding

  19. Economic Dispatch Using Genetic Algorithm Based Hybrid Approach

    International Nuclear Information System (INIS)

    Power Economic Dispatch (ED) is vital and essential daily optimization procedure in the system operation. Present day large power generating units with multi-valves steam turbines exhibit a large variation in the input-output characteristic functions, thus non-convexity appears in the characteristic curves. Various mathematical and optimization techniques have been developed, applied to solve economic dispatch (ED) problem. Most of these are calculus-based optimization algorithms that are based on successive linearization and use the first and second order differentiations of objective function and its constraint equations as the search direction. They usually require heat input, power output characteristics of generators to be of monotonically increasing nature or of piecewise linearity. These simplifying assumptions result in an inaccurate dispatch. Genetic algorithms have used to solve the economic dispatch problem independently and in conjunction with other AI tools and mathematical programming approaches. Genetic algorithms have inherent ability to reach the global minimum region of search space in a short time, but then take longer time to converge the solution. GA based hybrid approaches get around this problem and produce encouraging results. This paper presents brief survey on hybrid approaches for economic dispatch, an architecture of extensible computational framework as common environment for conventional, genetic algorithm and hybrid approaches based solution for power economic dispatch, the implementation of three algorithms in the developed framework. The framework tested on standard test systems for its performance evaluation. (authors)

  20. Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains.

    Science.gov (United States)

    Suresh, Sundari; Schlecht, Ulrich; Xu, Weihong; Miranda, Molly; Davis, Ronald W; Nislow, Corey; Giaever, Guri; St Onge, Robert P

    2016-01-01

    The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here. PMID:27587778

  1. Identification of genetic and chemical modulators of zebrafish mechanosensory hair cell death.

    Directory of Open Access Journals (Sweden)

    Kelly N Owens

    2008-02-01

    Full Text Available Inner ear sensory hair cell death is observed in the majority of hearing and balance disorders, affecting the health of more than 600 million people worldwide. While normal aging is the single greatest contributor, exposure to environmental toxins and therapeutic drugs such as aminoglycoside antibiotics and antineoplastic agents are significant contributors. Genetic variation contributes markedly to differences in normal disease progression during aging and in susceptibility to ototoxic agents. Using the lateral line system of larval zebrafish, we developed an in vivo drug toxicity interaction screen to uncover genetic modulators of antibiotic-induced hair cell death and to identify compounds that confer protection. We have identified 5 mutations that modulate aminoglycoside susceptibility. Further characterization and identification of one protective mutant, sentinel (snl, revealed a novel conserved vertebrate gene. A similar screen identified a new class of drug-like small molecules, benzothiophene carboxamides, that prevent aminoglycoside-induced hair cell death in zebrafish and in mammals. Testing for interaction with the sentinel mutation suggests that the gene and compounds may operate in different pathways. The combination of chemical screening with traditional genetic approaches is a new strategy for identifying drugs and drug targets to attenuate hearing and balance disorders.

  2. OPTIMIZING LOCALIZATION ROUTE USING PARTICLE SWARM-A GENETIC APPROACH

    Directory of Open Access Journals (Sweden)

    L. Lakshmanan

    2014-01-01

    Full Text Available One of the most key problems in wireless sensor networks is finding optimal algorithms for sending packets from source node to destination node. Several algorithms exist in literature, since some are in vital role other may not. Since WSN focus on low power consumption during packet transmission and receiving, finally we adopt by merging swarm particle based algorithm with genetic approach. Initially we order the nodes based on their energy criterion and then focusing towards node path; this can be done using Proactive route algorithm for finding optimal path between Source-Destination (S-D nodes. Fast processing and pre traversal can be done using selective flooding approach and results are in genetic. We have improved our results with high accuracy and optimality in rendering routes.

  3. Customer Targeting: A Neural Network Approach Guided by Genetic Algorithms

    OpenAIRE

    YongSeog Kim; W. Nick Street; Gary J. Russell; Filippo Menczer

    2005-01-01

    One of the key problems in database marketing is the identification and profiling of households that are most likely to be interested in a particular product or service. Principal component analysis (PCA) of customer background information followed by logistic regression analysis of response behavior is commonly used by database marketers. In this paper, we propose a new approach that uses artificial neural networks (ANNs) guided by genetic algorithms (GAs) to target households. We show that ...

  4. A genetic programming based business process mining approach

    OpenAIRE

    Turner, Christopher James

    2009-01-01

    As business processes become ever more complex there is a need for companies to understand the processes they already have in place. To undertake this manually would be time consuming. The practice of process mining attempts to automatically construct the correct representation of a process based on a set of process execution logs. The aim of this research is to develop a genetic programming based approach for business process mining. The focus of this research is on automated/semi automat...

  5. An imaging genetics approach to understanding social influence

    OpenAIRE

    Emily eFalk; Baldwin eWay; Agnes eJasinska

    2012-01-01

    Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain’s reward system. We next review neur...

  6. An imaging genetics approach to understanding social influence

    OpenAIRE

    Falk, Emily B.; Way, Baldwin M.; Agnes J Jasinska

    2012-01-01

    Normative social influences shape nearly every aspect of our lives, yet the biological processes mediating the impact of these social influences on behavior remain incompletely understood. In this Hypothesis, we outline a theoretical framework and an integrative research approach to the study of social influences on the brain and genetic moderators of such effects. First, we review neuroimaging evidence linking social influence and conformity to the brain's reward system. We next review neuro...

  7. Optimization of gridshell bar orientation using a simplified genetic approach

    OpenAIRE

    Bouhaya, Lina; Baverel, Olivier; Caron, Jean-François

    2015-01-01

    Gridshells are defined as structures that have the shape and rigidity of a double curvature shell but consist of a grid instead of a continuous surface. This study concerns those obtained by elastic deformation of an initially flat two-way grid. This paper presents a novel approach to generate gridshells on an imposed shape under imposed boundary conditions. A numerical tool based on a geometrical method, the compass method, is developed. It is coupled with genetic algorithms to optimize the ...

  8. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    Science.gov (United States)

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples. PMID:27086015

  9. Approaches to Learning in a Second Year Chemical Engineering Course.

    Science.gov (United States)

    Case, Jennifer M.; Gunstone, Richard F.

    2003-01-01

    Investigates student approaches to learning in a second year chemical engineering course by means of a qualitative research project which utilized interview and journal data from a group of 11 students. Identifies three approaches to learning: (1) conceptual; (2) algorithmic; and (3) information-based. Presents student responses to a series of…

  10. Discovering Fuzzy Censored Classification Rules (Fccrs: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Renu Bala

    2012-07-01

    Full Text Available Classification Rules (CRs are often discovered in the form of ‘If-Then’ Production Rules (PRs. PRs, being high level symbolic rules, are comprehensible and easy to implement. However, they are not capable of dealing with cognitive uncertainties like vagueness and ambiguity imperative to real word decision making situations. Fuzzy Classification Rules (FCRs based on fuzzy logic provide a framework for a flexible human like reasoning involving linguistic variables. Moreover, a classification system consisting of simple ‘If-Then’ rules is not competent in handling exceptional circumstances. In this paper, we propose a Genetic Algorithm approach to discover Fuzzy Censored Classification Rules (FCCRs. A FCCR is a Fuzzy Classification Rule (FCRs augmented with censors. Here, censors are exceptional conditions in which the behaviour of a rule gets modified. The proposed algorithm works in two phases. In the first phase, the Genetic Algorithm discovers Fuzzy Classification Rules. Subsequently, these Fuzzy Classification Rules are mutated to produce FCCRs in the second phase. The appropriate encoding scheme, fitness function and genetic operators are designed for the discovery of FCCRs. The proposed approach for discovering FCCRs is then illustrated on a synthetic dataset.

  11. Chemical named entities recognition: a review on approaches and applications.

    Science.gov (United States)

    Eltyeb, Safaa; Salim, Naomie

    2014-01-01

    The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to "text mine" these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted. PMID:24834132

  12. Genetic Evolutionary Approach for Cutting Forces Prediction in Hard Milling

    Science.gov (United States)

    Taylan, Fatih; Kayacan, Cengiz

    2011-11-01

    Hard milling is a very common used machining procedure in the last years. Therefore the prediction of cutting forces is important. The paper deals with this prediction using genetic evolutionary programming (GEP) approach to set mathematical expression for out cutting forces. In this study, face milling was performed using DIN1.2842 (90MnCrV8) cold work tool steel, with a hardness of 61 HRC. Experimental parameters were selected using stability measurements and simulations. In the hard milling experiments, cutting force data in a total of three axes were collected. Feed direction (Fx) and tangential direction (Fy) cutting forces generated using genetic evolutionary programming were modelled. Cutting speed and feed rate values were treated as inputs in the models, and average cutting force values as output. Mathematical expressions were created to predict average Fxand Fy forces that can be generated in hard material milling.

  13. An Airborne Conflict Resolution Approach Using a Genetic Algorithm

    Science.gov (United States)

    Mondoloni, Stephane; Conway, Sheila

    2001-01-01

    An airborne conflict resolution approach is presented that is capable of providing flight plans forecast to be conflict-free with both area and traffic hazards. This approach is capable of meeting constraints on the flight plan such as required times of arrival (RTA) at a fix. The conflict resolution algorithm is based upon a genetic algorithm, and can thus seek conflict-free flight plans meeting broader flight planning objectives such as minimum time, fuel or total cost. The method has been applied to conflicts occurring 6 to 25 minutes in the future in climb, cruise and descent phases of flight. The conflict resolution approach separates the detection, trajectory generation and flight rules function from the resolution algorithm. The method is capable of supporting pilot-constructed resolutions, cooperative and non-cooperative maneuvers, and also providing conflict resolution on trajectories forecast by an onboard FMC.

  14. Recent non-chemical approaches to estimate the shooting distance.

    Science.gov (United States)

    López-López, Maria; García-Ruiz, Carmen

    2014-06-01

    Shooting distance estimation offers useful information for the reconstruction of firearm related incidents. The muzzle to target distance is usually estimated by examining the bullet entrance hole and the gunshot residue pattern. To visualize the pattern the forensic analyst usually uses presumptive tests based on color chemical reactions that are applied using long and tedious proceedings. Due to the drawbacks of the chemical tests recent developments for shooting distance estimation not based on color chemical tests were described in the literature. The present review covers the approaches for shooting distance estimation published in the last 10 years considering two types of target, clothing and skin. PMID:24747671

  15. An assessment of the Central-China pig genetic diversity using Weitzman approach

    OpenAIRE

    Zhenzhen Liu; Xiuying Guo; Baoyu Li; Ming Wang; Xi Wang; Keliang Wu

    2010-01-01

    The genetic diversity of livestock breeds plays an important role in livestock production, but the significant loss of breeds is threatening genetic diversity of farm animal genetic resources (AnGR). The Weitzman approach which was accepted as a framework for assessment of genetic diversity on AnGR was exploited. In this study, several measurement indexes of genetic diversity, involving total genetic diversity, contributions of each breed to the total diversity, marginal diversities, conserva...

  16. An analytical approach to the implementation of genetically modified crops

    DEFF Research Database (Denmark)

    Borch, K.; Rasmussen, B.

    2000-01-01

    Public scepticism towards genetically modified (GM) crops is increasing. To address this, the risks and benefits of GM crops must be examined across scientific disciplines, and be discussed with the authorities, the agricultural industry and the consumers. In a feasibility study we have...... systematically analysed the challenges of the development and marketing of GM crops in Europe. A life-cycle inventory was used together with established technology foresight techniques in an interdisciplinary and empirical framework. The approach taken in this study established a dialogue between stakeholders...... and provided a framework for discussions about the future direction of GM crops....

  17. An analytical approach to the implementation of genetically modified crops.

    Science.gov (United States)

    Borch, K; Rasmussen, B

    2000-12-01

    Public scepticism towards genetically modified (GM) crops is increasing. To address this, the risks and benefits of GM crops must be examined across scientific disciplines, and be discussed with the authorities, the agricultural industry and the consumers. In a feasibility study we have systematically analysed the challenges of the development and marketing of GM crops in Europe. A life-cycle inventory was used together with established technology foresight techniques in an interdisciplinary and empirical framework. The approach taken in this study established a dialogue between stakeholders and provided a framework for discussions about the future direction of GM crops. PMID:11102658

  18. SURVEY OF GENETIC BASED APPROACH FOR MULTICAST ROUTING IN MANET

    Directory of Open Access Journals (Sweden)

    Sumathy S

    2012-12-01

    Full Text Available An independent, self-governing group of mobile wireless hosts communicate through wireless links by forming a temporary network (Mobile Ad-hoc Network in a dynamic manner without any fixedand centralized infrastructure. Since the nodes in MANET are not stationary, same path may not be taken always for routing between the sender and the receiver(s. So, routing in such situation is acomplicated task. In addition, the resources of the wireless nodes are limited. With the intention of saving the resources of the nodes in the network, multicasting can be used instead of multiple unicast data transmissions whenever a node needs to send same data in parallel to several destinations. The grouporiented services are the primary ones that support today’s need and trend of communication. In recent years, such services are provided with the help of MANETs. The residual energy of the battery of a mobile node is finite (before recharging is done, which is a constraint while developing multicast routing protocols. Genetic Algorithm (GA presents an improved solution for the multi-constrained multicast routing problem. By choosing proper fitness function and values for metrics such as initial population size, crossover and mutation that closely relates to the chosen scenario, the genetic algorithm optimizes the routes in terms of selected metrics. This paper focuses to provide a survey and analyses the categories of multicast routing protocols. In addition, this also covers the details of the application of genetic approach in finding multicast routes.

  19. Discovering Fuzzy Censored Classification Rules (Fccrs: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Renu Bala

    2012-08-01

    Full Text Available Classification Rules (CRs are often discovered in the form of ‘If-Then’ Production Rules (PRs. PRs, beinghigh level symbolic rules, are comprehensible and easy to implement. However, they are not capable ofdealing with cognitive uncertainties like vagueness and ambiguity imperative to real word decision makingsituations. Fuzzy Classification Rules (FCRs based on fuzzy logic provide a framework for a flexiblehuman like reasoning involving linguistic variables. Moreover, a classification system consisting of simple‘If-Then’ rules is not competent in handling exceptional circumstances. In this paper, we propose aGenetic Algorithm approach to discover Fuzzy Censored Classification Rules (FCCRs. A FCCR is aFuzzy Classification Rule (FCRs augmented with censors. Here, censors are exceptional conditions inwhich the behaviour of a rule gets modified. The proposed algorithm works in two phases. In the firstphase, the Genetic Algorithm discovers Fuzzy Classification Rules. Subsequently, these FuzzyClassification Rules are mutated to produce FCCRs in the second phase. The appropriate encodingscheme, fitness function and genetic operators are designed for the discovery of FCCRs. The proposedapproach for discovering FCCRs is then illustrated on a synthetic dataset.

  20. A decision analytic approach to exposure-based chemical prioritization.

    Directory of Open Access Journals (Sweden)

    Jade Mitchell

    Full Text Available The manufacture of novel synthetic chemicals has increased in volume and variety, but often the environmental and health risks are not fully understood in terms of toxicity and, in particular, exposure. While efforts to assess risks have generally been effective when sufficient data are available, the hazard and exposure data necessary to assess risks adequately are unavailable for the vast majority of chemicals in commerce. The US Environmental Protection Agency has initiated the ExpoCast Program to develop tools for rapid chemical evaluation based on potential for exposure. In this context, a model is presented in which chemicals are evaluated based on inherent chemical properties and behaviorally-based usage characteristics over the chemical's life cycle. These criteria are assessed and integrated within a decision analytic framework, facilitating rapid assessment and prioritization for future targeted testing and systems modeling. A case study outlines the prioritization process using 51 chemicals. The results show a preliminary relative ranking of chemicals based on exposure potential. The strength of this approach is the ability to integrate relevant statistical and mechanistic data with expert judgment, allowing for an initial tier assessment that can further inform targeted testing and risk management strategies.

  1. The Chemical Core of Chemistry I: A Conceptual Approach

    OpenAIRE

    Joachim Schummer

    1998-01-01

    Given the rich diversity of research fields usually ascribed to chemistry in a broad sense, the present paper tries to dig our characteristic parts of chemistry that can be conceptually distinguished from interdisciplinary, applied, and specialized subfields of chemistry, and that may be called chemistry in a very narrow sense, or 'the chemical core of chemistry'. Unlike historical, ontological, and 'anti-reductive' approaches, I use a conceptual approach together with some methodological imp...

  2. Controlling Risk Exposure in Periodic Environments: A Genetic Algorithm Approach

    CERN Document Server

    Navarro, Emeterio

    2007-01-01

    In this paper, we compare the performance of different agent's investment strategies in an investment scenario with periodic returns and different types and levels of noise. We consider an investment model, where an agent decides the percentage of budget to risk at each time step. Afterwards, agent's investment is evaluated in the market via a return on investment (RoI), which we assume is a stochastic process with unknown periodicities and different levels of noise. To control the risk exposure, we investigate approaches based on: technical analysis (Moving Least Squares, MLS), and evolutionary computation (Genetic Algorithms, GA). In our comparison, we also consider two reference strategies for zero-knowledge and complete-knowledge behaviors, respectively. In our approach, the performance of a strategy corresponds to the average budget that can be obtained with this strategy over a certain number of time steps. To this end, we perform some computer experiments, where for each strategy the budget obtained af...

  3. A genetic-neural artificial intelligence approach to resins optimization

    International Nuclear Information System (INIS)

    This work presents a preliminary study about the viability and adequacy of a new methodology for the definition of one of the main properties of ion exchange resins used for isotopic separation. Basically, the main problem is the definition of pelicule diameter in case of pelicular ion exchange resins, in order to achieve the best performance in the shortest time. In order to achieve this, a methodology was developed, based in two classic techniques of Artificial Intelligence (AI). At first, an artificial neural network (NN) was trained to map the existing relations between the nucleus radius and the resin's efficiency associated with the exchange time. Later on, a genetic algorithm (GA) was developed in order to find the best pelicule dimension. Preliminary results seem to confirm the potential of the method, and this can be used in any chemical process employing ion exchange resins. (author)

  4. Genetic modulation of oxytocin sensitivity: a pharmacogenetic approach.

    Science.gov (United States)

    Chen, F S; Kumsta, R; Dvorak, F; Domes, G; Yim, O S; Ebstein, R P; Heinrichs, M

    2015-01-01

    Intranasal administration of the neuropeptide oxytocin has been shown to influence a range of complex social cognitions and social behaviors, and it holds therapeutic potential for the treatment of mental disorders characterized by social functioning deficits such as autism, social phobia and borderline personality disorder. However, considerable variability exists in individual responses to oxytocin administration. Here, we undertook a study to investigate the role of genetic variation in sensitivity to exogenous oxytocin using a socioemotional task. In a randomized, double-blind, placebo-controlled experiment with a repeated-measures (crossover) design, we assessed the performance of 203 men on an emotion recognition task under oxytocin and placebo. We took a haplotype-based approach to investigate the association between oxytocin receptor gene variation and oxytocin sensitivity. We identified a six-marker haplotype block spanning the promoter region and intron 3 that was significantly associated with our measure of oxytocin sensitivity. Specifically, the TTCGGG haplotype comprising single-nucleotide polymorphisms rs237917-rs2268498-rs4564970-rs237897-rs2268495-rs53576 is associated with increased emotion recognition performance under oxytocin versus placebo, and the CCGAGA haplotype with the opposite pattern. These results on the genetic modulation of sensitivity to oxytocin document a significant source of individual differences with implications for personalized treatment approaches using oxytocin administration. PMID:26506050

  5. Human Genetic Marker for Resistance to Radiation and Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    DR. Howard B. Lieberman

    2001-05-11

    TO characterize the human HRDAD9 gene and evaluate its potential as a biomarker to predict susceptibility to the deleterious health effects potentially caused by exposure to radiations or chemicals present at DOE hazardous waste cleanup sites. HRAD9 is a human gene that is highly conserved throughout evolution. Related genes have been isolated from yeasts and mice, underscoring its biological significance. Most of our previous work involved characterization of the yeast gene cognate, wherein it was determined that the corresponding protein plays a significant role in promoting resistance of cells to radiations and chemicals, and in particular, controlling cell growth in response to DNA damage.

  6. Human Genetic Marker for Resistance to Radiation and Chemicals

    International Nuclear Information System (INIS)

    TO characterize the human HRDAD9 gene and evaluate its potential as a biomarker to predict susceptibility to the deleterious health effects potentially caused by exposure to radiations or chemicals present at DOE hazardous waste cleanup sites. HRAD9 is a human gene that is highly conserved throughout evolution. Related genes have been isolated from yeasts and mice, underscoring its biological significance. Most of our previous work involved characterization of the yeast gene cognate, wherein it was determined that the corresponding protein plays a significant role in promoting resistance of cells to radiations and chemicals, and in particular, controlling cell growth in response to DNA damage

  7. A computational approach to chemical etiologies of diabetes

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Brunak, Søren; Grandjean, Philippe

    2013-01-01

    Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic......, and offers thus promising guidance for future research in regard to the etiology and pathogenesis of complex diseases....

  8. Genetic effects of combined chemical-X-ray treatments in male mouse germ cells

    International Nuclear Information System (INIS)

    Several studies have shown that the yield of genetic damage induced by radiation in male mouse germ cells can be modified by chemical treatments. Pre-treatments with radio-protecting agents have given contradictory results but this appears to be largely attributable to the different germ cell stages tested and dependent upon the level of radiation damage induced. Pre-treatments which enhance the yield of genetic damage have been reported although, as yet, no tests have been conducted with radio-sensitizers. Another form of interaction between chemicals and radiation is specifically found with spermatogonial stem cells. Chemicals that kill cells can, by population depletion, substantially and predictably modify the genetic response to subsequent radiation exposure over a period of several days, or even weeks. Enhancement and reduction in the genetic yield can be attained, dependent upon the interval between treatments, with the modification also varying with the type of genetic damage scored. Post-treatment with one chemical (TEM) has been shown to reduce the genetic response to radiation exposure. (author)

  9. General approaches to the risk assessment of chemicals

    International Nuclear Information System (INIS)

    deciding upon the granting of permits for landfill sites or the discharge of toxic chemicals to water or air and in doing so they must take into account the hydrology, geology and climate of the specific locality. While the basic approach to chemical risk assessment will be the same, irrespective of the specific objective for which the assessment is carried out, the details will vary as a function of: the product type (pharmaceutical, pesticide, industrial chemical, etc.), the target population of interest (patient, environment, consumer, worker, etc.) and the exposure scenario (global, international, national, local)

  10. Chemical heterogeneities in the mantle: The equilibrium thermodynamic approach

    Science.gov (United States)

    Tirone, M.; Buhre, S.; Schmück, H.; Faak, K.

    2016-02-01

    This study attempts to answer a simple and yet fundamental question in relation to our understanding of the chemical evolution of deep Earth and planetary interiors. Given two initially separate assemblages (lithologies) in chemical equilibrium can we predict the chemical and mineralogical compositions of the two assemblages when they are put together to form a new equilibrated system? Perhaps a common perception is that given sufficient time, the two assemblages will homogenize chemically and mineralogically, however from a chemical thermodynamic point of view, this is not the case. Certain petrological differences in terms of bulk composition, mineralogy and mineral abundance remain unless other processes, like melting or mechanical mixing come into play. While there is not a standard procedure to address this problem, in this study it is shown that by applying chemical thermodynamic principles and some reasonable assumptions, it is possible to determine the equilibrium composition of each of the two assemblages. Some examples that consider typical mantle rocks, peridotite, lherzolite, dunite and eclogite described by simplified chemical systems are used to illustrate the general approach. A preliminary application to evaluate the effect of melting a heterogeneous mantle in complete chemical equilibrium using a thermodynamic formulation coupled with a two-phase geodynamic model shows that major element composition of the melt product generated by different peridotites is very similar. This may explain the relative homogeneity of major elements of MORBs which could be the product of melting a relatively uniform mantle, as commonly accepted, or alternatively a peridotitic mantle with different compositions but in chemical equilibrium.

  11. A Comprehensive Approach for Pectin Chemical and Functional Characterization

    DEFF Research Database (Denmark)

    de Sousa, António Felipe Gomes Teixeira

    In this work, a comprehensive approach for the chemical and functional analysis of pectin was used in order to relate the different extraction conditions used to the polymer structure and the final functional (mainly gelling) properties. A wide range of methods were utilized including chemical and...... chromatographic characterization methods (HPAEC and HPSEC), rheological measurements of elasticity, and biological epitopes detection using carbohydrate microarrays. The end product of this study is expected to contribute to the knowledge of pectin polymeric conformation and structure-function properties as well...

  12. Study on New Approaches for extended chemical management and REACH

    DEFF Research Database (Denmark)

    Lee, Jihyun

    2014-01-01

    existing chemical regulations in view of protecting vulnerable populations from “excessive total risk” and to explore the possibilities for improvement. Firstly, the completeness of the REACH exposure scenario was reviewed with the finding that the current scenario does not take into account territorial...... without controlling the quality of recycled materials, increased recycling of resources in a circular economy might increase undesirable recycling of micro-pollutants. Finally, a systemic approach based on sustainable resource flows was proposed for extended chemical management and the role of REACH in a...

  13. Evolving Approaches to Genetic Evaluation of Specific Cardiomyopathies.

    Science.gov (United States)

    Teo, Loon Yee Louis; Moran, Rocio T; Tang, W H Wilson

    2015-12-01

    The understanding of the genetic basis of cardiomyopathy has expanded significantly over the past 2 decades. The increasing availability, shortening diagnostic time, and lowering costs of genetic testing have provided researchers and physicians with the opportunity to identify the underlying genetic determinants for thousands of genetic disorders, including inherited cardiomyopathies, in effort to improve patient morbidities and mortality. As such, genetic testing has advanced from basic scientific research to clinical application and has been incorporated as part of patient evaluations for suspected inherited cardiomyopathies. Genetic evaluation framework of inherited cardiomyopathies typically encompasses careful evaluation of family history, genetic counseling, clinical screening of family members, and if appropriate, molecular genetic testing. This review summarizes the genetics, current guideline recommendations, and evidence supporting the genetic evaluation framework of five hereditary forms of cardiomyopathy: dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), arrhythmogenic right ventricular cardiomyopathy (ARVC), restrictive cardiomyopathy (RCM), and left ventricular noncompaction (LVNC). PMID:26472190

  14. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

    Science.gov (United States)

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

  15. Somatic cell genetics approach to dissecting mammalian DNA repair

    International Nuclear Information System (INIS)

    This review article examines the application of the methods and concepts of somatic cell genetics to the study of DNA repair. The first steps of this approach involve classical procedures of mutant isolation, complementation analysis, and mapping of genes using hybrid cells. Subsequent steps utilize the techniques of DNA-mediated gene transfer and methodologies of the recombinant DNA field. Several human repair genes have been cloned, but they have not been used to overproduce proteins thus far. This article highlights the more important developments and attempts to review in detail all of the isolated mutant cell lines that may be altered in the repair processes. Faster methods of gene cloning are greatly needed because the procedures for making secondary transformants from total genomic DNA are tedious

  16. A genetic epidemiology approach to cyber-security.

    Science.gov (United States)

    Gil, Santiago; Kott, Alexander; Barabási, Albert-László

    2014-01-01

    While much attention has been paid to the vulnerability of computer networks to node and link failure, there is limited systematic understanding of the factors that determine the likelihood that a node (computer) is compromised. We therefore collect threat log data in a university network to study the patterns of threat activity for individual hosts. We relate this information to the properties of each host as observed through network-wide scans, establishing associations between the network services a host is running and the kinds of threats to which it is susceptible. We propose a methodology to associate services to threats inspired by the tools used in genetics to identify statistical associations between mutations and diseases. The proposed approach allows us to determine probabilities of infection directly from observation, offering an automated high-throughput strategy to develop comprehensive metrics for cyber-security. PMID:25028059

  17. Chemical-genetic profile analysis of five inhibitory compounds in yeast

    Directory of Open Access Journals (Sweden)

    Alamgir Md

    2010-08-01

    Full Text Available Abstract Background Chemical-genetic profiling of inhibitory compounds can lead to identification of their modes of action. These profiles can help elucidate the complex interactions between small bioactive compounds and the cell machinery, and explain putative gene function(s. Results Colony size reduction was used to investigate the chemical-genetic profile of cycloheximide, 3-amino-1,2,4-triazole, paromomycin, streptomycin and neomycin in the yeast Saccharomyces cerevisiae. These compounds target the process of protein biosynthesis. More than 70,000 strains were analyzed from the array of gene deletion mutant yeast strains. As expected, the overall profiles of the tested compounds were similar, with deletions for genes involved in protein biosynthesis being the major category followed by metabolism. This implies that novel genes involved in protein biosynthesis could be identified from these profiles. Further investigations were carried out to assess the activity of three profiled genes in the process of protein biosynthesis using relative fitness of double mutants and other genetic assays. Conclusion Chemical-genetic profiles provide insight into the molecular mechanism(s of the examined compounds by elucidating their potential primary and secondary cellular target sites. Our follow-up investigations into the activity of three profiled genes in the process of protein biosynthesis provided further evidence concerning the usefulness of chemical-genetic analyses for annotating gene functions. We termed these genes TAE2, TAE3 and TAE4 for translation associated elements 2-4.

  18. Design and optimization of pulsed Chemical Exchange Saturation Transfer MRI using a multiobjective genetic algorithm

    Science.gov (United States)

    Yoshimaru, Eriko S.; Randtke, Edward A.; Pagel, Mark D.; Cárdenas-Rodríguez, Julio

    2016-02-01

    Pulsed Chemical Exchange Saturation Transfer (CEST) MRI experimental parameters and RF saturation pulse shapes were optimized using a multiobjective genetic algorithm. The optimization was carried out for RF saturation duty cycles of 50% and 90%, and results were compared to continuous wave saturation and Gaussian waveform. In both simulation and phantom experiments, continuous wave saturation performed the best, followed by parameters and shapes optimized by the genetic algorithm and then followed by Gaussian waveform. We have successfully demonstrated that the genetic algorithm is able to optimize pulse CEST parameters and that the results are translatable to clinical scanners.

  19. The terrorist threat nuclear, radiological, biological, chemical - a medical approach

    International Nuclear Information System (INIS)

    Since September 11, 2001, the fear of a large scale nuclear, biological and/or chemical terrorism is taken again into consideration at the highest level of national policies of risk prevention. The advent of international terrorism implies a cooperation between the military defense and the civil defense. The nuclear, radiological, biological and chemical (NRBC) experts of the health service of army and of civil defense will have to work together in case of major terror attack. This book presents this cooperation between civil and military experts in the NRBC domain: risk analysis, national defense plans, crisis management, syndromes and treatments. The different aspects linked with the use of nuclear, biological and chemical weapons are analyzed by the best experts from French medical and research institutes. All topics of each NRBC domain are approached: historical, basic, diagnostic, therapeutic and preventive. (J.S.)

  20. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

    Science.gov (United States)

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-01

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  1. Chemical genetic screening of KRAS-based synthetic lethal inhibitors for pancreatic cancer

    OpenAIRE

    Ji, Zhenyu; Mei, Fang C; Lory, Pedro L.; Gilbertson, Scott R.; Chen, Yijun; Cheng, Xiaodong

    2009-01-01

    Pancreatic cancer is one of the deadliest diseases largely due to difficulty in early diagnosis and the lack of effective treatments. KRAS is mutated in more than 90% of pancreatic cancer patients, and oncogenic KRAS contributes to pancreatic cancer tumorigenesis and progression. In this report, using an oncogenic KRASV12-based pancreatic cancer cell model, we developed a chemical genetic screen to identify small chemical inhibitors that selectively target pancreatic cancer cells with gain-of...

  2. The TSCA interagency testing committee`s approaches to screening and scoring chemicals and chemical groups: 1977-1983

    Energy Technology Data Exchange (ETDEWEB)

    Walker, J.D. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    This paper describes the TSCA interagency testing committee`s (ITC) approaches to screening and scoring chemicals and chemical groups between 1977 and 1983. During this time the ITC conducted five scoring exercises to select chemicals and chemical groups for detailed review and to determine which of these chemicals and chemical groups should be added to the TSCA Section 4(e) Priority Testing List. 29 refs., 1 fig., 2 tabs.

  3. Modeling monthly pan evaporations using fuzzy genetic approach

    Science.gov (United States)

    Kişi, Özgür; Tombul, Mustafa

    2013-01-01

    SummaryThis study investigates the ability of fuzzy genetic (FG) approach in estimation of monthly pan evaporations. Various monthly climatic data, that are, solar radiation, air temperature, relative humidity and wind speed from two stations, Antalya and Mersin, in Mediterranean Region of Turkey, were used as inputs to the FG technique so as to estimate monthly pan evaporations. In the first part of the study, FG models were compared with neuro-fuzzy (ANFIS), artificial neural networks (ANNs) and Stephens-Stewart (SS) methods in estimating pan evaporations of Antalya and Mersin stations, separately. Comparison of the models revealed that the FG models generally performed better than the ANFIS, ANN and SS models. In the second part of the study, models were compared to each other in two different applications. In the first application the input data of Antalya Station were used as inputs to the models to estimate pan evaporation data of Mersin Station. The pan evaporation data of Mersin Station were estimated using the input data of Antalya and Mersin stations in the second application. Comparison results indicated that the FG models performed better than the ANFIS and ANN models. Comparison of the accuracy of the applied models in estimating total pan evaporations showed that the FG model provided the closest estimate. It was concluded that monthly pan evaporations could be successfully estimated by the FG approach.

  4. Genetics in psychosomatic medicine : research designs and statistical approaches

    NARCIS (Netherlands)

    McCaffery, Jeanne M.; Snieder, Harold; Dong, Yanbin; de Geus, Eco

    2007-01-01

    It has become increasingly clear that genetic factors influence many of the behaviors and disease endpoints of interest to psychosomatic medicine researchers. There has been increasing interest in incorporating genetic variation markers into psychosomatic research. In this Statistical Corner article

  5. A problem-based learning approach to teaching medical genetics.

    OpenAIRE

    Moore, C.M.; Barnett, D R

    1992-01-01

    A newly developed problem-based medical genetics course that was integrated into the fourth-year medical school curriculum of the University of Texas Health Science Center at San Antonio is described. To provide a basic genetic background for the clinical rotations, a supplemental computer tutorial is required during the second year. These two formats prepare the medical students to recognize genetic diseases, to provide basic genetic counseling in their daily practice, and to appropriately r...

  6. Chemically Defined Medium and Caenorhabditis elegans: A Powerful Approach

    Science.gov (United States)

    Szewczyk, N. J.; Kozak, E.; Conley, C. A.

    2003-01-01

    C. elegans has been established as a powerful genetic system. Growth in a chemically defined medium (C. elegans Maintenance Medium (CeMM)) now allows standardization and systematic manipulation of the nutrients that animals receive. Liquid cultivation allows automated culturing and experimentation and should be of me in large-scale growth and screening of animals. Here we present our initial results from developing culture systems with CeMM. We find that CeMM is versatile and culturing is simple. CeMM can be used in a solid or liquid state, it can be stored unused for at least a year, unattended actively growing cultures may be maintained longer than with standard techniques, and standard C. elegans protocols work well with animals grown in defined medium. We also find that there are caveats of using defined medium. Animals in defined medium grow more slowly than on standard medium, appear to display adaptation to the defined medium, and display altered growth rates as they change defined medium composition. As was suggested with the introduction of C. elegans as a potential genetic system, use of defined medium with C. elegans should prove a powerful tool.

  7. Quantum-chemical approach to cohesive properties of metallic beryllium

    International Nuclear Information System (INIS)

    Calculations based upon the incremental approach, i.e. an expansion of the correlation energy in terms of one-body, two-body, and higher-order contributions from localized orbital groups, have been performed for metallic beryllium. We apply an embedding scheme which has been successfully applied recently to ground-state properties of magnesium and group 12 elements. This scheme forces localization in metallic-like model systems and allows for a gradual delocalization within the incremental approach. Quantum-chemical methods of the coupled-cluster and multi-reference configuration interaction type are used for evaluating individual increments. Results are given for the cohesive energy and lattice constants of beryllium, and it is shown that further development of the approach is needed for this difficult case

  8. Hybrid bioinorganic approach to solar-to-chemical conversion.

    Science.gov (United States)

    Nichols, Eva M; Gallagher, Joseph J; Liu, Chong; Su, Yude; Resasco, Joaquin; Yu, Yi; Sun, Yujie; Yang, Peidong; Chang, Michelle C Y; Chang, Christopher J

    2015-09-15

    Natural photosynthesis harnesses solar energy to convert CO2 and water to value-added chemical products for sustaining life. We present a hybrid bioinorganic approach to solar-to-chemical conversion in which sustainable electrical and/or solar input drives production of hydrogen from water splitting using biocompatible inorganic catalysts. The hydrogen is then used by living cells as a source of reducing equivalents for conversion of CO2 to the value-added chemical product methane. Using platinum or an earth-abundant substitute, α-NiS, as biocompatible hydrogen evolution reaction (HER) electrocatalysts and Methanosarcina barkeri as a biocatalyst for CO2 fixation, we demonstrate robust and efficient electrochemical CO2 to CH4 conversion at up to 86% overall Faradaic efficiency for ≥ 7 d. Introduction of indium phosphide photocathodes and titanium dioxide photoanodes affords a fully solar-driven system for methane generation from water and CO2, establishing that compatible inorganic and biological components can synergistically couple light-harvesting and catalytic functions for solar-to-chemical conversion. PMID:26305947

  9. Molecular genetics and livestock selection: Approaches, opportunities and risks

    International Nuclear Information System (INIS)

    developed and environmentally less favoured areas the use of these breeds presents a greater cause for concern. Local breeds are usually adapted to survive in their local environments eg with increased tolerance of extremes in temperature or in the face of particular disease or parasite challenge. Attempts at the inappropriate and/or unmanaged introduction of improved dairy breed into some areas has met with disastrous consequences. In 1993, 112 of the 783 cattle breeds worldwide were at risk of extinction. The greatest risk is the replacement of local stock that are adapted for survival in the face of disease challenge with disease sensitive stock in areas where standards and resources to provide extensive veterinary care are not available. Much work has been carried out over the past 10 or so years to produce genetic and physical maps of the bovine genome. In the first instance these maps were composed predominantly of anonymous markers, but more recently genes, and expressed sequence tags (ESTs) have been added to the genome maps of cattle. Use of genetic maps together with other molecular genetic approaches, like micro-array technology to examine gene expression, production-associated traits are under the control of several genes, which have varying levels of effect on the trait, and are generally referred to as Quantitative Trait Loci. To date considerable success has been reported in localising QTL for a wide range of traits, however two notable successes have identified the major genes involved in increased muscling and milk production. Knowledge of the loci controlling individual traits will allow the direct selection for favourable alleles at these loci. In the first instance this can be done by marker-assisted selection with markers linked to the gene involved in the trait. However, ultimately, knowledge of the allelic variation within that gene will allow more efficient selection to be carried out. There are several advantages of using markers in selection

  10. APPROACH FOR RESOURCE MANAGEMENT IN GRID ENVIRONMENTS USING GENETIC ALGORITHM

    Directory of Open Access Journals (Sweden)

    Seyed Javad Mirabedini

    2015-11-01

    Full Text Available The use of ‘proper energy computation system’ is the best method to investigate the problem of energy deficiency, since energy consumption in computational resources is proportional with the work load in the applied program. Also, the best method to improve the use of resources and decrease in energy consumption is dynamic integration of virtual machines which can be a base for the integration of resources in independent systems through virtualization technology, so that it is possible to use resources and equipment for long time and consequently assuring quicker return of investment. Today, grid computation is a new technology connecting heterogeneous computational resources to each other; thus, this structure operates as an individual and integrated virtual machine. Then, it is possible to implement very complex applied programs requiring high processing capacity and huge amount of input data on this virtual machine. In this regard, the purpose of this study is to present an approach for resource management in grid environments using PSO and Genetic algorithms, and also ants colony to find the location of virtual machines.

  11. Image fusion approach with noise reduction using Genetic algorithm

    Directory of Open Access Journals (Sweden)

    Gehad Mohamed Taher

    2013-12-01

    Full Text Available Image fusion is becoming a challenging field as for its importance to different applications, Multi focus image fusion is a type of image fusion that is used in medical fields, surveillances, and military issues to get the image all in focus from multi images every one is in focus in a different part, and for making the input images more accurate before making the fusing process we use Genetic Algorithm (GA for image de-noising as a preprocessing process. In our research paper we introduce a new approach that begin with image de-noising using GA and then apply the curvelet transform for image decomposition to get a multi focus image fusion image that is focused in all of its parts. The results show that Curvelet transform had been proven to be effective at detecting image activity along curves, and increasing the quality of the obtained fused images. And applying the mean fusion rule for fusing multi-focus images gives accurate results than PCA, contrast and mode fusion rule, Also, GA shows more accurate results in image de-noising after comparing it to contourlet transform.

  12. Translation and genetic criticism : genetic and editorial approaches to the untranslatable in Joyce and Beckett

    OpenAIRE

    Hulle, Van, Dirk

    2015-01-01

    Abstract: A genetics of translation may suggest a unidirectional link between two fields of research (genetic criticism applied to translations), but there are many ways in which translation and genetic criticism interact. This articles research hypothesis is that an exchange of ideas between translation studies and genetic criticism can be mutually beneficial in more than one way. Their main function is to enhance a form of textual awareness, and to this end they inform each other in at leas...

  13. Forward Genetic Approaches for Elucidation of Novel Regulators of Lyme Arthritis Severity

    Directory of Open Access Journals (Sweden)

    Kenneth K.C. Bramwell

    2014-06-01

    Full Text Available Patients experiencing natural infection with Borrelia burgdorferi display a spectrum of associated symptoms and severity, strongly implicating the impact of genetically determined host factors in the pathogenesis of Lyme disease. Herein, we provide a summary of the host genetic factors that have been demonstrated to influence the severity and chronicity of Lyme arthritis symptoms, and a review of the resources available, current progress, and added value of a forward genetic approach for identification of novel genetic regulators.

  14. Genetic variants in Alzheimer disease - molecular and brain network approaches.

    Science.gov (United States)

    Gaiteri, Chris; Mostafavi, Sara; Honey, Christopher J; De Jager, Philip L; Bennett, David A

    2016-07-01

    Genetic studies in late-onset Alzheimer disease (LOAD) are aimed at identifying core disease mechanisms and providing potential biomarkers and drug candidates to improve clinical care of AD. However, owing to the complexity of LOAD, including pathological heterogeneity and disease polygenicity, extraction of actionable guidance from LOAD genetics has been challenging. Past attempts to summarize the effects of LOAD-associated genetic variants have used pathway analysis and collections of small-scale experiments to hypothesize functional convergence across several variants. In this Review, we discuss how the study of molecular, cellular and brain networks provides additional information on the effects of LOAD-associated genetic variants. We then discuss emerging combinations of these omic data sets into multiscale models, which provide a more comprehensive representation of the effects of LOAD-associated genetic variants at multiple biophysical scales. Furthermore, we highlight the clinical potential of mechanistically coupling genetic variants and disease phenotypes with multiscale brain models. PMID:27282653

  15. AMAZON RAINFOREST COSMETICS: CHEMICAL APPROACH FOR QUALITY CONTROL

    Directory of Open Access Journals (Sweden)

    Mariko Funasaki

    2016-02-01

    Full Text Available The market for natural cosmetics featuring ingredients derived from Amazon natural resources is growing worldwide. However, there is neither enough scientific basis nor quality control of these ingredients. This paper is an account of the chemical constituents and their biological activities of fourteen Amazonian species used in cosmetic industry, including açaí (Euterpe oleracea, andiroba (Carapa guianensis, bacuri (Platonia insignis, Brazil nut (Bertholletia excelsa, buriti (Mauritia vinifera or M. flexuosa, cumaru (Dipteryx odorata, cupuaçu (Theobroma grandiflorum, guarana (Paullinia cupana, mulateiro (Calycophyllum spruceanum, murumuru (Astrocaryum murumuru, patawa (Oenocarpus bataua or Jessenia bataua, pracaxi (Pentaclethra macroloba, rosewood (Aniba rosaeodora, and ucuuba (Virola sebifera. Based on the reviewed articles, we selected chemical markers for the quality control purpose and evaluated analytical methods. Even though chromatographic and spectroscopic methods are major analytical techniques in the studies of these species, molecular approaches will also be important as used in food and medicine traceability. Only a little phytochemical study is available about most of the Amazonian species and some species such as açaí and andiroba have many reports on chemical constituents, but studies on biological activities of isolated compounds and sampling with geographical variation are limited.

  16. Marine Derived Polysaccharides for Biomedical Applications: Chemical Modification Approaches

    Directory of Open Access Journals (Sweden)

    Paola Laurienzo

    2008-09-01

    Full Text Available Polysaccharide-based biomaterials are an emerging class in several biomedical fields such as tissue regeneration, particularly for cartilage, drug delivery devices and gelentrapment systems for the immobilization of cells. Important properties of the polysaccharides include controllable biological activity, biodegradability, and their ability to form hydrogels. Most of the polysaccharides used derive from natural sources; particularly, alginate and chitin, two polysaccharides which have an extensive history of use in medicine, pharmacy and basic sciences, and can be easily extracted from marine plants (algae kelp and crab shells, respectively. The recent rediscovery of poly-saccharidebased materials is also attributable to new synthetic routes for their chemical modification, with the aim of promoting new biological activities and/or to modify the final properties of the biomaterials for specific purposes. These synthetic strategies also involve the combination of polysaccharides with other polymers. A review of the more recent research in the field of chemical modification of alginate, chitin and its derivative chitosan is presented. Moreover, we report as case studies the results of our recent work concerning various different approaches and applications of polysaccharide-based biomaterials, such as the realization of novel composites based on calcium sulphate blended with alginate and with a chemically modified chitosan, the synthesis of novel alginate-poly(ethylene glycol copolymers and the development of a family of materials based on alginate and acrylic polymers of potential interest as drug delivery systems.

  17. Ancestral genome inference using a genetic algorithm approach.

    Science.gov (United States)

    Gao, Nan; Yang, Ning; Tang, Jijun

    2013-01-01

    Recent advancement of technologies has now made it routine to obtain and compare gene orders within genomes. Rearrangements of gene orders by operations such as reversal and transposition are rare events that enable researchers to reconstruct deep evolutionary histories. An important application of genome rearrangement analysis is to infer gene orders of ancestral genomes, which is valuable for identifying patterns of evolution and for modeling the evolutionary processes. Among various available methods, parsimony-based methods (including GRAPPA and MGR) are the most widely used. Since the core algorithms of these methods are solvers for the so called median problem, providing efficient and accurate median solver has attracted lots of attention in this field. The "double-cut-and-join" (DCJ) model uses the single DCJ operation to account for all genome rearrangement events. Because mathematically it is much simpler than handling events directly, parsimony methods using DCJ median solvers has better speed and accuracy. However, the DCJ median problem is NP-hard and although several exact algorithms are available, they all have great difficulties when given genomes are distant. In this paper, we present a new algorithm that combines genetic algorithm (GA) with genomic sorting to produce a new method which can solve the DCJ median problem in limited time and space, especially in large and distant datasets. Our experimental results show that this new GA-based method can find optimal or near optimal results for problems ranging from easy to very difficult. Compared to existing parsimony methods which may severely underestimate the true number of evolutionary events, the sorting-based approach can infer ancestral genomes which are much closer to their true ancestors. The code is available at http://phylo.cse.sc.edu. PMID:23658708

  18. Modeling drug- and chemical- induced hepatotoxicity with systems biology approaches

    Directory of Open Access Journals (Sweden)

    SudinBhattacharya

    2012-12-01

    Full Text Available We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of ‘toxicity pathways’ is described in the context of the 2007 US National Academies of Science report, “Toxicity testing in the 21st Century: A Vision and A Strategy”. Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically-based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular “virtual tissue” model of the liver lobule that combines molecular circuits in individual hepatocytes with cell-cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the AhR toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsymTM to understand drug-induced liver injury (DILI, the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.

  19. Potential International Approaches to Ownership/Control of Human Genetic Resources.

    Science.gov (United States)

    Rhodes, Catherine

    2016-09-01

    In its governance activities for genetic resources, the international community has adopted various approaches to their ownership, including: free access; common heritage of mankind; intellectual property rights; and state sovereign rights. They have also created systems which combine elements of these approaches. While governance of plant and animal genetic resources is well-established internationally, there has not yet been a clear approach selected for human genetic resources. Based on assessment of the goals which international governance of human genetic resources ought to serve, and the implications for how they will be accessed and utilised, it is argued that common heritage of mankind will be the most appropriate approach to adopt to their ownership/control. It does this with the aim of stimulating discussion in this area and providing a starting point for deeper consideration of how a common heritage of mankind, or similar, regime for human genetic resources would function and be implemented. PMID:26297608

  20. The genetic code degeneracy and the amino acids chemical composition are connected

    OpenAIRE

    Negadi, Tidjani

    2009-01-01

    We show that our recently published Arithmetic Model of the genetic code based on Godel Encoding is robust against symmetry transformations, specially Rumer s one U > G, A > C, and constitutes a link between the degeneracy structure and the chemical composition of the 20 canonical amino acids. As a result, several remarkable atomic patterns involving hydrogen, carbon, nucleon and atom numbers are derived. This study has no obvious practical application(s) but could, we hope, add some new know...

  1. Combining Single (Mixed) Metric Approach and Genetic Algorithm for QoS Routing Problem

    Institute of Scientific and Technical Information of China (English)

    胡世余; 谢剑英

    2004-01-01

    A hybrid algorithm for the delay constrained least cost path problem is proposed through combination of single (mixed) metric approach and genetic algorithm. Compared with the known genetic algorithm for the same problem, the new algorithm adopts integral coding scheme and new genetic operator, which reduces the search space and improves the efficiency of genetic operation. Meanwhile, the single (mixed) approach accelerates the convergence speed. Simulation results indicate that the proposed algorithm can find near-optimal even optimal solutions within moderate numbers of generations.

  2. Bioethical – Theological and Legal approach in genetic testing of adult persons

    Directory of Open Access Journals (Sweden)

    George Katsimigas

    2012-07-01

    Full Text Available Thorough genetic testing gives possibility's diagnosis of genetic diseases or identity individuals, who genetic predisposed for disease outbreak Aims: To present/identify the ethical and religious issues, which arise from the application of genetic testing in humans. Furthermore, the principles from the European and Greek legislation regarding genetic testing will be discussed. Materials & Methods: A literature review based on both review and research literature, conducted during the period of (1993-2010, derived from MEDLINE, SCOPUS and ΙΑΤΡΟΤΕΚ databases using as key words: Bioethics, genetic testing, bioethics, access, genetic information, orthodox ethics, Legislation. Results: Genetic testing for disease prevention is of primary importance. The main ethical concerns however, are related to the dissemination/ disclosure and use of this information from insurance companies, healthcare authorities, scientists, forensic departments/services and employers. Similarly, the orthodox religion accepts the use of genetic testing for the prevention and treatment of diseases as long as there is no break of confidentiality. Finally, considering the legal issues, it is apparent that genetic information is regarded as personal information and as such it is protected from the national (Greek and international law. Conclusions: It is necessary to ensure that the public authorities protect the rights of their citizens regarding genetic testing and all insurance companies, employers, schools etc. should not be allowed to have access to genetic information. Such an approach will ensure that social discrimination, obstructions or other inequalities between people on the basis of genetic information is avoided.

  3. Genetic approaches to study aging in Drosophila melanogaster

    OpenAIRE

    Poirier, Luc; Seroude, Laurent

    2005-01-01

    The process of aging can be described as a progressive decline in an organism's function that invariably results in death. This decline results from the activities of intrinsic genetic factors within an organism. The relative contributions of the biological and environmental components to senescence are hard to measure, however different strategies have been devised in Drosophila melanogaster to isolate and identify genetic influences on aging. These strategies include selective breeding, qua...

  4. Improved and simplified recombineering approach for influenza virus reverse genetics

    OpenAIRE

    Liu, Qinfang; Wang, Shuai; Ma, Guangpeng; Pu, Juan; Forbes, Nicole E.; Brown, Earl G.; Liu, Jin-Hua

    2009-01-01

    Typical reverse genetics systems for generating influenza viruses require the insertion of each genome segments by DNA ligation into vectors for genome synthesis and expression. Herein is described the construction and use of a novel pair of plasmid vectors for cloning all eight genome segments of influenza A virus by homologous recombination for influenza virus reverse genetics. Plasmids, pLLBA and pLLBG, were constructed to possess opposing RNA polymerase I and RNA polymerase II transcripti...

  5. Introduction to Focus Issue: Quantitative Approaches to Genetic Networks

    Science.gov (United States)

    Albert, Réka; Collins, James J.; Glass, Leon

    2013-06-01

    All cells of living organisms contain similar genetic instructions encoded in the organism's DNA. In any particular cell, the control of the expression of each different gene is regulated, in part, by binding of molecular complexes to specific regions of the DNA. The molecular complexes are composed of protein molecules, called transcription factors, combined with various other molecules such as hormones and drugs. Since transcription factors are coded by genes, cellular function is partially determined by genetic networks. Recent research is making large strides to understand both the structure and the function of these networks. Further, the emerging discipline of synthetic biology is engineering novel gene circuits with specific dynamic properties to advance both basic science and potential practical applications. Although there is not yet a universally accepted mathematical framework for studying the properties of genetic networks, the strong analogies between the activation and inhibition of gene expression and electric circuits suggest frameworks based on logical switching circuits. This focus issue provides a selection of papers reflecting current research directions in the quantitative analysis of genetic networks. The work extends from molecular models for the binding of proteins, to realistic detailed models of cellular metabolism. Between these extremes are simplified models in which genetic dynamics are modeled using classical methods of systems engineering, Boolean switching networks, differential equations that are continuous analogues of Boolean switching networks, and differential equations in which control is based on power law functions. The mathematical techniques are applied to study: (i) naturally occurring gene networks in living organisms including: cyanobacteria, Mycoplasma genitalium, fruit flies, immune cells in mammals; (ii) synthetic gene circuits in Escherichia coli and yeast; and (iii) electronic circuits modeling genetic networks

  6. Controlling bloat : individual and population based approaches in genetic programming

    OpenAIRE

    Silva, Sara Guilherme Oliveira da

    2008-01-01

    Genetic Programming (GP) is the automated learning of computer programs. Basically a search process, it is capable of solving complex problems by evolving populations of computer programs, using Darwinian evolution and Mendelian genetics as inspiration. Theoretically, GP can solve any problem whose candidate solutions can be measured and compared, making it a widely applicable technique. Furthermore, the solutions found by GP are usually provided in a format that users can understand and modi...

  7. Genetics of the Musculoskeletal System: A Pleiotropic Approach

    OpenAIRE

    Karasik, David; Kiel, Douglas P

    2008-01-01

    The risk of osteoporotic fracture can be viewed as a function of loading conditions and the ability of the bone to withstand the load. Skeletal loads are dominated by muscle action. Recently, it has become clear that bone and muscle share genetic determinants. Involution of the musculoskeletal system manifests as bone loss (osteoporosis) and muscle wasting (sarcopenia). Therefore, the consideration of pleiotropy is an important aspect in the study of the genetics of osteoporosis and sarcopeni...

  8. A novel approach to automatic music composing: Using genetic algorithm

    OpenAIRE

    Daylamani Zad, Damon; Araabi, Babak N.; Lucas, Caru

    2006-01-01

    Artificial music composition is one of the ever rising problems of computer science. Genetic Algorithm has been one of the most useful means in our hands to solve optimization problems. By use of precise assumptions and adequate fitness function it is possible to change the music composing into an optimization problem. This paper proposes a new genetic algorithm for composing music. Considering entropy of the notes distribution as a factor of fitness function and developing mutation and cross...

  9. A quantum informational approach for dissecting chemical reactions

    CERN Document Server

    Duperrouzel, Corinne; Boguslawski, Katharina; Barcza, Gergerly; Legeza, Örs; Ayers, Paul W

    2014-01-01

    We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected which allows us to monitor the interplay of back-bonding and $\\pi$-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

  10. Chemical reaction network approaches to Biochemical Systems Theory.

    Science.gov (United States)

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R

    2015-11-01

    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. PMID:26363083

  11. Multi-stage genetic fuzzy systems based on the iterative rule learning approach

    OpenAIRE

    González Muñoz, Antonio; Herrera Triguero, Francisco

    1997-01-01

    Genetic algorithms (GAs) represent a class of adaptive search techniques inspired by natural evolution mechanisms. The search properties of GAs make them suitable to be used in machine learning processes and for developing fuzzy systems, the so-called genetic fuzzy systems (GFSs). In this contribution, we discuss genetics-based machine learning processes presenting the iterative rule learning approach, and a special kind of GFS, a multi-stage GFS based on the iterative rule...

  12. A genetic algorithm approach in interface and surface structure optimization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian [Iowa State Univ., Ames, IA (United States)

    2010-01-01

    The thesis is divided into two parts. In the first part a global optimization method is developed for the interface and surface structures optimization. Two prototype systems are chosen to be studied. One is Si[001] symmetric tilted grain boundaries and the other is Ag/Au induced Si(111) surface. It is found that Genetic Algorithm is very efficient in finding lowest energy structures in both cases. Not only existing structures in the experiments can be reproduced, but also many new structures can be predicted using Genetic Algorithm. Thus it is shown that Genetic Algorithm is a extremely powerful tool for the material structures predictions. The second part of the thesis is devoted to the explanation of an experimental observation of thermal radiation from three-dimensional tungsten photonic crystal structures. The experimental results seems astounding and confusing, yet the theoretical models in the paper revealed the physics insight behind the phenomena and can well reproduced the experimental results.

  13. A genetic algorithm approach in interface and surface structure optimization

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian

    2010-05-16

    The thesis is divided into two parts. In the first part a global optimization method is developed for the interface and surface structures optimization. Two prototype systems are chosen to be studied. One is Si[001] symmetric tilted grain boundaries and the other is Ag/Au induced Si(111) surface. It is found that Genetic Algorithm is very efficient in finding lowest energy structures in both cases. Not only existing structures in the experiments can be reproduced, but also many new structures can be predicted using Genetic Algorithm. Thus it is shown that Genetic Algorithm is a extremely powerful tool for the material structures predictions. The second part of the thesis is devoted to the explanation of an experimental observation of thermal radiation from three-dimensional tungsten photonic crystal structures. The experimental results seems astounding and confusing, yet the theoretical models in the paper revealed the physics insight behind the phenomena and can well reproduced the experimental results.

  14. Genes, Culture and Conservatism-A Psychometric-Genetic Approach.

    Science.gov (United States)

    Schwabe, Inga; Jonker, Wilfried; van den Berg, Stéphanie M

    2016-07-01

    The Wilson-Patterson conservatism scale was psychometrically evaluated using homogeneity analysis and item response theory models. Results showed that this scale actually measures two different aspects in people: on the one hand people vary in their agreement with either conservative or liberal catch-phrases and on the other hand people vary in their use of the "?" response category of the scale. A 9-item subscale was constructed, consisting of items that seemed to measure liberalism, and this subscale was subsequently used in a biometric analysis including genotype-environment interaction, correcting for non-homogeneous measurement error. Biometric results showed significant genetic and shared environmental influences, and significant genotype-environment interaction effects, suggesting that individuals with a genetic predisposition for conservatism show more non-shared variance but less shared variance than individuals with a genetic predisposition for liberalism. PMID:26590135

  15. Optimization of a Reduced Chemical Kinetic Model for HCCI Engine Simulations by Micro-Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A reduced chemical kinetic model (44 species and 72 reactions) for the homogeneous charge compression ignition (HCCI) combustion of n-heptane was optimized to improve its autoignition predictions under different engine operating conditions. The seven kinetic parameters of the optimized model were determined by using the combination of a micro-genetic algorithm optimization methodology and the SENKIN program of CHEMKIN chemical kinetics software package. The optimization was performed within the range of equivalence ratios 0.2-1.2, initial temperature 310-375 K and initial pressure 0.1-0.3 MPa. The engine simulations show that the optimized model agrees better with the detailed chemical kinetic model (544 species and 2 446 reactions) than the original model does.

  16. Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database

    International Nuclear Information System (INIS)

    We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are 'unbiased' insofar as contributions from detectable secondary structure have been minimized (RCCSu). We have used this approach to derive a set of RCCSu values for 13Cα and 13Cβ for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of 13Cα and 13Cβ chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCSmax-ent). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCSpeptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCSstruct-stat). We show that the RCCSmax-ent values are strikingly similar to published RCCSpeptide and RCCSstruct-stat values. By contrast, the RCCSu values differ significantly from both published types of random coil chemical shift values. The differences (RCCSpeptide-RCCSu) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCSu values appear to be consistent with the current concept of the 'random coil' as the state in which the geometry of the polypeptide ensemble samples the allowed region of (φ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine

  17. Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

    International Nuclear Information System (INIS)

    A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionary biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended

  18. Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

    Energy Technology Data Exchange (ETDEWEB)

    Burgess-Herbert, Sarah L., E-mail: sarah.burgess@alum.mit.edu [American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellow at the US Environmental Protection Agency (EPA), 2009–10 (United States); Euling, Susan Y. [National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency, Washington, DC 20460 (United States)

    2013-09-15

    A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionary biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended.

  19. A Fuzzy Genetic Algorithm Approach to an Adaptive Information Retrieval Agent.

    Science.gov (United States)

    Martin-Bautista, Maria J.; Vila, Maria-Amparo; Larsen, Henrik Legind

    1999-01-01

    Presents an approach to a Genetic Information Retrieval Agent Filter (GIRAF) that filters and ranks documents retrieved from the Internet according to users' preferences by using a Genetic Algorithm and fuzzy set theory to handle the imprecision of users' preferences and users' evaluation of the retrieved documents. (Author/LRW)

  20. A molecular-genetic approach to studying source-sink interactions in Arabidopsis thalian. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, S. I.

    2000-06-01

    This is a final report describing the results of the research funded by the DOE Energy Biosciences Program grant entitled ''A Molecular-Genetic Approach to Studying Source-Sink Interactions in Arabidiopsis thaliana''.

  1. Chemical Stimulants and Genetic Sexing Boost the SIT: Evidence from Ceratitis capitata and Bactrocera Dorsalis in Hawaii

    Science.gov (United States)

    Genetic and chemical means have been developed to significantly improve the effectiveness of the sterile insect technique against tephritid fruit flies in recent years. Beginning with the development of genetic sexing techniques some 25 years ago, all-male strains of several species of fruit flies h...

  2. Correlation and regression analyses of genetic effects for different types of cells in mammals under radiation and chemical treatment

    International Nuclear Information System (INIS)

    Data about genetic mutations under radiation and chemical treatment for different types of cells have been analyzed with correlation and regression analyses. Linear correlation between different genetic effects in sex cells and somatic cells have found. The results may be extrapolated on sex cells of human and mammals. (authors)

  3. The Genetic Approach in Pulmonary Fibrosis: Can It Provide Clues to This Complex Disease?

    OpenAIRE

    Lawson, William E.; Loyd, James E.

    2006-01-01

    Multiple investigators have undertaken genetic studies in idiopathic pulmonary fibrosis populations in attempts to define genetic links to disease in hopes that this would improve understanding of disease pathogenesis and target pathways for therapy. Multiple genes have been evaluated using a candidate gene approach with limited success, with results suggesting a disease modifier effect rather than a disease causing effect. Using this approach, associations have been observed between idiopath...

  4. AN EXPERT BASED INITIAL GENERATION OF GENETIC ALGORITHM WITH ADAPTIVE PROBABILITY APPROACH FOR QUADRATIC OPF

    OpenAIRE

    BHASKAR, Mithun; BENARJI, Mohan; MAHESWARAPU, Sydulu

    2012-01-01

    This paper presents a novel and superior Genetic Algorithm (GA) based resolver for Optimal Power flow (OPF) problem. Here, the main contrast to other Genetic Algorithm based approaches is that a novel expert based initial generation of population and adaptive probability approach (variable Cross over probability and mutation probability) is adopted in selection of offspring together with roulette wheel technique which reduces the computation time and increases the quality considerably. Select...

  5. Hormones as Mediators of Phenotypic and Genetic Integration: an Evolutionary Genetics Approach.

    Science.gov (United States)

    Cox, Robert M; McGlothlin, Joel W; Bonier, Frances

    2016-08-01

    Evolutionary endocrinology represents a synthesis between comparative endocrinology and evolutionary genetics. This synthesis can be viewed through the breeder's equation, a cornerstone of quantitative genetics that, in its univariate form, states that a population's evolutionary response is the product of the heritability of a trait and selection on that trait (R = h(2)S). Under this framework, evolutionary endocrinologists have begun to quantify the heritability of, and the strength of selection on, a variety of hormonal phenotypes. With specific reference to our work on testosterone and corticosterone in birds and lizards, we review these studies while emphasizing the challenges of applying this framework to hormonal phenotypes that are inherently plastic and mediate adaptive responses to environmental variation. Next, we consider the untapped potential of evolutionary endocrinology as a framework for exploring multivariate versions of the breeder's equation, with emphasis on the role of hormones in structuring phenotypic and genetic correlations. As an extension of the familiar concepts of phenotypic integration and hormonal pleiotropy, we illustrate how the hormonal milieu of an individual acts as a local environment for the expression of genes and phenotypes, thereby influencing the quantitative genetic architecture of multivariate phenotypes. We emphasize that hormones are more than mechanistic links in the translation of genotype to phenotype: by virtue of their pleiotropic effects on gene expression, hormones structure the underlying genetic variances and covariances that determine a population's evolutionary response to selection. PMID:27252188

  6. The Multiplexed Chemical Kinetic Photoionization Mass Spectrometer: A New Approach To Isomer-resolved Chemical Kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Osborne, David L.; Zou, Peng; Johnsen, Howard; Hayden, Carl C.; Taatjes, Craig A.; Knyazev, Vadim D.; North, Simon W.; Peterka, Darcy S.; Ahmed, Musahid; Leone, Stephen R.

    2008-08-28

    We have developed a multiplexed time- and photon-energy?resolved photoionizationmass spectrometer for the study of the kinetics and isomeric product branching of gasphase, neutral chemical reactions. The instrument utilizes a side-sampled flow tubereactor, continuously tunable synchrotron radiation for photoionization, a multi-massdouble-focusing mass spectrometer with 100percent duty cycle, and a time- and positionsensitive detector for single ion counting. This approach enables multiplexed, universal detection of molecules with high sensitivity and selectivity. In addition to measurement of rate coefficients as a function of temperature and pressure, different structural isomers can be distinguished based on their photoionization efficiency curves, providing a more detailed probe of reaction mechanisms. The multiplexed 3-dimensional data structure (intensity as a function of molecular mass, reaction time, and photoionization energy) provides insights that might not be available in serial acquisition, as well as additional constraints on data interpretation.

  7. A genetic-algorithm-based neural network approach for EDXRF analysis

    International Nuclear Information System (INIS)

    In energy dispersive X-ray fluorescence (EDXRF), quantitative elemental content analysis becomes difficult due to the existence of the noise, the spectrum peak superposition, element matrix effect, etc. In this paper, a hybrid approach of genetic algorithm (GA) and back propagation (BP) neural network is proposed without considering the complex relationship between the elemental content and peak intensity. The aim of GA-optimized BP is to get better network initial weights and thresholds. The starting point of this approach is that the reciprocal of the mean square error of the initialization BP neural network is set as the fitness value of the individuals in GA; and the initial weights and thresholds are replaced by individuals, then the optimal individual is searched by selecting, crossover and mutation operations, finally a new BP neural network model is established with the optimal initial weights and thresholds. The quantitative analysis results of titanium and iron contents in five types of mineral samples show that the relative errors of 76.7% samples are below 2%, compared to chemical analysis data, which demonstrates the effectiveness of the proposed method. (authors)

  8. Production and Characterization of Chemically Inactivated Genetically Engineered Clostridium difficile Toxoids.

    Science.gov (United States)

    Vidunas, Eugene; Mathews, Antony; Weaver, Michele; Cai, Ping; Koh, Eun Hee; Patel-Brown, Sujata; Yuan, Hailey; Zheng, Zi-Rong; Carriere, Marjolaine; Johnson, J Erik; Lotvin, Jason; Moran, Justin

    2016-07-01

    A recombinant Clostridium difficile expression system was used to produce genetically engineered toxoids A and B as immunogens for a prophylactic vaccine against C. difficile-associated disease. Although all known enzymatic activities responsible for cytotoxicity were genetically abrogated, the toxoids exhibited residual cytotoxic activity as measured in an in vitro cell-based cytotoxicity assay. The residual cytotoxicity was eliminated by treating the toxoids with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide. Mass spectrometry and amino acid analysis of the EDC-inactivated toxoids identified crosslinks, glycine adducts, and β-alanine adducts. Surface plasmon resonance analysis demonstrated that modifications resulting from the chemical treatment did not appreciably affect recognition of epitopes by both toxin A- and B-specific neutralizing monoclonal antibodies. Compared to formaldehyde-inactivated toxoids, the EDC/N-hydroxysuccinimide-inactivated toxoids exhibited superior stability in solution with respect to reversion of cytotoxic activity. PMID:27233688

  9. Problems and solutions in the estimation of genetic risks from radiation and chemicals

    International Nuclear Information System (INIS)

    Extensive investigations with mice on the effects of various physical and biological factors, such as dose rate, sex and cell stage, on radiation-induced mutation have provided an evaluation of the genetics hazards of radiation in man. The mutational results obtained in both sexes with progressive lowering of the radiation dose rate have permitted estimation of the mutation frequency expected under the low-level radiation conditions of most human exposure. Supplementing the studies on mutation frequency are investigations on the phenotypic effects of mutations in mice, particularly anatomical disorders of the skeleton, which allow an estimation of the degree of human handicap associated with the occurrence of parallel defects in man. Estimation of the genetic risk from chemical mutagens is much more difficult, and the research is much less advanced. Results on transmitted mutations in mice indicate a poor correlation with mutation induction in non-mammalian organisms

  10. Energy Efficient Routing in Wireless Sensor Networks: A Genetic Approach

    CERN Document Server

    Chakraborty, Ayon; Naskar, Mrinal Kanti

    2011-01-01

    The key parameters that need to be addressed while designing protocols for sensor networks are its energy awareness and computational feasibility in resource constrained sensor nodes. Variation in the distances of nodes from the Base Station and differences in inter-nodal distances are primary factors causing unequal energy dissipation among the nodes. Thus energy difference among the nodes increases with time resulting in degraded network performance. The LEACH and PEGASIS schemes which provided elegant solutions to the problem suffer due to randomization of cluster heads and greedy chain formation respectively. In this paper, we propose a Genetic algorithm inspired ROUting Protocol (GROUP) which shows enhanced performance in terms of energy efficiency and network lifetime over other schemes. GROUP increases the network performance by ensuring a sub-optimal energy dissipation of the individual nodes despite their random deployment. It employs modern heuristics like Genetic Algorithms along with Simulated Ann...

  11. An Improved Hybrid Genetic Algorithm for Chemical Plant Layout Optimization with Novel Non-overlapping and Toxic Gas Dispersion Constraints

    Institute of Scientific and Technical Information of China (English)

    XU Yuan; WANG Zhenyu; ZHU Qunxiong

    2013-01-01

    New approaches for facility distribution in chemical plants are proposed including an improved non-overlapping constraint based on projection relationships of facilities and a novel toxic gas dispersion constraint.In consideration of the large number of variables in the plant layout model,our new method can significantly reduce the number of variables with their own projection relationships.Also,as toxic gas dispersion is a usual incident in a chemical plant,a simple approach to describe the gas leakage is proposed,which can clearly represent the constraints of potential emission source and sitting facilities.For solving the plant layout model,an improved genetic algorithm (GA) based on infeasible solution fix technique is proposed,which improves the globe search ability of GA.The case study and experiment show that a better layout plan can be obtained with our method,and the safety factors such as gas dispersion and minimum distances can be well handled in the solution.

  12. A Dynamic Programming Approach to Individual Initialization in Genetic Programming

    Czech Academy of Sciences Publication Activity Database

    Křen, T.; Neruda, Roman

    Los Alamitos: IEEE, 2015, s. 1752-1757. ISBN 978-1-4799-8696-5. [SMC 2015. International Conference on Systems, Man and Cybernetics. Hong Kong (HK), 09.10.2015-12.10.2015] R&D Projects: GA ČR GA15-18108S Grant ostatní: GA UK(CZ) 187115; SVV(CZ) 260 224 Institutional support: RVO:67985807 Keywords : genetic programming * initialization * dynamic programming Subject RIV: IN - Informatics, Computer Science

  13. A Reverse Genetic Approach to Test Functional Redundancy During Embryogenesis

    OpenAIRE

    Rikin, Amir; Rosenfeld, Gabriel E.; McCartin, Kellie; Evans, Todd

    2010-01-01

    Gene function during embryogenesis is typically defined by loss-of-function experiments, for example by targeted mutagenesis (knockout) in the mouse. In the zebrafish model, effective reverse genetic techniques have been developed using microinjection of gene-specific antisense morpholinos. Morpholinos target an mRNA through specific base-pairing and block gene function transiently by inhibiting translation or splicing for several days during embryogenesis (knockdown). However, in vertebrates...

  14. A genetic programming hyper-heuristic approach to automated packing

    OpenAIRE

    Hyde, Matthew

    2010-01-01

    This thesis presents a programme of research which investigated a genetic programming hyper-heuristic methodology to automate the heuristic design process for one, two and three dimensional packing problems. Traditionally, heuristic search methodologies operate on a space of potential solutions to a problem. In contrast, a hyper-heuristic is a heuristic which searches a space of heuristics, rather than a solution space directly. The majority of hyper-heuristic research papers, so far, hav...

  15. Genetics of intracerebral hemorrhage: Insights from candidate gene approaches

    OpenAIRE

    Baoqiong Liu; Le Zhang; Qidong Yang

    2012-01-01

    Intracerebral hemorrhage (ICH) is a heterogeneous disease with genetic factors playing an important role. Association studies on a wide range of candidate pathways suggest a weak but significant effect for several alleles with ICH risk. Among the most widely investigated genes are those involved in the renin-angiotensin-aldosterone system (e.g., angiotensin-converting enzyme), coagulation pathway (e.g., Factor XIII, Factor VII, platelet-activating factor acetylhydrolase, Factor V Leiden, and ...

  16. Genetic modulation of oxytocin sensitivity : a pharmacogenetic approach

    OpenAIRE

    Chen, Frances S.; Kumsta, Robert; Dvorak, Fabian; Domes, Gregor; Yim, O. S.; Ebstein, Richard P.; Heinrichs, Markus

    2015-01-01

    Intranasal administration of the neuropeptide oxytocin has been shown to influence a range of complex social cognitions and social behaviors, and it holds therapeutic potential for the treatment of mental disorders characterized by social functioning deficits such as autism, social phobia and borderline personality disorder. However, considerable variability exists in individual responses to oxytocin administration. Here, we undertook a study to investigate the role of genetic variation in se...

  17. A Genetic Approach to the History of the Magellanic Clouds

    OpenAIRE

    Guglielmo, Magda; Lewis, Geraint F.; Bland-Hawthorn, Joss

    2014-01-01

    The history of the Magellanic Clouds is investigated using N-body hydrodynamic simulations where the initial conditions are set by a genetic algorithm. This technique allows us to identify possible orbits for the Magellanic Clouds around the Milky Way, by directly comparing the simulations with observational constraints. We explore the parameter space of the interaction between the Magellanic Clouds and the Milky Way, considering as free parameters the proper motions of the Magellanic Clouds,...

  18. AI AND SAR APPROACHES FOR PREDICTING CHEMICAL CARCINOGENICITY: SURVEY AND STATUS REPORT

    Science.gov (United States)

    A wide variety of artificial intelligence (AI) and structure-activity relationship (SAR approaches have been applied to tackling the general problem of predicting rodent chemical carcinogenicity. Given the diversity of chemical structures and mechanisms relative to this endpoin...

  19. A Genetic-Algorithms-Based Approach for Programming Linear and Quadratic Optimization Problems with Uncertainty

    Directory of Open Access Journals (Sweden)

    Weihua Jin

    2013-01-01

    Full Text Available This paper proposes a genetic-algorithms-based approach as an all-purpose problem-solving method for operation programming problems under uncertainty. The proposed method was applied for management of a municipal solid waste treatment system. Compared to the traditional interactive binary analysis, this approach has fewer limitations and is able to reduce the complexity in solving the inexact linear programming problems and inexact quadratic programming problems. The implementation of this approach was performed using the Genetic Algorithm Solver of MATLAB (trademark of MathWorks. The paper explains the genetic-algorithms-based method and presents details on the computation procedures for each type of inexact operation programming problems. A comparison of the results generated by the proposed method based on genetic algorithms with those produced by the traditional interactive binary analysis method is also presented.

  20. A New Approach to Tuning Heuristic Parameters of Genetic Algorithms

    Czech Academy of Sciences Publication Activity Database

    Holeňa, Martin

    2006-01-01

    Roč. 3, č. 3 (2006), s. 562-569. ISSN 1790-0832. [AIKED'06. WSEAS International Conference on Artificial Intelligence, Knowledge Engineering and Data Bases. Madrid, 15.02.2006-17.02.2006] R&D Projects: GA ČR(CZ) GA201/05/0325; GA ČR(CZ) GA201/05/0557 Institutional research plan: CEZ:AV0Z10300504 Keywords : evolutionary optimization * genetic algorithms * heuristic parameters * parameter tuning * artificial neural network s * convergence speed * population diversity Subject RIV: IN - Informatics, Computer Science

  1. AGROBACTERIUM-MEDIATED GENETIC TRANSFORMATION OF SORGHUM USING TISSUE CULTURE-BASED AND POLLEN-MEDIATED APPROACHES

    OpenAIRE

    Elkonin L.A.; O.N. Nosova; J.V. Italianskaya

    2012-01-01

    Genetic transformation is a powerful tool for genetic improvement of arable crops. Genetic engineering approaches are especially important for modification of starch and protein contents, vitamin and micronutrient concentration, improvement of nutritive value of protein fractions, and increase tolerance to environmental stresses. Application of transgenic technologies for genetic improvement of sorghum, a highly productive heat tolerant and drought resistant crop, is extremely important since...

  2. Genetic algorithm approach to estimate transport energy demand in Turkey

    International Nuclear Information System (INIS)

    Transport energy modeling is a subject of current interest among transport engineers and scientists concerned with problems of sustainable transport. Transport energy planning is not possible without a reasonable knowledge of past and present energy consumption and likely future demands. In this study, three forms of the energy demand equations are developed in order to improve transport energy demand estimation efficiency for future projections based on genetic algorithm (GA) notion. The Genetic Algorithm Transport Energy Demand Estimation (GATEDE) model is developed using population, gross domestic product and vehicle-km. All equations proposed here are linear and non-linear, of which one is linear, second is exponential and third is quadratic. The quadratic form of the GATEDE model provided better-fit solution to the observed data and can be used with a high correlation coefficient for Turkey's future transport energy projections. It is expected that this study will be helpful in developing highly applicable and productive planning for transport energy policies. The GATEDE gives transport energy demand in comparison with the other transport energy demand projections. The GATEDE model plans the sectoral energy demand of Turkey until 2020

  3. Genetics of intracerebral hemorrhage: Insights from candidate gene approaches

    Directory of Open Access Journals (Sweden)

    Baoqiong Liu

    2012-01-01

    Full Text Available Intracerebral hemorrhage (ICH is a heterogeneous disease with genetic factors playing an important role. Association studies on a wide range of candidate pathways suggest a weak but significant effect for several alleles with ICH risk. Among the most widely investigated genes are those involved in the renin-angiotensin-aldosterone system (e.g., angiotensin-converting enzyme, coagulation pathway (e.g., Factor XIII, Factor VII, platelet-activating factor acetylhydrolase, Factor V Leiden, and beta1-tubulin, lipid metabolism (e.g., apolipoproteins (ApoE, Apo(a, ApoH, homocysteine metabolism (e.g., methylenetetrahydrofolate reductase, inflammation (e.g., interleukin-6 and tumor necrosis-alpha and other candidate pathways. To identify the robustness of the above associations with ICH, a search of Pubmed (1988 through December 2011 was performed, with searches limited to English-language studies conducted among adult human subjects. This article presents a review of the examined literature on the genetics of ICH.

  4. Drosophila wing modularity revisited through a quantitative genetic approach.

    Science.gov (United States)

    Muñoz-Muñoz, Francesc; Carreira, Valeria Paula; Martínez-Abadías, Neus; Ortiz, Victoria; González-José, Rolando; Soto, Ignacio M

    2016-07-01

    To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo-distal axis, as suggested by developmental, biomechanical, and evolutionary evidence. To achieve these goals we perform a multilevel analysis of covariation combining the techniques of geometric morphometrics and quantitative genetics. Our results indicate that the Drosophila wing is indeed organized into two main modules, the wing base and the wing blade. The patterns of integration and modularity were highly concordant at the phenotypic, genetic, environmental, and developmental levels. Besides, we found that modularity at the developmental level was considerably higher than modularity at other levels, suggesting that in the Drosophila wing direct developmental interactions are major contributors to total phenotypic shape variation. We propose that the precise time at which covariance-generating developmental processes occur and/or the magnitude of variation that they produce favor proximo-distal, rather than anterior-posterior, modularity in the Drosophila wing. PMID:27272402

  5. Genetics

    Science.gov (United States)

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

  6. The Sociopolitical Importance of Genetic, Phenomenological Approaches to Science Teaching and Learning

    Science.gov (United States)

    Bazzul, Jesse

    2015-01-01

    This article discusses Wolff-Michael Roth's theoretical framework for a phenomenological, genetic approach to science teaching and learning based on the work of Edmund Husserl. This approach advocates the inclusion of student lifeworlds in science education and underlines the importance of thinking about subjectivity in both science and science…

  7. A Genetic Algorithms-based Approach for Optimized Self-protection in a Pervasive Service Middleware

    DEFF Research Database (Denmark)

    Zhang, Weishan; Ingstrup, Mads; Hansen, Klaus Marius;

    2009-01-01

    constraints of heterogeneous devices and networks. In this paper, we present a Genetic Algorithms-based approach for obtaining optimized security configurations at run time, supported by a set of security OWL ontologies and an event-driven framework. This approach has been realized as a prototype for self...

  8. Genetic and chemical modifiers of a CUG toxicity model in Drosophila.

    Directory of Open Access Journals (Sweden)

    Amparo Garcia-Lopez

    Full Text Available Non-coding CUG repeat expansions interfere with the activity of human Muscleblind-like (MBNL proteins contributing to myotonic dystrophy 1 (DM1. To understand this toxic RNA gain-of-function mechanism we developed a Drosophila model expressing 60 pure and 480 interrupted CUG repeats in the context of a non-translatable RNA. These flies reproduced aspects of the DM1 pathology, most notably nuclear accumulation of CUG transcripts, muscle degeneration, splicing misregulation, and diminished Muscleblind function in vivo. Reduced Muscleblind activity was evident from the sensitivity of CUG-induced phenotypes to a decrease in muscleblind genetic dosage and rescue by MBNL1 expression, and further supported by the co-localization of Muscleblind and CUG repeat RNA in ribonuclear foci. Targeted expression of CUG repeats to the developing eye and brain mushroom bodies was toxic leading to rough eyes and semilethality, respectively. These phenotypes were utilized to identify genetic and chemical modifiers of the CUG-induced toxicity. 15 genetic modifiers of the rough eye phenotype were isolated. These genes identify putative cellular processes unknown to be altered by CUG repeat RNA, and they include mRNA export factor Aly, apoptosis inhibitor Thread, chromatin remodelling factor Nurf-38, and extracellular matrix structural component Viking. Ten chemical compounds suppressed the semilethal phenotype. These compounds significantly improved viability of CUG expressing flies and included non-steroidal anti-inflammatory agents (ketoprofen, muscarinic, cholinergic and histamine receptor inhibitors (orphenadrine, and drugs that can affect sodium and calcium metabolism such as clenbuterol and spironolactone. These findings provide new insights into the DM1 phenotype, and suggest novel candidates for DM1 treatments.

  9. Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach.

    Science.gov (United States)

    Eslami-Mossallam, Behrouz; Schram, Raoul D; Tompitak, Marco; van Noort, John; Schiessel, Helmut

    2016-01-01

    Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function. PMID:27272176

  10. Feature selection using a genetic algorithm-based hybrid approach

    Directory of Open Access Journals (Sweden)

    Luis Felipe Giraldo

    2010-04-01

    Full Text Available The present work proposes a hybrid feature selection model aimed at reducing training time whilst maintaining classification accuracy. The model includes adlusting a decision tree for producing feature subsets. Such subsets’ statistical relevance was evaluated from their resulting classification error. Evaluation involved using the k-nearest neighbors’ rule. Dimension reduction techniques usually assume an element of error; however, the hybrid selection model was tuned by means of genetic algorithms in this work. They simultaneously minimise the number of fea- tures and training error. Contrasting with conventional methods, this model also led to quantifying the relevance of each training set’s features. The model was tested on speech signals (hypernasality classification and ECG identification (ischemic cardiopathy. In the case of speech signals, the database consisted of 90 children (45 recordings per sample; the ECG database had 100 electrocardiograph records (50 recordings per sample. Results showed average reduction rates of up to 88%, classification error being less than 6%.

  11. Data Mining Using Neural–Genetic Approach: A Review

    Directory of Open Access Journals (Sweden)

    Parvez Rahi

    2014-04-01

    Full Text Available In the advance age of technology, there is an increasing availability of digital documents in various languages in various fields. Data mining is gaining popularity in field of knowledge discovery. Data mining is the knowledge discovery process by which we can analyze the large amounts of data from various data repositories and summarizing it into information useful to us. Due to its importance of extracting information/ knowledge from the large data repositories, data mining has become an essential part of human life in various fields. Data mining has a very wide area of applications, and these applications have enriched the human life in various fields including scientific, medical, business, education etc. Here in this paper we will discuss the emphasis of Neural Network and Genetic Algorithm in the field of data mining.

  12. A Novel Approach of Query Optimization for Genetic Population

    Directory of Open Access Journals (Sweden)

    Ishtiaq Ahmed

    2012-03-01

    Full Text Available In relational database large information is maintained and organized so that user can get the desired information in predictable and reliable fashion through the query processing. Retrieving these results in timely manner is Query Optimization. Optimization is a process of choosing most efficient way to execute a SQL query. This is important step in processing of any data manipulation language because in RDBMS, as in large and complicated system performance is key issue. Its an issue that you need to deal with on an ongoing basis so performance must be built in. This paper will provide the reader general concepts of query optimization in relational database system. I will define the implementation plan using join ordering to broaden the potential of database engine through the use of Genetic algorithm in the field of database area in the context of query optimization [12].

  13. Modelling of chemical reaction in foods: a multiresponse approach.

    NARCIS (Netherlands)

    Boekel, van M.A.J.S.

    1998-01-01

    The quality of foods depends on several factors. One of these factors is the occurrence of (bio)chemical changes taking place during the post-harvest period and during processing, storage and distribution. In order to optimise quality it is of utmost importance to control (bio)chemical changes as mu

  14. The statutory approach: the control of chemical products

    International Nuclear Information System (INIS)

    The evaluation and management of risks linked with chemical products and in particular with petroleum products is now performed using all the available tools developed by the OECD or the European Union in order to harmonize the procedures between member states. This paper describes the statutory liabilities linked to the trade of chemical products of industrial use in the case of new and of existing chemical substances (classification, labelling, risk evaluation and reduction, physico-chemical properties, toxicological and eco-toxicological studies, neutralization, limitation of trade and use, import/export, protection of the ozone layer, etc..). It refers to the legal framework (orders, by-laws, decrees, guidelines..) defined by the OECD and the European Community and recalls the organization and administration of the competent authorities for the control of chemical products. (J.S.)

  15. A new approach for the combined chemical and mineral classification of the inorganic matter in coal. 1. Chemical and mineral classification systems

    Energy Technology Data Exchange (ETDEWEB)

    Stanislav V. Vassilev; Christina G. Vassileva [Bulgarian Academy of Sciences, Sofia (Bulgaria). Central Laboratory of Mineralogy and Crystallography

    2009-02-15

    This work introduces and evaluates a new approach for the combined chemical and mineral classification of the inorganic matter in coal. Thirty-seven coal samples from Australia, Bulgaria, USA, Japan, Canada, South Africa, China, Spain, and Ukraine, which differ considerably in their geology, rank, age, ash yield, chemistry and mineralogy, were used to establish the classifications. The chemical classification system was organized according to the contents and significant positive or negative correlations of ash-forming elements in coal ashes using three composition-based criteria, namely: (1) sum of Si, Al, K, and Ti oxides; (2) sum of Ca, Mg, S, and Na oxides; and (3) Fe oxide. This approach resulted in four chemical coal ash types (sialic, calsialic, ferrisialic, and ferricalsialic) further divided into seven subtypes (with high, medium and low acid tendencies) based on the sum of Si, Al, K, and Ti oxides. The more important mineral classification system was organized according to the contents, genesis, and behaviour of mineral classes and species in coals also using three composition-based criteria, namely: (1) silicates + oxyhydroxides; (2) carbonates; and (3) sulphides + sulphates + phosphates. This approach resulted in four mineral coal types (silicate, silicate-carbonate, silicate-sulphide, and silicate-sulphide-carbonate or mixed) further divided into seven subtypes (with high, medium and low detrital tendencies) based on the sum of silicates and oxyhydroxides. The chemical and mineral coal types and subtypes are characterized and relationships and distinctions between them also are described herein. The benefit of this new classification approach is the use of significant correlations and actual element associations, and well-defined and genetically described mineral classes and species in coal. Potential applications of the classification schemes are described in part 2 of the present work. 41 refs., 3 figs., 6 tabs.

  16. Ecological consequences, genetic and chemical variations in fragmented populations of a medicinal plant, justicia adhatoda and implications for its conservation

    International Nuclear Information System (INIS)

    Justicia adhatoda from Kohat Plateau was selected for genetic diversity studies, due to its fragmented habitat, importance in traditional and pharmaceutical medicine and a lack of population structure studies. We had two hypotheses: that habitat loss posed a greater threat to populations than loss of genetic diversity, and that chemical diversity would be higher among different populations than within populations. Genetic diversity within and among populations was evaluated using PBA (P450 based analogue) markers. AMOVA analysis revealed that there was higher genetic diversity within populations (90%) than among populations (10%). No genetic drift was observed, i.e., genetic diversity within populations was maintained despite fewer numbers of individuals in fragmented populations. Surveys of J. adhatoda populations revealed that they were growing in harsh conditions and were imperiled due to extensive harvesting for commercial and domestic purposes. Chemical diversity was evaluated by GC-MS (Gas Chromatograph-Mass Spectrometry) analysis of 90% methanol and 1:2 chloroform:methanol extracts. GC-MS analysis of both the extracts showed nine and 18 chemical compounds, respectively, with higher chemical variations among populations. It is therefore recommended that efforts for the conservation of severely fragmented populations of J. adhatoda must be carried out along with sustainable harvesting. (author)

  17. Induction of Neural Progenitor-Like Cells from Human Fibroblasts via a Genetic Material-Free Approach.

    Directory of Open Access Journals (Sweden)

    Fahimeh Mirakhori

    Full Text Available A number of studies generated induced neural progenitor cells (iNPCs from human fibroblasts by viral delivering defined transcription factors. However, the potential risks associated with gene delivery systems have limited their clinical use. We propose it would be safer to induce neural progenitor-like cells from human adult fibroblasts via a direct non-genetic alternative approach.Here, we have reported that seven rounds of TAT-SOX2 protein transduction in a defined chemical cocktail under a 3D sphere culture gradually morphed fibroblasts into neuroepithelial-like colonies. We were able to expand these cells for up to 20 passages. These cells could give rise to cells that expressed neurons and glia cell markers both in vitro and in vivo.These results show that our approach is beneficial for the genetic material-free generation of iNPCs from human fibroblasts where small chemical molecules can provide a valuable, viable strategy to boost and improve induction in a 3D sphere culture.

  18. Sharing results from complex disease genetics studies: a community based participatory research approach

    OpenAIRE

    Boyer, Bert B.; Mohatt, Gerald V; Pasker, Renee L.; Drew, Elaine M; McGlone, Kathleen K.

    2007-01-01

    OBJECTIVES: Dissemination of research results to communities builds capacity of the community to understand and utilize the results. The objective of this manuscript was to propose a culturally appropriate approach to disseminate complex disease genetics research findings in small Alaska Native communities. STUDY DESIGN: The Center for Alaska Native Health Research is a community-based participatory research project (CBPR) directed at understanding the interactions between genetic, nutrition...

  19. A systematic approach to assessing the clinical significance of genetic variants

    OpenAIRE

    Duzkale, H; Shen, J; McLaughlin, H; Alfares, A; Kelly, MA; Pugh, TJ; Funke, BH; Rehm, HL; Lebo, MS

    2013-01-01

    Molecular genetic testing informs diagnosis, prognosis, and risk assessment for patients and their family members. Recent advances in low-cost, high-throughput DNA sequencing and computing technologies have enabled the rapid expansion of genetic test content, resulting in dramatically increased numbers of DNA variants identified per test. To address this challenge, our laboratory has developed a systematic approach to thorough and efficient assessments of variants for pathogenicity determinat...

  20. A combined genetic and multi medium approach revels new secondary metabolites in Aspergillus nidulans

    OpenAIRE

    Klejnstrup, Marie Louise; Nielsen, Morten Thrane; Frisvad, Jens Christian; Mortensen, Uffe Hasbro; Larsen, Thomas Ostenfeld

    2011-01-01

    Secondary metabolites are a diverse group of metabolites which serve as important natural sources of drugs for treating diseases. The availability of full genome sequences of several filamentous fungi has revealed a large genetic potential for production of secondary metabolites that are not observed under standard laboratory conditions. Genetic approaches have proven a fruitfull strategy towards the production and identification of these unknown metabolites. Examples include deletion of the ...

  1. Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach

    OpenAIRE

    Pascual, Laura; Xu, Jiaxin; Biais, Benoit; Maucourt, Mickael; Ballias, Patricia; Bernillon, Stéphane; Deborde, Catherine; Jacob, Daniel; Desgroux, Aurore; Faurobert, Mireille; Bouchet, Jean-Paul; Gibon, Yves; Moing, Annick

    2013-01-01

    Integrative systems biology proposes new approaches to decipher the variation of phenotypic traits. In an effort to link the genetic variation and the physiological and molecular bases of fruit composition, the proteome (424 protein spots), metabolome (26 compounds), enzymatic profile (26 enzymes), and phenotypes of eight tomato accessions, covering the genetic diversity of the species, and four of their F1 hybrids, were characterized at two fruit developmental stages (cell expansion and oran...

  2. Utilizing Systems Genetics Approaches to Identify Novel Molecular Mechanisms in Cardiovascular Diseases

    OpenAIRE

    Romay, Milagros De La Caridad

    2016-01-01

    Despite the success of focused, reductionist approaches in characterizing the pathophysiology of cardiovascular diseases (CVDs), current estimates predict that 24 million deaths annually will be due to CVDs by 2030. Emphasizing the use of genetic variation in combination with mathematical modeling and integration of next generation –omics profiling technologies, systems genetics characterizes the flow of biological information in physiologic and pathologic states to allow investigators to und...

  3. Search for novel genetic risk factors for venous thrombosis: a dual approach

    OpenAIRE

    van Minkelen, Rick

    2008-01-01

    Venous thrombosis (VT) is a multicausal disease that is caused by the interaction of both genetic and acquired risk factors. The aim of the studies described in this thesis was to identify novel genes or genomic regions that contribute to the susceptibility of VT. We used two different approaches to achieve this goal: the hypothesis-based candidate gene approach and the discovery-based genome-wide approach. The candidate genes investigated are factor VII-activating protease, coagulation facto...

  4. Hybrid genetic algorithm approach for selective harmonic control

    Energy Technology Data Exchange (ETDEWEB)

    Dahidah, Mohamed S.A. [Faculty of Engineering, Multimedia University, 63100, Jalan Multimedia-Cyberjaya, Selangor (Malaysia); Agelidis, Vassilios G. [School of Electrical and Information Engineering, The University of Sydney, NSW (Australia); Rao, Machavaram V. [Faculty of Engineering and Technology, Multimedia University, 75450, Jalan Ayer Keroh Lama-Melaka (Malaysia)

    2008-02-15

    The paper presents an optimal solution for a selective harmonic elimination pulse width modulated (SHE-PWM) technique suitable for a high power inverter used in constant frequency utility applications. The main challenge of solving the associated non-linear equations, which are transcendental in nature and, therefore, have multiple solutions, is the convergence, and therefore, an initial point selected considerably close to the exact solution is required. The paper discusses an efficient hybrid real coded genetic algorithm (HRCGA) that reduces significantly the computational burden, resulting in fast convergence. An objective function describing a measure of the effectiveness of eliminating selected orders of harmonics while controlling the fundamental, namely a weighted total harmonic distortion (WTHD) is derived, and a comparison of different operating points is reported. It is observed that the method was able to find the optimal solution for a modulation index that is higher than unity. The theoretical considerations reported in this paper are verified through simulation and experimentally on a low power laboratory prototype. (author)

  5. Hybrid genetic algorithm approach for selective harmonic control

    International Nuclear Information System (INIS)

    The paper presents an optimal solution for a selective harmonic elimination pulse width modulated (SHE-PWM) technique suitable for a high power inverter used in constant frequency utility applications. The main challenge of solving the associated non-linear equations, which are transcendental in nature and, therefore, have multiple solutions, is the convergence, and therefore, an initial point selected considerably close to the exact solution is required. The paper discusses an efficient hybrid real coded genetic algorithm (HRCGA) that reduces significantly the computational burden, resulting in fast convergence. An objective function describing a measure of the effectiveness of eliminating selected orders of harmonics while controlling the fundamental, namely a weighted total harmonic distortion (WTHD) is derived, and a comparison of different operating points is reported. It is observed that the method was able to find the optimal solution for a modulation index that is higher than unity. The theoretical considerations reported in this paper are verified through simulation and experimentally on a low power laboratory prototype

  6. Chemical Mixture Risk Assessment Additivity-Based Approaches

    Science.gov (United States)

    Powerpoint presentation includes additivity-based chemical mixture risk assessment methods. Basic concepts, theory and example calculations are included. Several slides discuss the use of "common adverse outcomes" in analyzing phthalate mixtures.

  7. Gradient Bundle Analysis: A Full Topological Approach to Chemical Bonding

    CERN Document Server

    Morgenstern, Amanda

    2016-01-01

    The "chemical bond" is a central concept in molecular sciences, but there is no consensus as to what a bond actually is. Therefore, a variety of bonding models have been developed, each defining the structure of molecules in a different manner with the goal of explaining and predicting chemical properties. This thesis describes the initial development of gradient bundle analysis (GBA), a chemical bonding model that creates a high resolution picture of chemical interactions within the charge density framework. GBA is based on concepts from the quantum theory of atoms in molecules (QTAIM), but uses a more complete picture of the topology and geometry of the electron charge density to understand and predict bonding interactions. Gradient bundles are defined as volumes bounded by zero-flux surfaces (ZFSs) in the gradient of the charge density with well-defined energies. The structure of gradient bundles provides an avenue for detecting the locations of valence electrons, which correspond to reactive regions in a ...

  8. Chemical-Engineering Approach for Evaluation of Vapour Permeation Data.

    Czech Academy of Sciences Publication Activity Database

    Sedláková, Zuzana; Morávková, Lenka; Vejražka, Jiří; Izák, Pavel

    Ozarow Mazowiecki: Nobell Compressing sp. z o.o, 2015 - (Kosinsky, K.; Urbanczyk, M.; Žerko, S.), E-026 ISBN N. [Euromembrane Conference 2015. Aachen (DE), 06.09.2015-10.09.2015] R&D Projects: GA MŠk(CZ) LD14094 Institutional support: RVO:67985858 Keywords : organic vapour permeation * membrane separation * chemical-engineering model Subject RIV: CI - Industrial Chemistry, Chemical Engineering

  9. Approaches to the evaluation of chemical-induced immunotoxicity.

    OpenAIRE

    Krzystyniak, K; Tryphonas, H; Fournier, M

    1995-01-01

    The immune system plays a crucial role in maintaining health; however, accumulating evidence indicates that this system can be the target for immunotoxic effects caused by a variety of chemicals including the environmental pollutants of polychlorinated biphenyls, chlorinated dibenzo-p-dioxins, pesticides, and heavy metals. Adverse chemical-induced immunomodulation, which is studied within the discipline of immunotoxicology, may be expressed either as immunosuppression/immunodepression or immu...

  10. Genetic algorithm based image binarization approach and its quantitative evaluation via pooling

    Science.gov (United States)

    Hu, Huijun; Liu, Ya; Liu, Maofu

    2015-12-01

    The binarized image is very critical to image visual feature extraction, especially shape feature, and the image binarization approaches have been attracted more attentions in the past decades. In this paper, the genetic algorithm is applied to optimizing the binarization threshold of the strip steel defect image. In order to evaluate our genetic algorithm based image binarization approach in terms of quantity, we propose the novel pooling based evaluation metric, motivated by information retrieval community, to avoid the lack of ground-truth binary image. Experimental results show that our genetic algorithm based binarization approach is effective and efficiency in the strip steel defect images and our quantitative evaluation metric on image binarization via pooling is also feasible and practical.

  11. Technical Efficiency of The Vietnam's Manufacture of Chemical and Chemical Products: A Dual Approach

    OpenAIRE

    Tran Ngo Thi Minh Tam

    2007-01-01

    This paper is on its way to estimate the technical efficiency (TE) level and identify the sources of technical inefficiency (TIE) of the Vietnam Manufacture of Chemicals and Chemical Products (MCCP) or the chemical industry, using the stochastic frontier cost function and the sample data of 95 MCCP's firms drawn from the Economic Census for Enterprises conducted by the General Statistic Office in 2002. The empirical results show that the mean TE of the industry is 1.50, implying that the cost...

  12. Maximizing lifetime of wireless sensor networks using genetic approach

    DEFF Research Database (Denmark)

    Wagh, Sanjeev; Prasad, Ramjee

    2014-01-01

    nodes are deployed in an inaccessible location for particular mission, it is difficult to exchange or recharge the nodes battery. Hence the important issues to design the sensor network for maximum time duration of network and also for low power operation of the nodes. The proposal is to select the...... cluster head intelligently using auction data of node i.e. its local battery power, topology strength and external battery support. The network lifetime is the centre focus of the research paper which explores intelligently selection of cluster head using auction based approach. The multi...

  13. FORMATION OF THE CONCEPT OF TRANSACTION: HISTORICAL-GENETIC APPROACH

    Directory of Open Access Journals (Sweden)

    Irina Valerievna Marushchak

    2016-04-01

    Full Text Available Evolution of the theory of transactions represents the difficult, uneven process including stages of metaforization, conceptualization and operatsionalization. From vague understanding of a role of transactions in division and cooperation of labour in society, economists have passed to measurement of transaction costs on micro- and macrolevels of economy. At the same time, the basic for institutionalism category of transaction remains insufficiently precisely and is still unstable and unambiguously certain, also its classifications are open for discussions.In article the analysis of various concepts of transactions is carried out, the corresponding approaches, their achievements and areas of discussions are allocated. It is revealed that during the development the theory of transactions has accepted a little unilateral character connected with the narrowed interpretation of transactions as market exchanges of property titles, and also their negative interpretations from positions of transaction costs. It is shown that transaction can be understood in a broad sense as an exchange of its parties of various actions; such broad approach allows to consider complexity and interdisciplinary nature of transactions. The transactional paradigm is considered as set of the concepts and theories united by the general focusing of the analysis on non-material aspects and elements of economic systems, including roles of transaction and economic relations. Within a transactional paradigm there is possible an accounting of those concepts which don’t belong to the theory of transaction costs, and also have other disciplinary nature.Purpose – systematization of evolution of views and approaches within the theory of transactions as fundamental components of the institutional and evolutionary economic theory.Methodology: methodology of research includes the descriptive, comparative and evolutionary analysis.Results: analysis of evolution of the transaction theory

  14. Protection against genetic hazards from environmental chemical mutagens: experience with ionizing radiation

    International Nuclear Information System (INIS)

    In radiation protection, the recurrent theme is, and always has been, dose limitation whether it is for occupational workers, individual members of the public or the population as a whole. The key words are 'dose' and 'limitation'. The quantitative system of dose limitation has been achieved because of a number of conceptual developments in our understanding of the mechanism of radiation action, development of radiation dosimetry, the accumulation of a vast body of quantitative information on dose-effect relationships and the effects of various biological and physical variables that affect these relationships of data on patterns and levels of exposures likely to be encountered to make estimates of the effects expected to result from such exposures, and balancing of risks to society against the benefits derived, the latter a matter of informed judgement. The philosophy has always been to avoid all unnecessary exposures and to limit the necessary exposures (justified by the benefits expected) to as low a level as reasonably achievable, social and economic factors being taken into acccount. The introduction of the concept that the system of dose limitation to the population should be based on genetic risks has stressed the need for careful planning to ensure that our genetic heritage is not endangered. Transfer of this knowledge to the field of chemical protection is discussed. (Auth.)

  15. Germ cell toxicity: significance in genetic and fertility effects of radiation and chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Oakberg, E.F.

    1983-01-01

    The response of the male and female to radiation and chemicals is different. Any loss of oocytes in the female cannot be replaced, and if severe enough, will result in a shortening of the reproductive span. In the male, a temporary sterile period may be induced owing to destruction of the differentiating spermatogonia, but the stem cells are the most resistant spermatogonial type, are capable of repopulating the seminiferous epithelium, and fertility usually returns. The response of both the male and female changes with development of the embryonic to the adult gonad, and with differentiation and maturation in the adult. The primordial germ cells, early oocytes, and differentiating spermatogonia of the adult male are unusually sensitive to the cytotoxic action of noxious agents, but each agent elicits a specific response owing to the intricate biochemical and physiological changes associated with development and maturation of the gametes. The relationship of germ cell killing to fertility is direct, and long-term fertility effects can be predicted from histological analysis of the gonads. The relationship to genetic effects, on the other hand, is indirect, and acts primarily by limiting the cell stages available for testing, by affecting the distribution of mitotically active stem cells among the different stages of the mitotic cycle, and thereby, changing both the type and frequency of genetic effects observed. 100 references, 38 figures, 7 tables.

  16. Chemical genetics reveals an RGS/G-protein role in the action of a compound.

    Directory of Open Access Journals (Sweden)

    Kevin Fitzgerald

    2006-04-01

    Full Text Available We report here on a chemical genetic screen designed to address the mechanism of action of a small molecule. Small molecules that were active in models of urinary incontinence were tested on the nematode Caenorhabditis elegans, and the resulting phenotypes were used as readouts in a genetic screen to identify possible molecular targets. The mutations giving resistance to compound were found to affect members of the RGS protein/G-protein complex. Studies in mammalian systems confirmed that the small molecules inhibit muscarinic G-protein coupled receptor (GPCR signaling involving G-alphaq (G-protein alpha subunit. Our studies suggest that the small molecules act at the level of the RGS/G-alphaq signaling complex, and define new mutations in both RGS and G-alphaq, including a unique hypo-adapation allele of G-alphaq. These findings suggest that therapeutics targeted to downstream components of GPCR signaling may be effective for treatment of diseases involving inappropriate receptor activation.

  17. Germ cell toxicity: significance in genetic and fertility effects of radiation and chemicals

    International Nuclear Information System (INIS)

    The response of the male and female to radiation and chemicals is different. Any loss of oocytes in the female cannot be replaced, and if severe enough, will result in a shortening of the reproductive span. In the male, a temporary sterile period may be induced owing to destruction of the differentiating spermatogonia, but the stem cells are the most resistant spermatogonial type, are capable of repopulating the seminiferous epithelium, and fertility usually returns. The response of both the male and female changes with development of the embryonic to the adult gonad, and with differentiation and maturation in the adult. The primordial germ cells, early oocytes, and differentiating spermatogonia of the adult male are unusually sensitive to the cytotoxic action of noxious agents, but each agent elicits a specific response owing to the intricate biochemical and physiological changes associated with development and maturation of the gametes. The relationship of germ cell killing to fertility is direct, and long-term fertility effects can be predicted from histological analysis of the gonads. The relationship to genetic effects, on the other hand, is indirect, and acts primarily by limiting the cell stages available for testing, by affecting the distribution of mitotically active stem cells among the different stages of the mitotic cycle, and thereby, changing both the type and frequency of genetic effects observed. 100 references, 38 figures, 7 tables

  18. Viable chemical approach for patterning nanoscale magnetoresistive random access memory

    International Nuclear Information System (INIS)

    A reactive ion etching process with alternating Cl2 and H2 exposures has been shown to chemically etch CoFe film that is an integral component in magnetoresistive random access memory (MRAM). Starting with systematic thermodynamic calculations assessing various chemistries and reaction pathways leading to the highest possible vapor pressure of the etch products reactions, the potential chemical combinations were verified by etch rate investigation and surface chemistry analysis in plasma treated CoFe films. An ∼20% enhancement in etch rate was observed with the alternating use of Cl2 and H2 plasmas, in comparison with the use of only Cl2 plasma. This chemical combination was effective in removing metal chloride layers, thus maintaining the desired magnetic properties of the CoFe films. Scanning electron microscopy equipped with energy-dispersive x-ray spectroscopy showed visually and spectroscopically that the metal chloride layers generated by Cl2 plasma were eliminated with H2 plasma to yield a clean etch profile. This work suggests that the selected chemistries can be used to etch magnetic metal alloys with a smooth etch profile and this general strategy can be applied to design chemically based etch processes to enable the fabrication of highly integrated nanoscale MRAM devices

  19. Viable chemical approach for patterning nanoscale magnetoresistive random access memory

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Taeseung; Kim, Younghee; Chen, Jack Kun-Chieh; Chang, Jane P., E-mail: jpchang@seas.ucla.edu [Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095 (United States)

    2015-03-15

    A reactive ion etching process with alternating Cl{sub 2} and H{sub 2} exposures has been shown to chemically etch CoFe film that is an integral component in magnetoresistive random access memory (MRAM). Starting with systematic thermodynamic calculations assessing various chemistries and reaction pathways leading to the highest possible vapor pressure of the etch products reactions, the potential chemical combinations were verified by etch rate investigation and surface chemistry analysis in plasma treated CoFe films. An ∼20% enhancement in etch rate was observed with the alternating use of Cl{sub 2} and H{sub 2} plasmas, in comparison with the use of only Cl{sub 2} plasma. This chemical combination was effective in removing metal chloride layers, thus maintaining the desired magnetic properties of the CoFe films. Scanning electron microscopy equipped with energy-dispersive x-ray spectroscopy showed visually and spectroscopically that the metal chloride layers generated by Cl{sub 2} plasma were eliminated with H{sub 2} plasma to yield a clean etch profile. This work suggests that the selected chemistries can be used to etch magnetic metal alloys with a smooth etch profile and this general strategy can be applied to design chemically based etch processes to enable the fabrication of highly integrated nanoscale MRAM devices.

  20. A network dynamics approach to chemical reaction networks

    Science.gov (United States)

    van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

    2016-04-01

    A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

  1. A network dynamics approach to chemical reaction networks

    NARCIS (Netherlands)

    van der Schaft, Abraham; Rao, S.; Jayawardhana, B.

    2016-01-01

    A treatment of chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a ve

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

    Science.gov (United States)

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

    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.

  3. Population-genetic approach to standardization of radiation and non-radiation factors

    International Nuclear Information System (INIS)

    Numerous studies demonstrate the importance of genetic predisposition in the development of wide range of pathologies and unfavorable effects caused by different factors. This prompts to account for genetic factors in the risk assessment of unfavorable effects. Current approaches used to solve this problem are far from perfect. On the one hand, recommendations on occupational selection bas ed on genetic signs are presently considered as human rights violation. On the other hand, to medically inform an individual with certain genetic characteristics about possible unfavorable health effects due to occupational hazard has little effect. Finally, a vast number of polymorphic genes in human genome (at least 30%) hampers accounting for all possible factors of genetic predisposition to the increasing number of environmental factors. Therefore, the current situation proves it appropriate to develop the new approach to account for genetic predisposition of individuals that would be free of flaws considered above. A possible basis for such an approach is the assessment of genotype specific relative risk (G.S.R.R.) that accounts for genetic predisposition (susceptibility) of individuals to the effects of unfavorable factors. The study used results from 65 studies. This effort was undertaken to study the association between 32 diseases and unfavorable effects and 17 genetic polymorphic systems. Data analysis included calculation of relative risk (R.R.) of specific diseases or effects development in individuals with different genotypes. Genotype-specific relative risk (G.S.R.R.) of diseases and unfavorable effects in individuals with 'sensitive' genotypes was calculated. Since about the third of genes in human genome are polymorphic, and therefore, a considerable number of genes can be involved in genetic predisposition of an individual to a specific unfavorable effect, an averaged G.S.R.R. of diseases and unfavorable effects was calculated for integral characteristics on

  4. Electrochemical approaches for chemical and biological analysis on Mars

    Science.gov (United States)

    Kounaves, Samuel P.

    2003-01-01

    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  5. Genetic improvement of long grain aromatic rices through mutation approach

    International Nuclear Information System (INIS)

    In the export market, the price of basmati rice is two to three times higher than non-basmati rice. Traditional tall basmati variety Taroari Basmati, followed by Basmati 370 has supremacy over other basmati rice due to their exclusive quality. The breeding efforts of Basmati rices have resulted in the development of improved varieties, such as Pusa Basmati 1, which currently occupies a large area in the basmati zone. However, the variety has now become highly susceptible to blast, which is causing severe yield losses. The present investigation deals with the development of non-lodging, high yielding, long grain aromatic rices, employing a mutation approach of gamma rays (γ) irradiation. Mutant lines were developed from three elite basmati cultivars, i.e. Basmati 370, Pusa Basmati 1 and Pakistan Basmati. A mutant line derived from Basmati 370, CR 2007-1(IET 17276), is found to be highly promising in the basmati growing areas of Haryana and Punjab in the multi location trials. This promising mutant line consistently shows significant yield superiority over Pusa Basmati (5.36%) and Taroari Basmati (64.04%) and has all the desirable basmati grain quality traits that are closer to Taroari Basmati. It is also resistant to rice neck blast, moderately resistant to brown spot and also to biotype 1 of rice gall midge. The other mutants developed under the study have also shown higher yield potential than Pusa Basmatil 1, the highest yielding basmati cultivar that is being currently grown, but their quality characteristics could not reach the standard of Basmati rice. (author)

  6. Genetic evaluation of popcorn families using a Bayesian approach via the independence chain algorithm

    Directory of Open Access Journals (Sweden)

    Marcos Rodovalho

    2014-11-01

    Full Text Available The objective of this study was to examine genetic parameters of popping expansion and grain yield in a trial of 169 halfsib families using a Bayesian approach. The independence chain algorithm with informative priors for the components of residual and family variance (inverse-gamma prior distribution was used. Popping expansion was found to be moderately heritable, with a posterior mode of h2 of 0.34, and 90% Bayesian confidence interval of 0.22 to 0.44. The heritability of grain yield (family level was moderate (h2 = 0.4 with Bayesian confidence interval of 0.28 to 0.49. The target population contains sufficient genetic variability for subsequent breeding cycles, and the Bayesian approach is a useful alternative for scientific inference in the genetic evaluation of popcorn.

  7. National Ignition Facility: Impacts of chemical accidents and comparison of chemical and radiological accident approaches

    International Nuclear Information System (INIS)

    An environmental assessment was conducted to estimate potential impacts or consequences associated with constructing and operating the proposed National Ignition Facility (NIF). The multidisciplinary assessment covered topics ranging from radiological and chemical health and safety to socioeconomic and land-use issues. The impacts of five chemical accidents that could occur at NIF are compared, and the extent of their consequences for workers and off-site populations are discussed. Each of the five accident scenarios was modeled by a chemical release and dispersion model with a toxicological criterion for evaluating potential irreversible human health effects. Results show that most of the chemical release scenarios considered will not impair the general public in taking protective actions in the event of an accidental release. The two exceptions are the mercury release (equipment failure) scenarios for the conceptual design and the enhanced design. In general, the predicted maximum threat zones are significantly less than the distance to the point of nearest public access

  8. Tomato Derived Polysaccharides for Biotechnological Applications: Chemical and Biological Approaches

    Directory of Open Access Journals (Sweden)

    Barbara Nicolaus

    2008-06-01

    Full Text Available Recent studies concerning the isolation and purification of exopolysaccharides from suspension-cultured tomato (Lycopersicon esculentum L. var. San Marzano cells and the description of a simple, rapid and low environmental impact method with for obtaining polysaccharides from solid tomato-processing industry wastes are reported. Their chemical composition, rheological properties and partial primary structure were determined on the basis of spectroscopic analyses (UV, IR, GC-MS, 1H-, 13C-NMR. Moreover, the anticytotoxic activities of exopolysaccharides obtained from cultured tomato cells were tested in a brine shrimp bioassay and the preparation of biodegradable film by chemical processing of polysaccharides from solid tomato industry waste was also reported.

  9. Environmental Contamination Genetic Consequences Monitoring on the Former Semipalatinsk Test Site: General Approach

    International Nuclear Information System (INIS)

    genetic monitoring of natural populations of plants and animals and the theoretic approach for their fulfillment. We also consider the main issues of research work on assessment and forecast of the remote genetic consequences of nuclear tests at STS: 1) assessment of the environmental radiation situation; determination of the indicator species of plants and animals and the criteria encompassing the different levels from the molecular one through the genetic to the population one; 2) study of the dose dependence of the genetic effects under the chronic ionizing radiation; 3) analysis of mutation process dynamics in the following generations of population under various exposure condition; 4) study of the possible ways of population adaptation to the chronic impact of various radiation doses; 5) analysis of relation between different genetic changes in exposed population and ecology alterations, etc

  10. BARC 2009 Annual Report TO NC-1037: Genetic and functional genomic approaches to improve production and quality of pork

    Science.gov (United States)

    The NC-1037 project addresses “Genetic and functional genomic approaches to improve production and quality of pork.” It has 2 objectives: 1) Further understand the dynamic genetic mechanisms that influence production efficiency and quality of pork; and 2) Discover genetic mechanisms controlling anim...

  11. Chemical named entities recognition: a review on approaches and applications

    OpenAIRE

    Eltyeb, Safaa; Salim, Naomie

    2014-01-01

    The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to “text mine” these extracted data and determine contextual relationships helps research scientists, particularly those in drug developmen...

  12. AMAZON RAINFOREST COSMETICS: CHEMICAL APPROACH FOR QUALITY CONTROL

    OpenAIRE

    Mariko Funasaki; Hileia dos Santos Barroso; Valdelira Lia Araújo Fernandes; Ingrid Sabino Menezes

    2016-01-01

    The market for natural cosmetics featuring ingredients derived from Amazon natural resources is growing worldwide. However, there is neither enough scientific basis nor quality control of these ingredients. This paper is an account of the chemical constituents and their biological activities of fourteen Amazonian species used in cosmetic industry, including açaí (Euterpe oleracea), andiroba (Carapa guianensis), bacuri (Platonia insignis), Brazil nut (Bertholletia excelsa), buriti (Mauritia vi...

  13. A Genetic Algorithm Approach for Group Formation in Collaborative Learning Considering Multiple Student Characteristics

    Science.gov (United States)

    Moreno, Julian; Ovalle, Demetrio A.; Vicari, Rosa M.

    2012-01-01

    Considering that group formation is one of the key processes in collaborative learning, the aim of this paper is to propose a method based on a genetic algorithm approach for achieving inter-homogeneous and intra-heterogeneous groups. The main feature of such a method is that it allows for the consideration of as many student characteristics as…

  14. Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century

    International Nuclear Information System (INIS)

    Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization of drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment

  15. Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century

    Energy Technology Data Exchange (ETDEWEB)

    Mortensen, Holly M., E-mail: mortensen.holly@epa.gov [Office of Research and Development, US Environmental Protection Agency, National Center for Computational Toxicology, US EPA, 109 TW Alexander Dr., Mailcode B205-01, Research Triangle Park, NC 27711 (United States); Euling, Susan Y. [Office of Research and Development, US Environmental Protection Agency, National Center for Environmental Assessment, US EPA, 1200 Pennsylvania Ave., NW, Mail Code 8623P, Washington, DC 20460 (United States)

    2013-09-15

    Response to environmental chemicals can vary widely among individuals and between population groups. In human health risk assessment, data on susceptibility can be utilized by deriving risk levels based on a study of a susceptible population and/or an uncertainty factor may be applied to account for the lack of information about susceptibility. Defining genetic susceptibility in response to environmental chemicals across human populations is an area of interest in the NAS' new paradigm of toxicity pathway-based risk assessment. Data from high-throughput/high content (HT/HC), including -omics (e.g., genomics, transcriptomics, proteomics, metabolomics) technologies, have been integral to the identification and characterization of drug target and disease loci, and have been successfully utilized to inform the mechanism of action for numerous environmental chemicals. Large-scale population genotyping studies may help to characterize levels of variability across human populations at identified target loci implicated in response to environmental chemicals. By combining mechanistic data for a given environmental chemical with next generation sequencing data that provides human population variation information, one can begin to characterize differential susceptibility due to genetic variability to environmental chemicals within and across genetically heterogeneous human populations. The integration of such data sources will be informative to human health risk assessment.

  16. At the brink of supercoloniality: genetic, behavioral and chemical assessments of population structure of the desert ant Cataglyphis niger

    Directory of Open Access Journals (Sweden)

    Maya eSaar

    2014-05-01

    Full Text Available The nesting habits of ants play an important role in structuring ant populations. They vary from monodomy, a colony occupies a single nest, via polydomy, a colony occupies multiple adjacent nests, to supercoloniality, a colony spans over large territories comprising dozen to thousands nests without having any boundaries. The population structure of the desert ant Cataglyphis niger, previously considered to form supercolonies, was studied using genetic, chemical and behavioral tools in plots of 50x50 meters at two distinct populations. At the Palmahim site, the plot comprised 15 nests that according to the genetic analysis constituted three colonies. Likewise at the Rishon Leziyyon site 14 nests constituted 5 genetic colonies. In both sites, both chemical analysis and the behavioral (aggression tests confirmed the colony genetic architecture. The behavioral tests also revealed that aggression between colonies within a population was higher than that exhibited between colonies of different populations, suggesting the occurrence of the nasty neighbor phenomenon. In contrast to supercolony structure previously reported in another population of this species, the presently studied populations were composed of polydomous colonies. However, both the genetic and chemical data revealed that the inter-colonial differences between sites were larger than those within site, suggesting some within-site population viscosity. Thus, C. niger exhibits flexible nesting characteristics, from polydomy to supercoloniality, and can be considered at the brink of supercoloniality. We attribute the differences in population structure among sites to the intensity of intraspecific competition.

  17. Harmonization of risk management approaches: radiation and chemical exposures

    Energy Technology Data Exchange (ETDEWEB)

    Srinivasan, P. [Bhabha Atomic Research Centre, Radiation Safety Systems Div., Mumbai (India)

    2006-07-01

    Assessment of occupational and public risk from the environmental pollutants like chemicals, radiation, etc demands that the effects be considered not only from each individual pollutant, but from the combination of all the pollutants. An integrated risk assessment system needs to be in place to have an overall risk perspective for the benefit of policy makers and decision takers to try to achieve risk reduction in totality. The basis for risk-based radiation dose limits is derived from epidemiological studies, which provide a rich source of data largely unavailable to chemical risk assessors. In addition, use of the principle of optimization as expressed in the ALARA concept has resulted in a safety culture, which is much more than just complying with stipulated limits. The conservative hypothesis of no-threshold dose-effect relation (ICRP) is universally assumed. The end-points and the severity of different classes of pollutants and even different pollutants in a same class vary over a wide range. Hence, it is difficult to arrive at a quantitative value for the net detriment that weighs the various types of end-points and various classes of pollutants. Once the risk due to other pollutants is quantified by some acceptable methodology, it can be expressed in terms of the Risk Equivalent Radiation Dose (R.E.R.D.) for easy comparison with options involving radiation exposure. This paper is an effort to use to quantify and present the risk due to exposure to chemicals and radiation in a common scale for the purpose of easy comparison to facilitate decision taking. (authors)

  18. Harmonization of risk management approaches: radiation and chemical exposures

    International Nuclear Information System (INIS)

    Assessment of occupational and public risk from the environmental pollutants like chemicals, radiation, etc demands that the effects be considered not only from each individual pollutant, but from the combination of all the pollutants. An integrated risk assessment system needs to be in place to have an overall risk perspective for the benefit of policy makers and decision takers to try to achieve risk reduction in totality. The basis for risk-based radiation dose limits is derived from epidemiological studies, which provide a rich source of data largely unavailable to chemical risk assessors. In addition, use of the principle of optimization as expressed in the ALARA concept has resulted in a safety culture, which is much more than just complying with stipulated limits. The conservative hypothesis of no-threshold dose-effect relation (ICRP) is universally assumed. The end-points and the severity of different classes of pollutants and even different pollutants in a same class vary over a wide range. Hence, it is difficult to arrive at a quantitative value for the net detriment that weighs the various types of end-points and various classes of pollutants. Once the risk due to other pollutants is quantified by some acceptable methodology, it can be expressed in terms of the Risk Equivalent Radiation Dose (R.E.R.D.) for easy comparison with options involving radiation exposure. This paper is an effort to use to quantify and present the risk due to exposure to chemicals and radiation in a common scale for the purpose of easy comparison to facilitate decision taking. (authors)

  19. Probabilistic Approach to Risk Analysis of Chemical Spills at Sea

    Institute of Scientific and Technical Information of China (English)

    Magda Bogalecka; Krzysztof Kolowrocki

    2006-01-01

    Risk analysis of chemical spills at sea and their consequences for sea environment are discussed. Mutual interactions between the process of the sea accident initiating events, the process of the sea environment threats, and the process of the sea environment degradation are investigated. To describe these three particular processes, the separate semi-Markov models are built. Furthermore, these models are jointed into one general model of these processes interactions.Moreover, some comments on the method for statistical identification of the considered models are proposed.

  20. Early quark production and approach to chemical equilibrium

    Science.gov (United States)

    Gelfand, D.; Hebenstreit, F.; Berges, J.

    2016-04-01

    We perform real-time lattice simulations of out-of-equilibrium quark production in non-Abelian gauge theory in 3 +1 dimensions. Our simulations include the backreaction of quarks onto the dynamical gluon sector, which is particularly relevant for strongly correlated quarks. We observe fast isotropization and universal behavior of quarks and gluons at weak coupling and establish a quantitative connection to previous pure glue results. In order to understand the strongly correlated regime, we perform simulations for a large number of flavors and compare them to those obtained with two light quark flavors. By doing this we are able to provide estimates of the chemical equilibration time.

  1. Terrorist threat, chemical, biological, radiological, nuclear medical approach

    International Nuclear Information System (INIS)

    The different aspects linked to the use of nuclear, radiological, biological and or chemical weapons are gathered in this work. They concern history, fundamental aspect, diagnosis, therapy and prevention. The part devoted to the nuclear aspect concern the accidents in relation with ionizing radiations, the radiation syndrome, the contribution and limits of dosimetry, the treatment of medullary aplasia, the evaluation and treatment of an internal contamination, new perspectives on the use of cytokine for the treatment of accidental irradiated persons, alternative to the blood transfusion. (N.C.)

  2. Germ cell toxicity: significance in genetic and fertility effects of radiation and chemicals

    International Nuclear Information System (INIS)

    The primordial germ cells originate in the region of the caudal end of the primitive streak, root of the allantois, and yolk sac splanchnopleure, and migrate to the gonadal ridges where they divide to form the oogonia of the female and gonocytes of the male. In the female, the transition to oocytes occurs in utero, and the female mammal is born with a finite number of oocytes that cannot be replaced. By contrast, the gonocytes of the male initiate divisions soon after birth to form the spermatogonial stem cells, which persist throughout reproductive life of the male and are capable of regenerating the seminiferous epithelium after injury. As a result of these basic differences in gametogenesis, the response of the male and female to radiation and chemicals is different. The response of both the male and female changes with development of the embryonic to the adult gonad, and with differentiation and maturation in the adult. The primordial germ cells, early oocytes, and differentiating spermatogonia of the adult male are unusually sensitive to the cytotoxic action of noxious agents, but each agent elicits a specific response owing to the intricate biochemical and physiological changes associated with development and maturation of the gametes. The relationship of germ cell killing to fertility is direct, and long-term fertility effects can be predicted from histological analysis of the gonads. The relationship to genetic effects, on the other hand, is indirect, and acts primarily by limiting the cell stages available for testing, by affecting the distribution of mitotically active stem cells among the different stages of the mitotic cycle, and thereby changing both the type and frequency of genetic effects observed

  3. A fuzzy genetic approach for network reconfiguration to enhance voltage stability in radial distribution systems

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, N.C. [Faculty of Engineering and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450 Melaka (Malaysia); Prasad, K. [Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450 Melaka (Malaysia)

    2006-11-15

    This paper presents a fuzzy genetic approach for reconfiguration of radial distribution systems (RDS) so as to maximize the voltage stability of the network for a specific set of loads. The network reconfiguration involves a mechanism for selection of the best set of branches to be opened, one from each loop, such that the reconfigured RDS possesses desired performance characteristics. This discrete solution space is better handled by the proposed scheme, which maximizes a suitable optimizing function (computed using two different approaches). In the first approach, this function is chosen as the average of a voltage stability index of all the buses in the RDS, while in the second approach, the complete RDS is reduced to a two bus equivalent system and the optimizing function is the voltage stability index of this reduced two bus system. The fuzzy genetic algorithm uses a suitable coding and decoding scheme for maintaining the radial nature of the network at every stage of genetic evolution, and it also uses a fuzzy rule based mutation controller for efficient search of the solution space. This method, tested on 69 bus and 33 bus RDSs, shows promising results for the both approaches. It is also observed that the network losses are reduced when the voltage stability is enhanced by the network reconfiguration. (author)

  4. A fuzzy genetic approach for network reconfiguration to enhance voltage stability in radial distribution systems

    International Nuclear Information System (INIS)

    This paper presents a fuzzy genetic approach for reconfiguration of radial distribution systems (RDS) so as to maximize the voltage stability of the network for a specific set of loads. The network reconfiguration involves a mechanism for selection of the best set of branches to be opened, one from each loop, such that the reconfigured RDS possesses desired performance characteristics. This discrete solution space is better handled by the proposed scheme, which maximizes a suitable optimizing function (computed using two different approaches). In the first approach, this function is chosen as the average of a voltage stability index of all the buses in the RDS, while in the second approach, the complete RDS is reduced to a two bus equivalent system and the optimizing function is the voltage stability index of this reduced two bus system. The fuzzy genetic algorithm uses a suitable coding and decoding scheme for maintaining the radial nature of the network at every stage of genetic evolution, and it also uses a fuzzy rule based mutation controller for efficient search of the solution space. This method, tested on 69 bus and 33 bus RDSs, shows promising results for the both approaches. It is also observed that the network losses are reduced when the voltage stability is enhanced by the network reconfiguration

  5. Gene Prioritization for Imaging Genetics Studies Using Gene Ontology and a Stratified False Discovery Rate Approach

    Science.gov (United States)

    Patel, Sejal; Park, Min Tae M.; Chakravarty, M. Mallar; Knight, Jo

    2016-01-01

    Imaging genetics is an emerging field in which the association between genes and neuroimaging-based quantitative phenotypes are used to explore the functional role of genes in neuroanatomy and neurophysiology in the context of healthy function and neuropsychiatric disorders. The main obstacle for researchers in the field is the high dimensionality of the data in both the imaging phenotypes and the genetic variants commonly typed. In this article, we develop a novel method that utilizes Gene Ontology, an online database, to select and prioritize certain genes, employing a stratified false discovery rate (sFDR) approach to investigate their associations with imaging phenotypes. sFDR has the potential to increase power in genome wide association studies (GWAS), and is quickly gaining traction as a method for multiple testing correction. Our novel approach addresses both the pressing need in genetic research to move beyond candidate gene studies, while not being overburdened with a loss of power due to multiple testing. As an example of our methodology, we perform a GWAS of hippocampal volume using both the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA2) and the Alzheimer's Disease Neuroimaging Initiative datasets. The analysis of ENIGMA2 data yielded a set of SNPs with sFDR values between 10 and 20%. Our approach demonstrates a potential method to prioritize genes based on biological systems impaired in a disease. PMID:27092072

  6. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection.

    Science.gov (United States)

    Thounaojam, Dalton Meitei; Khelchandra, Thongam; Singh, Kh Manglem; Roy, Sudipta

    2016-01-01

    This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter. PMID:27127500

  7. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection

    Science.gov (United States)

    Thounaojam, Dalton Meitei; Khelchandra, Thongam; Singh, Kh. Manglem; Roy, Sudipta

    2016-01-01

    This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter.

  8. New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach

    Czech Academy of Sciences Publication Activity Database

    Petretto, E.; Bottolo, L.; Langley, S. R.; Heinig, M.; McDermott-Roe, Ch.; Sarwar, R.; Pravenec, Michal; Hübner, N.; Aitman, T. J.; Cook, S.A.; Richardson, S.

    2010-01-01

    Roč. 6, č. 4 (2010), e1000737. ISSN 1553-734X R&D Projects: GA ČR(CZ) GA301/08/0166; GA MŠk(CZ) 1M0520; GA ČR GAP301/10/0290 Grant ostatní: EC(XE) LSHG-CT-2005-019015; Fondation Leducq(FR) 06 CVD 03 Institutional research plan: CEZ:AV0Z50110509 Keywords : expression profiles * Bayesian multi- tissue approach * genetical genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.515, year: 2010

  9. New approach for direct chemical synthesis of hexagonal Co nanoparticles

    Science.gov (United States)

    Abel, Frank M.; Tzitzios, Vasilis; Hadjipanayis, George C.

    2016-02-01

    In this paper, we explore the possibility of producing hexagonal Cobalt nanoparticles, with high saturation magnetization by direct chemical synthesis. The nanoparticles were synthesized by reduction of anhydrous cobalt (II) chloride by NaBH4 in tetraglyme at temperatures in the range of 200-270 °C under a nitrogen-hydrogen atmosphere. The reactions were done at high temperatures to allow for the formation of as-made hexagonal cobalt. The size of the particles was controlled by the addition of different surfactants. The best magnetic properties so far were obtained on spherical hexagonal Co nanoparticles with an average size of 45 nm, a saturation magnetization of 143 emu/g and coercivity of 500 Oe. the saturation magnetization and coercivity were further improved by annealing the Co nanoparticles leading to saturation magnetization of 160 emu/g and coercivity of 540 Oe.

  10. The Trouble with Chemical Energy: Why Understanding Bond Energies Requires an Interdisciplinary Systems Approach

    OpenAIRE

    Cooper, Melanie M.; Klymkowsky, Michael W.

    2013-01-01

    Helping students understand “chemical energy” is notoriously difficult. Many hold inconsistent ideas about what energy is, how and why it changes during the course of a chemical reaction, and how these changes are related to bond energies and reaction dynamics. There are (at least) three major sources for this problem: 1) the way biologists talk about chemical energy (which is also the way we talk about energy in everyday life); 2) the macroscopic approach to energy concepts that is common in...

  11. Supervised extensions of chemography approaches: case studies of chemical liabilities assessment

    OpenAIRE

    Ovchinnikova, Svetlana I; Bykov, Arseniy A; Tsivadze, Aslan Yu.; Dyachkov, Evgeny P; Kireeva, Natalia V

    2014-01-01

    Chemical liabilities, such as adverse effects and toxicity, play a significant role in modern drug discovery process. In silico assessment of chemical liabilities is an important step aimed to reduce costs and animal testing by complementing or replacing in vitro and in vivo experiments. Herein, we propose an approach combining several classification and chemography methods to be able to predict chemical liabilities and to interpret obtained results in the context of impact of structural chan...

  12. Neuro-genetic hybrid approach for the solution of non-convex economic dispatch problem

    International Nuclear Information System (INIS)

    ED (Economic Dispatch) is non-convex constrained optimization problem, and is used for both on line and offline studies in power system operation. Conventionally, it is solved as convex problem using optimization techniques by approximating generator input/output characteristic. Curves of monotonically increasing nature thus resulting in an inaccurate dispatch. The GA (Genetic Algorithm) has been used for the solution of this problem owing to its inherent ability to address the convex and non-convex problems equally. This approach brings the solution to the global minimum region of search space in a short time and then takes longer time to converge to near optimal results. GA based hybrid approaches are used to fine tune the near optimal results produced by GA. This paper proposes NGH (Neuro Genetic Hybrid) approach to solve the economic dispatch with valve point effect. The proposed approach combines the GA with the ANN (Artificial Neural Network) using SI (Swarm Intelligence) learning rule. The GA acts as a global optimizer and the neural network fine tunes the GA results to the desired targets. Three machines standard test system has been tested for validation of the approach. Comparing the results with GA and NGH model based on back-propagation learning, the proposed approach gives contrast improvements showing the promise of the approach. (author)

  13. A genetic-algorithm-based neutral network approach for radioactive activity prediction

    International Nuclear Information System (INIS)

    In this paper, a genetic-algorithm-based artificial neural network (GAANN) model radioactivity prediction is proposed, which is verified by measuring results from Long Range Alpha Detector (LRAD). GAANN can integrate capabilities of approximation of Artificial Neural Networks (ANN) and of global optimization of Genetic Algorithms (GA) so that the hybrid model can enhance capability of generalization and prediction accuracy, theoretically. With this model, both the number of hidden nodes and connection weights matrix in ANN are optimized using genetic operation. The real data sets are applied to the introduced method and the results are discussed and compared with the traditional Back Propagation (BP) neural network, showing the feasibility and validity of the proposed approach. (authors)

  14. Human genetic marker for resistance to radiations and chemicals. 1997 annual progress report

    International Nuclear Information System (INIS)

    'The specific aims listed in the original application will essentially be pursued as indicated. The major goal of the grant is to characterize a human homologue of the fission yeast Schizosaccharomyces pombe rad9 checkpoint control, radioresistance and chemoresistance gene, which is called HRAD9. The purpose is to gain information about the gene, including its structure and function, such that it can potentially be developed as a human genetic marker indicative of hypersensitivity to the deleterious effects associated with exposure to radiations or certain chemicals. The specific aims are divided into two major sections. The first section includes experiments designed to characterize the HRAD9 gene at the molecular level. Specifically, the genomic version of the gene will be isolated and its DNA sequence determined, in vitro mutagenesis will be used to assess structure/function relationships, and expression in cells and tissues will be examined. The second major set of aims focuses on determining the role of HRAD9 in radio/chemoresponsiveness and cancer. For this aim, human HRAD9 mutants will be constructed and characterized. In addition, the status of HRAD9 in cancer cells and tissues will be assessed.'

  15. Tactical approach to maneuvering within the chemical contamination labyrinth

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, T.W. [Department of Energy, Oak Ridge, TN (United States)

    1990-12-31

    The Department of Energy (DOE) recognized the need and accepts the responsibility for understanding the reality and mitigating the consequence of the complex chemical contamination legacy it inherited as well as controlling, reducing, and eliminating extant emissions and effluents. The key to maneuvering through this complicated and multifaceted labyrinth of concerns, from which a meaningful, high quality, and cost-effective restoration/mitigation machine is then set in motions, is the ability to perform accurate, factual, and explicit health and environmental/ecological risk assessments. Likewise, the common denominator for carrying out this essential task is to have access to comprehensive and reliable data of known quality with which to perform those analyses. DOE is committed to identifying the data universe; to technically scrutinize and ensure the quality of that data; to develop efficient and cost-effective means to maximize the handling, utilization, and sharing of that universe; and to undertake those assessments. DOE views this as an effort that can only be accomplished through a merging of the technical excellence that exists within federal and state agencies, academia, and industry. The task at hand is so large that only by integrating that intelligence base can we hope to accomplish the goals of establishing meaningful standards, developing functional and effective solutions, and providing quality guidance at a national scale.

  16. Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus).

    Science.gov (United States)

    Ahrens, Collin W; James, Elizabeth A

    2016-05-01

    Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity. PMID:26865733

  17. Kinetics of methane fermentation yield in biogas reactors: Genetic variation and association with chemical composition in maize

    International Nuclear Information System (INIS)

    Maize (Zea mays L.) is the most competitive crop for methane production in Germany. Methane fermentation yield per unit of dry matter (MFY) is a determinant of methane yield, but little information is available on this trait. Our objectives were to investigate the kinetics of MFY during fermentation of maize, estimate quantitative-genetic parameters for different traits related to MFY and examine the relationship of MFY with chemical composition and silage quality. Whole-plant material of 16 inbreds and their 32 testcrosses was analyzed for MFY over 35 days of fermentation using a discontinuous laboratory assay. Data were also generated on chemical composition and in vitro digestible organic matter (IVDOM). Significant genotypic variances and high heritabilities were observed for MFY at early fermentation stages (up to 5 days) probably due to different concentrations of easily degradable chemical components. However, genotypic variances and heritability of MFY reduced as fermentation progressed, because of complete or partial degradation of all chemical components. Further, there were strong correlations of MFY with chemical components at early fermentation stages but not at later stages. Therefore, MFY at later stages, which is closer to potential MFY, does not seem to be amenable to selection. High heritability of IVDOM and its strong correlation with MFY in testcrosses indicated its possible use for preliminary or indirect selection. Keeping in view the magnitude of genetic variance that was low for MFY and high for dry matter yield (DMY), the other component of methane yield, more emphasis on breeding for DMY seems appropriate. -- Highlights: ► We investigated methane fermentation yield (MFY) of diverse germplasm of maize. ► The kinetics of MFY and its correlations with chemical composition were examined. ► Genetic variance and heritability for MFY decreased with fermentation time. ► Complete fermentation (35 d) reduced correlations of MFY with chemical

  18. Use of Genetic algorithm based approaches in scheduling of FMS: A Review

    Directory of Open Access Journals (Sweden)

    Hameshbabu Nanvala

    2011-03-01

    Full Text Available Scheduling in an FMS environment is more complex and difficult than in a conventional manufacturing environment. Therefore, determining an optimal schedule and controlling an FMS is considered a difficult task. To achieve high performance for an FMS, a good scheduling system should make a right decision at a right time according to system conditions. In recent years, the use of Meta heuristic based approaches sch as Tabu Search, Simulated Annealing and genetic algorithms increased for scheduling in a flexible manufacturing system (FMS. These ,do not guarantee to find an optimal schedule, but have the ability to find near to optimum solutions in a short time. This work presents a review on use of genetic algorithms based approaches in scheduling of flexible manufacturing systems.

  19. An integrative systems genetics approach reveals potential causal genes and pathways related to obesity

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Zhernakova, Daria V.; Westra, Harm-Jan; Cirera Salicio, Susanna; Fredholm, Merete; Franke, Lude; Kadarmideen, Haja

    2015-01-01

    BACKGROUND: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the...... porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. METHODS: Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential...... expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected...

  20. Neutron spectrometry and dosimetry based on a new approach called Genetic Artificial Neural Networks

    International Nuclear Information System (INIS)

    Artificial Neural Networks and Genetic Algorithms are two relatively young research areas that were subject to a steadily growing interest during the past years. The structure of a neural network is a significant contributing factor to its performance and the structure is generally heuristically chosen. The use of evolutionary algorithms as search techniques has allowed different properties of neural networks to be evolved. This paper focuses on the intersection on neural networks and evolutionary computation, namely on how evolutionary algorithms can be used to assist neural network design and training, as a novel approach. In this research, a new evolvable artificial neural network modelling approach is presented, which utilizes an optimization process based on the combination of genetic algorithms and artificial neural networks, and is applied in the design of a neural network, oriented to solve the neutron spectrometry and simultaneous dosimetry problems, using only the count rates measured with a Bonner spheres spectrometer system as entrance data. (author)

  1. GENETIC ALGORITHM BASED HYBRID APPROACH FOR CLUSTERING TIME SERIES FINANCIAL DATA

    Directory of Open Access Journals (Sweden)

    Chandrika.J

    2014-08-01

    Full Text Available Stock market data is a high dimensional time series financial data that poses unique computational challenges. Stock data is variable in terms of time, predicting the future trend of the prices is a challenging task. The factors that influence the predictability of stock data cannot be judged as the same factors may or may not influence the value of the stock all the time. We propose a data mining approach for the prediction of the movement of stock market. It includes using the genetic algorithm for pre processing and a hybrid clustering approach of Hierarchical clustering and Fuzzy C-Means for clustering. The genetic algorithm helps in dimensionality reduction and clustering helps to create feature vectors that help in prediction.

  2. Chemical Genetics of Rapamycin-Insensitive TORC2 in S. cerevisiae

    Directory of Open Access Journals (Sweden)

    Joseph I. Kliegman

    2013-12-01

    Full Text Available Current approaches for identifying synergistic targets use cell culture models to see if the combined effect of clinically available drugs is better than predicted by their individual efficacy. New techniques are needed to systematically and rationally identify targets and pathways that may be synergistic targets. Here, we created a tool to screen and identify molecular targets that may synergize with new inhibitors of target of rapamycin (TOR, a conserved protein that is a major integrator of cell proliferation signals in the nutrient-signaling pathway. Although clinical results from TOR complex 1 (TORC1-specific inhibition using rapamycin analogs have been disappointing, trials using inhibitors that also target TORC2 have been promising. To understand this increased therapeutic efficacy and to discover secondary targets for combination therapy, we engineered Tor2 in S. cerevisiae to accept an orthogonal inhibitor. We used this tool to create a chemical epistasis miniarray profile (ChE-MAP by measuring interactions between the chemically inhibited Tor2 kinase and a diverse library of deletion mutants. The ChE-MAP identified known TOR components and distinguished between TORC1- and TORC2-dependent functions. The results showed a TORC2-specific interaction with the pentose phosphate pathway, a previously unappreciated TORC2 function that suggests a role for the complex in balancing the high energy demand required for ribosome biogenesis.

  3. An Alternative Educational Approach for an Inorganic Chemistry Laboratory Course in Industrial and Chemical Engineering

    Science.gov (United States)

    Garces, Andres; Sanchez-Barba, Luis Fernando

    2011-01-01

    We describe an alternative educational approach for an inorganic chemistry laboratory module named "Experimentation in Chemistry", which is included in Industrial Engineering and Chemical Engineering courses. The main aims of the new approach were to reduce the high levels of failure and dropout on the module and to make the content match the…

  4. A New Software Reliability Growth Model: Genetic-Programming-Based Approach

    OpenAIRE

    Zainab ALRahamneh; Mohammad Reyalat; Alaa F. Sheta; Sulieman Bani-Ahmad; Saleh Al-Oqeili

    2011-01-01

    A variety of Software Reliability Growth Models (SRGM) have been presented in literature. These models suffer many problems when handling various types of project. The reason is; the nature of each project makes it difficult to build a model which can generalize. In this paper we propose the use of Genetic Programming (GP) as an eVolutionary computation approach to handle the software reliability modeling problem. GP deals with one of the key issues in computer science which is called automat...

  5. TNFRSF13B Genetic variability an anthropological - evolutionary approach to Biomedical Research

    OpenAIRE

    Sazzini, Marco

    2009-01-01

    In the recent years TNFRSF13B coding variants have been implicated by clinical genetics studies in Common Variable Immunodeficiency (CVID), the most common clinically relevant primary immunodeficiency in individuals of European ancestry, but their functional effects in relation to the development of the disease have not been entirely established. To examine the potential contribution of such variants to CVID, the more comprehensive perspective of an evolutionary approach was applied in this s...

  6. Method of transient identification based on a possibilistic approach, optimized by genetic algorithm

    International Nuclear Information System (INIS)

    This work develops a method for transient identification based on a possible approach, optimized by Genetic Algorithm to optimize the number of the centroids of the classes that represent the transients. The basic idea of the proposed method is to optimize the partition of the search space, generating subsets in the classes within a partition, defined as subclasses, whose centroids are able to distinguish the classes with the maximum correct classifications. The interpretation of the subclasses as fuzzy sets and the possible approach provided a heuristic to establish influence zones of the centroids, allowing to achieve the 'don't know' answer for unknown transients, that is, outside the training set. (author)

  7. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

    KAUST Repository

    Klingbeil, Guido

    2012-02-01

    We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimize data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximizes parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie [14]. In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system\\'s size. © 2006 IEEE.

  8. Genetic algorithm learning as a robust approach to RNA editing site prediction

    Directory of Open Access Journals (Sweden)

    Gopal Shuba

    2006-03-01

    Full Text Available Abstract Background RNA editing is one of several post-transcriptional modifications that may contribute to organismal complexity in the face of limited gene complement in a genome. One form, known as C → U editing, appears to exist in a wide range of organisms, but most instances of this form of RNA editing have been discovered serendipitously. With the large amount of genomic and transcriptomic data now available, a computational analysis could provide a more rapid means of identifying novel sites of C → U RNA editing. Previous efforts have had some success but also some limitations. We present a computational method for identifying C → U RNA editing sites in genomic sequences that is both robust and generalizable. We evaluate its potential use on the best data set available for these purposes: C → U editing sites in plant mitochondrial genomes. Results Our method is derived from a machine learning approach known as a genetic algorithm. REGAL (RNA Editing site prediction by Genetic Algorithm Learning is 87% accurate when tested on three mitochondrial genomes, with an overall sensitivity of 82% and an overall specificity of 91%. REGAL's performance significantly improves on other ab initio approaches to predicting RNA editing sites in this data set. REGAL has a comparable sensitivity and higher specificity than approaches which rely on sequence homology, and it has the advantage that strong sequence conservation is not required for reliable prediction of edit sites. Conclusion Our results suggest that ab initio methods can generate robust classifiers of putative edit sites, and we highlight the value of combinatorial approaches as embodied by genetic algorithms. We present REGAL as one approach with the potential to be generalized to other organisms exhibiting C → U RNA editing.

  9. The Chemical and Genetic Characteristics of Szechuan Pepper (Zanthoxylum bungeanum and Z. armatum) Cultivars and Their Suitable Habitat

    OpenAIRE

    Xiang, Li; Liu, Yue; Xie, Caixiang; Li, Xiwen; Yu, Yadong; Ye, Meng; Chen, Shilin

    2016-01-01

    Szechuan peppers, famous for their unique sensation and flavor, are widely used as a food additive and traditional herbal medicine. Zanthoxylum bungeanum and Z. armatum are both commonly recognized as Szechuan peppers, but they have different tastes and effects. The chemical components, genetic characteristics, and suitable habitat of six cultivars were analyzed in this study. The results indicated that Z. armatum contained a larger proportion of volatile oil, whereas Z. bungeanum produced a ...

  10. The chemical and genetic characteristics of Szechuan pepper (Zanthoxylum bungeanum and Z. armatum) cultivars and their suitable habitat

    OpenAIRE

    Li eXiang; Yue eLiu; Caixiang eXie; Xiwen eLi; Yadong eYu; Meng eYe; Shilin eChen

    2016-01-01

    Szechuan peppers, famous for their unique sensation and flavor, are widely used as a food additive and traditional herbal medicine. Zanthoxylum bungeanum and Z. armatum are both commonly recognized as Szechuan peppers, but they have different tastes and effects. The chemical components, genetic characteristics, and suitable habitat of six cultivars were analyzed in this study. The results indicated that Z. armatum contained a larger proportion of volatile oil, whereas Z. bungeanum produced a ...

  11. Chemical-genetic disruption of clathrin function spares adaptor complex 3–dependent endosome vesicle biogenesis

    OpenAIRE

    Zlatic, Stephanie A.; Grossniklaus, Emily J.; Ryder, Pearl V.; Salazar, Gloria; Mattheyses, Alexa L.; Peden, Andrew A.; Faundez, Victor

    2013-01-01

    A role for clathrin in AP-3–dependent vesicle biogenesis has been inferred from biochemical interactions and colocalization between this adaptor and clathrin. The functionality of these molecular associations, however, is controversial. We comprehensively explore the role of clathrin in AP-3–dependent vesicle budding, using rapid chemical-genetic perturbation of clathrin function with a clathrin light chain–FKBP chimera oligomerizable by the drug AP20187. We find that AP-3 interacts and coloc...

  12. Chemical proteomics approaches for identifying the cellular targets of natural products.

    Science.gov (United States)

    Wright, M H; Sieber, S A

    2016-05-01

    Covering: 2010 up to 2016Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied "in situ" - in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide-alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss 'competitive mode' approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed. PMID:27098809

  13. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach

    OpenAIRE

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A.; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-01-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected...

  14. Endometriosis: A New Cellular and Molecular Genetic Approach for understanding the pathogenesis and evolutivity

    Directory of Open Access Journals (Sweden)

    Jean eBouquet De Joliniere

    2014-05-01

    Full Text Available ABSTRACT. Endometriosis is a benign disease with high prevalence in women of reproductive age estimated between 10 and 15% and is associated with considerable morbidity. Its etiology and pathogenesis are controversial but it is believed to involve multiple genetic, environmental, immunological, angiogenic and endocrine processes. Altered expressions of growth factors, cytokines, adhesion molecules, matrix metalloproteinases, and enzymes for estrogen synthesis and metabolism have been frequently observed in this condition. The possibility of genetic basis of endometriosis is demonstrated in studies of familial disease, in which the incidence of endometriosis is higher for first-degree relatives of probands as compared to controls. This review describes mainly the cellular, cytochemical, cytogenetic and molecular genetic features of endometriotic lesions and cultured endometriotic cells. In attempts to identify candidate gene (s involved in the pathogenesis of endometriosis, a tissue-based approaches including conventional cytogenetics (RHG-banding, loss of heterozygosity (LOH and Comparative Genomic Hybridization (CGH were employed. In addition to the karyotipic anomalies, consistent chromosome instability was confirmed by CGH and Fluorescence in Situ Hybridization (FISH. The nature and significance of the molecular genetic aberrations in relation to the locations and function of oncogenes and tumor supressor genes will be discussed. At last, a possible pathogenic role of embryonic duct remnants was observed in 7 female foetal reproductive tract in endometriosis and may induce a discussion about the begining of ovarian tumors and malignant proliferations

  15. An alternative approach to modeling genetic merit of feed efficiency in dairy cattle.

    Science.gov (United States)

    Lu, Y; Vandehaar, M J; Spurlock, D M; Weigel, K A; Armentano, L E; Staples, C R; Connor, E E; Wang, Z; Bello, N M; Tempelman, R J

    2015-09-01

    Genetic improvement of feed efficiency (FE) in dairy cattle requires greater attention given increasingly important resource constraint issues. A widely accepted yet occasionally contested measure of FE in dairy cattle is residual feed intake (RFI). The use of RFI is limiting for several reasons, including interpretation, differences in recording frequencies between the various component traits that define RFI, and potential differences in genetic versus nongenetic relationships between dry matter intake (DMI) and FE component traits. Hence, analyses focusing on DMI as the response are often preferred. We propose an alternative multiple-trait (MT) modeling strategy that exploits the Cholesky decomposition to provide a potentially more robust measure of FE. We demonstrate that our proposed FE measure is identical to RFI provided that genetic and nongenetic relationships between DMI and component traits of FE are identical. We assessed both approaches (MT and RFI) by simulation as well as by application to 26,383 weekly records from 50 to 200 d in milk on 2,470 cows from a dairy FE consortium study involving 7 institutions. Although the proposed MT model fared better than the RFI model when simulated genetic and nongenetic associations between DMI and FE component traits were substantially different from each other, no meaningful differences were found in predictive performance between the 2 models when applied to the consortium data. PMID:26210274

  16. An alternative approach for neural network evolution with a genetic algorithm: crossover by combinatorial optimization.

    Science.gov (United States)

    García-Pedrajas, Nicolás; Ortiz-Boyer, Domingo; Hervás-Martínez, César

    2006-05-01

    In this work we present a new approach to crossover operator in the genetic evolution of neural networks. The most widely used evolutionary computation paradigm for neural network evolution is evolutionary programming. This paradigm is usually preferred due to the problems caused by the application of crossover to neural network evolution. However, crossover is the most innovative operator within the field of evolutionary computation. One of the most notorious problems with the application of crossover to neural networks is known as the permutation problem. This problem occurs due to the fact that the same network can be represented in a genetic coding by many different codifications. Our approach modifies the standard crossover operator taking into account the special features of the individuals to be mated. We present a new model for mating individuals that considers the structure of the hidden layer and redefines the crossover operator. As each hidden node represents a non-linear projection of the input variables, we approach the crossover as a problem on combinatorial optimization. We can formulate the problem as the extraction of a subset of near-optimal projections to create the hidden layer of the new network. This new approach is compared to a classical crossover in 25 real-world problems with an excellent performance. Moreover, the networks obtained are much smaller than those obtained with classical crossover operator. PMID:16343847

  17. Approaches to quality management and accreditation in a genetic testing laboratory.

    Science.gov (United States)

    Berwouts, Sarah; Morris, Michael A; Dequeker, Elisabeth

    2010-09-01

    Medical laboratories, and specifically genetic testing laboratories, provide vital medical services to different clients: clinicians requesting a test, patients from whom the sample was collected, public health and medical-legal instances, referral laboratories and authoritative bodies. All expect results that are accurate and obtained in an efficient and effective manner, within a suitable time frame and at acceptable cost. There are different ways of achieving the end results, but compliance with International Organization for Standardization (ISO) 15189, the international standard for the accreditation of medical laboratories, is becoming progressively accepted as the optimal approach to assuring quality in medical testing. We present recommendations and strategies designed to aid genetic testing laboratories with the implementation of a quality management system, including key aspects such as document control, external quality assessment, internal quality control, internal audit, management review, validation, as well as managing the human side of change. The focus is on pragmatic approaches to attain the levels of quality management and quality assurance required for accreditation according to ISO 15189, within the context of genetic testing. Attention is also given to implementing efficient and effective quality improvement. PMID:20720559

  18. A generalized quantum chemical approach for nano- and bio-electronics

    OpenAIRE

    Jiang, Jun

    2005-01-01

    A generalized quantum chemical approach for electron transport in molecular devices is developed. It allows to treat the devices where the metal electrodes and the molecule are either chemically or physically bonded on equal footing. Effects of molecular length and hydrogen bonding on the current-voltage (I-V) characteristics of molecular devices are discussed. An extension to include the vibration motions of the molecule has been derived and implemented. It provides the inelastic electron tu...

  19. The Genetics of Obsessive-Compulsive Disorder and Tourette Syndrome: An Epidemiological and Pathway-Based Approach for Gene Discovery

    Science.gov (United States)

    Grados, Marco A.

    2010-01-01

    Objective: To provide a contemporary perspective on genetic discovery methods applied to obsessive-compulsive disorder (OCD) and Tourette syndrome (TS). Method: A review of research trends in genetics research in OCD and TS is conducted, with emphasis on novel approaches. Results: Genome-wide association studies (GWAS) are now in progress in OCD…

  20. Controlling organic chemical hazards in food manufacturing: a hazard analysis critical control points (HACCP) approach.

    Science.gov (United States)

    Ropkins, K; Beck, A J

    2002-08-01

    Hazard analysis by critical control points (HACCP) is a systematic approach to the identification, assessment and control of hazards. Effective HACCP requires the consideration of all hazards, i.e., chemical, microbiological and physical. However, to-date most 'in-place' HACCP procedures have tended to focus on the control of microbiological and physical food hazards. In general, the chemical component of HACCP procedures is either ignored or limited to applied chemicals, e.g., food additives and pesticides. In this paper we discuss the application of HACCP to a broader range of chemical hazards, using organic chemical contaminants as examples, and the problems that are likely to arise in the food manufacturing sector. Chemical HACCP procedures are likely to result in many of the advantages previously identified for microbiological HACCP procedures: more effective, efficient and economical than conventional end-point-testing methods. However, the high costs of analytical monitoring of chemical contaminants and a limited understanding of formulation and process optimisation as means of controlling chemical contamination of foods are likely to prevent chemical HACCP becoming as effective as microbiological HACCP. PMID:12224422

  1. A combined genetic and multi medium approach revels new secondary metabolites in Aspergillus nidulans

    DEFF Research Database (Denmark)

    Klejnstrup, Marie Louise; Nielsen, Morten Thrane; Frisvad, Jens Christian; Mortensen, Uffe Hasbro; Larsen, Thomas Ostenfeld

    Secondary metabolites are a diverse group of metabolites which serve as important natural sources of drugs for treating diseases. The availability of full genome sequences of several filamentous fungi has revealed a large genetic potential for production of secondary metabolites that are not...... observed under standard laboratory conditions. Genetic approaches have proven a fruitfull strategy towards the production and identification of these unknown metabolites. Examples include deletion of the cclA1 and laeA2 genes in A. nidulans which affects the expression of secondary metabolites including...... monodictyphenone and terrequinone A respectively. We have deleted the cclA gene in A. nidulans and grown the mutants on several complex media to provoke the production of secondary metabolites. This resulted in the production of several metabolites not previously reported from A. nidulans. Some of these have been...

  2. Estimating energy demand of Turkey based on economic indicators using genetic algorithm approach

    International Nuclear Information System (INIS)

    This study deals with estimation of energy demand based on economic indicators in Turkey. The genetic algorithm energy demand (GAEDM) Model is developed based on past data using the genetic algorithm approach. The economic indicators that are used during the model development are: gross national product (GNP), population and import and export figures of Turkey. Two forms of the GAEDM model are developed to estimate energy demand. The GAEDM can be used for estimating the energy demand in the future by optimizing the parameter value using available data. The future energy demand is calculated under different scenarios. The current models overestimate the energy demand in the years 2020 and 2025. The relative estimation errors of the GAEDM model are the lowest when they are compared with the Ministry of Energy and Natural Resources (MENR) projection

  3. Branch-pipe-routing approach for ships using improved genetic algorithm

    Science.gov (United States)

    Sui, Haiteng; Niu, Wentie

    2016-05-01

    Branch-pipe routing plays fundamental and critical roles in ship-pipe design. The branch-pipe-routing problem is a complex combinatorial optimization problem and is thus difficult to solve when depending only on human experts. A modified genetic-algorithm-based approach is proposed in this paper to solve this problem. The simplified layout space is first divided into threedimensional (3D) grids to build its mathematical model. Branch pipes in layout space are regarded as a combination of several two-point pipes, and the pipe route between two connection points is generated using an improved maze algorithm. The coding of branch pipes is then defined, and the genetic operators are devised, especially the complete crossover strategy that greatly accelerates the convergence speed. Finally, simulation tests demonstrate the performance of proposed method.

  4. Target identification strategies in plant chemical biology

    OpenAIRE

    Dejonghe, Wim; Russinova, Eugenia

    2014-01-01

    The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharma...

  5. Some chemical influence on genetic effects of ionizing radiation and biodosimetry problems

    International Nuclear Information System (INIS)

    Complete text of publication follows. Radiation sensitivity is a quantitative character from genetic point of view and the distribution of this character values in populations is characterized by a binomial curve. So, 50% of the population have the mean values of radiosensitivity (x ± 0.67σ), 95% of individuals have radiosensitivity values equal to x ± 1.96σ and 5% of the population have this characters ranged from x ± 1.96σ to x ± 3σ, with division into the supersensitive fraction (2.5%) and the superresistant one (2.5%). Radiosensitivity as well as other quantitative characters is caused by the interaction of some pairs of polymeric genes determining a lot of physiological and biochemical organism features. Thus, irradiation in the same dose can induce different level of mutations or other biological effects in different humans. Besides, radiosensitivity depends to a great degree upon environmental factors. For instance, a level of radiosensitivity depends on physical activity, nervous and psychological state, hormonal balance etc. A diet can change an individual radioresistance - food rich in vitamins, microelements, adaptogens and so on favors the increase in individual radioresistance. Many food stuffs contain radioprotectors or antimutagens. So, tea, coffee, cocoa, chocolate, mushrooms and other products have melanin, which is a very effective radioprotector not only against acute irradiation, but even against chronic one according to out data. On the contrary some substances in our food such as residual amounts of fertilizers or herbicides can be mutagenic or increase mutagenic action of radiation. In the last case we observed synergetic or antagonistic effects. Radioadaptive response is one of the most significant factors which can be responsible for uncorrected radiation dose evaluation by biodosimetry methods. This phenomenon decreases effects of ionizing radiation approximately twice. Adaptive reaction can be induced by low radiation dose as well

  6. Induction of novel genetic recombinants through chemical mutagenesis of microspores in Indian Mustard B. juncea

    International Nuclear Information System (INIS)

    The microspore embryogenesis and DH production protocol developed in our lab [In Vitro Cellular and Development Biology - Plant. 2005, 41: 266-273] was used for microspores isolation and their chemical mutagenesis to widen the genetic base of three widely cultivated B. juncea species, Pusa Bold, Varuna and Bio- 902. The regenerated three to four leaf growth stage plantlets were diploidized, hardened and transplanted to develop doubled haploid plants. The microspores of genotype BIO-902 treated with either ENU/EMS did not produce any embryos while the control produced 85.4 ± 10.9 embryos/ Petri dish. Treatment with 5.0 μM ENU/EMS resulted in maximum embryo induction from the other two genotypes, Pusa Bold and Varuna. Irrespective of the concentration used, EMS mutated microspores produced embryos with higher frequency (239) as compared to those treated with ENU (106). The control embryos exhibited 85 to 90% germination against the mutant microspore derived embryos (16.7 to 31.5%). Overall lower concentrations of EMS (1.0 to 2.5 μM) compared to that of ENU (2.5 to 5.0 μM) promoted higher frequency of positive mutants with promising yield potential. Both EMS and ENU generated considerable variability for agro morphological and biochemical traits; appressed pod phenotype, number of pods, leaf size, total glucosinolate content and FA profile. Desirable phenotypes with reduced glucosinolate ( 100 μM) per g oil free meal were recovered from 2.5 to 5.0 μM EMS mutagenesis. Mutants with 45% oleic acid (against 40-45% erucic and 15-20% oleic in controls) were obtained in mutagenized plants from EMS (2.5 μM) and ENU (5.0 μM ). Useful variability was identified in mutant plants for their disease response to the most devastating fungal diseases Albugo candida (DI 0.6-2.0) and Alternaria brassicae (DI 1.3- 2.6) under artificial inoculation. (author)

  7. Tower of Babel: variation in ethical approaches, concepts of welfare and attitudes to genetic manipulation.

    Science.gov (United States)

    Appleby, M C

    1999-01-01

    Attitudes to animal biotechnology are diverse, partly because people have different viewpoints and often do not recognize or acknowledge this to be so. First, people adopt different ethical approaches. If an opponent of genetic manipulation says 'I don't like the idea of altering animals' biology' and a proponent replies '...but it is useful', they are failing to communicate, because one is asking whether the action is right or wrong, whereas the other emphasizes the consequences. Another approach focuses on the person carrying out the action. Many people have hybrid views combining elements of these different approaches. Second, people's concepts of welfare vary, emphasizing animal minds, bodies or natures--or a combination of these. A proponent who argues that a particular genetic change will not cause suffering is unlikely to reassure an opponent who puts more emphasis on naturalness than on feelings or health. An improved dialogue, in which people attempt to understand one another's viewpoints, may enable common principles to be established and practical measures to be taken that enable more cooperation in attempts to improve both human and animal welfare. PMID:11933932

  8. Genetic evaluation of popcorn families using a Bayesian approach via the independence chain algorithm

    OpenAIRE

    Marcos Rodovalho; Freddy Mora; Osvin Arriagada; Carlos Maldonado; Emmanuel Arnhold; Carlos Alberto Scapim

    2014-01-01

    The objective of this study was to examine genetic parameters of popping expansion and grain yield in a trial of 169 halfsib families using a Bayesian approach. The independence chain algorithm with informative priors for the components of residual and family variance (inverse-gamma prior distribution) was used. Popping expansion was found to be moderately heritable, with a posterior mode of h2 of 0.34, and 90% Bayesian confidence interval of 0.22 to 0.44. The heritability of gra...

  9. An Approach to Assembly Sequence Plannning Based on Hierarchical Strategy and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    Niu Xinwen; Ding Han; Xiong Youlun

    2001-01-01

    Using group and subassembly cluster methods, the hierarchical structure of a product is.generated automatically, which largely reduces the complexity of planning. Based on genetic algofithn the optimal of assembly sequence of each stracture level can be obtained by sequence-bysequence search. As a result, a better assembly sequence of the product can be generated by combining the assembly sequences of all hierarchical structures, which provides more parallelism and flexibility for assembly operations. An industrial example is solved by this new approach.

  10. Compromise Approach-Based Genetic Algorithm for Constrained Multiobjective Portfolio Selection Model

    Science.gov (United States)

    Li, Jun

    In this paper, fuzzy set theory is incorporated into a multiobjective portfolio selection model for investors’ taking into three criteria: return, risk and liquidity. The cardinality constraint, the buy-in threshold constraint and the round-lots constraints are considered in the proposed model. To overcome the difficulty of evaluation a large set of efficient solutions and selection of the best one on non-dominated surface, a compromise approach-based genetic algorithm is presented to obtain a compromised solution for the proposed constrained multiobjective portfolio selection model.

  11. Genetic algorithm-fuzzy based dynamic motion planning approach for a mobile robot

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Presents the mobile robots dynamic motion planning problem with a task to find an obstacle-free route that requires minimum travel time from the start point to the destination point in a changing environment, due to the obstacle's moving. An Genetic Algorithm fuzzy(GA-Fuzzy)based optimal approach proposed to find any obstacle-free path and the GA used to select the optimal one, points ont that using this learned knowledge off line, a mobile robot can navigate to its goal point when it faces new scenario on-line. Concludes with the opti mal rule base given and the simulation results showing its effectiveness.

  12. An iterative consensus-building approach to revising a genetics/genomics competency framework for nurse education in the UK

    OpenAIRE

    Kirk, Maggie; Tonkin, Emma; Skirton, Heather

    2013-01-01

    KIRK M., TONKIN E. & SKIRTON H. (2014) An iterative consensus-building approach to revising a genetics/genomics competency framework for nurse education in the UK. Journal of Advanced Nursing 70(2), 405–420. doi: 10.1111/jan.12207 AimTo report a review of a genetics education framework using a consensus approach to agree on a contemporary and comprehensive revised framework. BackgroundAdvances in genomic health care have been significant since the first genetics education framework for nurses...

  13. A clinical approach to the diagnosis of patients with leukodystrophies and genetic leukoencephelopathies

    Science.gov (United States)

    Leventer, Richard J.; van der Knaap, Marjo S.; van Hove, Johan; Pizzino, Amy; McNeill, Nathan H.; Helman, Guy; Simons, Cas; Schmidt, Johanna L.; Rizzo, William B.

    2015-01-01

    Leukodystrophies (LD) and genetic leukoencephalopathies (gLE) are disorders that result in white matter abnormalities in the central nervous system (CNS). Magnetic resonance (MR) imaging (MRI) has dramatically improved and systematized the diagnosis of LDs and gLEs, and in combination with specific clinical features, such as Addison's disease in Adrenoleukodystrophy or hypodontia in Pol-III related or 4H leukodystrophy, can often resolve a case with a minimum of testing. The diagnostic odyssey for the majority LD and gLE patients, however, remains extensive – many patients will wait nearly a decade for a definitive diagnosis and at least half will remain unresolved. The combination of MRI, careful clinical evaluation and next generation genetic sequencing holds promise for both expediting the diagnostic process and dramatically reducing the number of unresolved cases. Here we present a workflow detailing the Global Leukodystrophy Initiative (GLIA) consensus recommendations for an approach to clinical diagnosis, including salient clinical features suggesting a specific diagnosis, neuroim-aging features and molecular genetic testing. We also discuss recommendations on the use of broad-spectrum next-generation sequencing in instances of ambiguous MRI or clinical findings. We conclude with a proposal for systematic trials of genome-wide agnostic testing as a first line diagnostic in LDs and gLEs given the increasing number of genes associated with these disorders. PMID:25655951

  14. New Approaches for Crop Genetic Adaptation to the Abiotic Stresses Predicted with Climate Change

    Directory of Open Access Journals (Sweden)

    Robert Redden

    2013-05-01

    Full Text Available Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural production for an expanding population, but to achieve this under more adverse environmental conditions. It is now possible to systematically explore the genetic variation in historic local landraces by using GPS locators and world climate maps to describe the natural selection for local adaptation, and to identify candidate germplasm for tolerances to extreme stresses. The physiological and biochemical components of these expressions can be genomically investigated with candidate gene approaches and next generation sequencing. Wild relatives of crops have largely untapped genetic variation for abiotic and biotic stress tolerances, and could greatly expand the available domesticated gene pools to assist crops to survive in the predicted extremes of climate change, a survivalomics strategy. Genomic strategies can assist in the introgression of these valuable traits into the domesticated crop gene pools, where they can be better evaluated for crop improvement. The challenge is to increase agricultural productivity despite climate change. This calls for the integration of many disciplines from eco-geographical analyses of genetic resources to new advances in genomics, agronomy and farm management, underpinned by an understanding of how crop adaptation to climate is affected by genotype × environment interaction.

  15. The theological and legal approach of prenatal and preimplantation genetic control

    Directory of Open Access Journals (Sweden)

    George Katsimigas

    2012-04-01

    Full Text Available Aim: The investigation of the theological and legal questions derived from the application of prenatal and preimplantation genetic control on human embryos. Moreover, the review of the European and Greek legislation with regard to the prenatal and preimplantation control. Material and Method: A literature review based on both review and research literature, conducted during the period of 1984-2009, derived from MEDLINE, SCOPUS and ΙΑΤΡΟΤΕΚ databases using as key words Prenatal diagnosis , Bioethics, Orthodox ethics, preimplantation genetic diagnosis, Legislation. Results: The orthodox theology adopts a negative view for the abortion of fetus, which it is considered murder in any stage of growth. The legal approach brought two basic questions a the securing of consent from the examined individual and b the constitutional protection of fetus' life. Conclusions: The orthodox theology, through their teaching places the moral criteria for facing the moral questions derived from the application of prenatal and preimplantation genetic control on human embryos. Also, the Greek citizens need to be informed for all the diagnostic examinations on embryos that should be provided by all public health organizations.

  16. An alternative approach to the Boltzmann distribution through the chemical potential

    Science.gov (United States)

    D'Anna, Michele; Job, Georg

    2016-05-01

    The Boltzmann distribution is one of the most significant results of classical physics. Despite its importance and its wide range of application, at high school level it is mostly presented without any derivation or link to some basic ideas. In this contribution we present an approach based on the chemical potential that allows to derive it directly from the basic idea of thermodynamical equilibrium.

  17. Improving Students' Chemical Literacy Levels on Thermochemical and Thermodynamics Concepts through a Context-Based Approach

    Science.gov (United States)

    Cigdemoglu, Ceyhan; Geban, Omer

    2015-01-01

    The aim of this study was to delve into the effect of context-based approach (CBA) over traditional instruction (TI) on students' chemical literacy level related to thermochemical and thermodynamics concepts. Four eleventh-grade classes with 118 students in total taught by two teachers from a public high school in 2012 fall semester were enrolled…

  18. Two Experiments to Approach the Boltzmann Factor: Chemical Reaction and Viscous Flow

    Science.gov (United States)

    Fazio, Claudio; Battaglia, Onofrio R.; Guastella, Ivan

    2012-01-01

    In this paper we discuss a pedagogical approach aimed at pointing out the role played by the Boltzmann factor in describing phenomena usually perceived as regulated by different mechanisms of functioning. Experimental results regarding some aspects of a chemical reaction and of the viscous flow of some liquids are analysed and described in terms…

  19. Microwave-irradiation-assisted hybrid chemical approach for titanium dioxide nanoparticle synthesis: microbial and cytotoxicological evaluation.

    Science.gov (United States)

    Ranjan, Shivendu; Dasgupta, Nandita; Rajendran, Bhavapriya; Avadhani, Ganesh S; Ramalingam, Chidambaram; Kumar, Ashutosh

    2016-06-01

    Titanium dioxide nanoparticles (TNPs) are widely used in the pharmaceutical and cosmetics industries. It is used for protection against UV exposure due to its light-scattering properties and high refractive index. Though TNPs are increasingly used, the synthesis of TNPs is tedious and time consuming; therefore, in the present study, microwave-assisted hybrid chemical approach was used for TNP synthesis. In the present study, we demonstrated that TNPs can be synthesized only in 2.5 h; however, the commonly used chemical approach using muffle furnace takes 5 h. The activity of TNP depends on the synthetic protocol; therefore, the present study also determined the effect of microwave-assisted hybrid chemical approach synthetic protocol on microbial and cytotoxicity. The results showed that TNP has the best antibacterial activity in decreasing order from Escherichia coli, Bacillus subtilis, and Staphylococcus aureus. The IC50 values of TNP for HCT116 and A549 were found to be 6.43 and 6.04 ppm, respectively. Cell death was also confirmed from trypan blue exclusion assay and membrane integrity loss was observed. Therefore, the study determines that the microwave-assisted hybrid chemical approach is time-saving; hence, this technique can be upgraded from lab scale to industrial scale via pilot plant scale. Moreover, it is necessary to find the mechanism of action at the molecular level to establish the reason for greater bacterial and cytotoxicological toxicity. Graphical abstract A graphical representation of TNP synthesis. PMID:26976013

  20. An Artificial Neural Network Approach to the Solution of Molecular Chemical Equilibrium

    CERN Document Server

    Ramos, A A

    2005-01-01

    A novel approach is presented for the solution of instantaneous chemical equilibrium problems. The chemical equilibrium can be considered, due to its intrinsically local character, as a mapping of the three-dimensional parameter space spanned by the temperature, hydrogen density and electron density into many one-dimensional spaces representing the number density of each species. We take advantage of the ability of artificial neural networks to approximate non-linear functions and construct neural networks for the fast and efficient solution of the chemical equilibrium problem in typical stellar atmosphere physical conditions. The neural network approach has the advantage of providing an analytic function, which can be rapidly evaluated. The networks are trained with a learning set (that covers the entire parameter space) until a relative error below 1% is reached. It has been verified that the networks are not overtrained by using an additional verification set. The networks are then applied to a snapshot of...

  1. The economic and environmental value of genetic improvements in fattening pigs: An integrated dynamic model approach.

    Science.gov (United States)

    Niemi, J K; Sevón-Aimonen, M-L; Stygar, A H; Partanen, K

    2015-08-01

    The selection of animals for improved performance affects the profitability of pig fattening and has environmental consequences. The goal of this paper was to examine how changes in genetic and market parameters impact the biophysical (feeding patterns, timing of slaughter, nitrogen excretion) and economic (return per pig space unit) results describing pig fattening in a Finnish farm. The analysis can be viewed as focusing on terminal line breeding goals. An integrated model using recursive stochastic dynamic programming and a biological pig growth model was used to estimate biophysical results and economic values. Combining these models allowed us to provide more accurate estimates for the value of genetic improvement and, thus, provide better feedback to animal breeding programs than the traditional approach, which is based on fixed management patterns. Besides the benchmark scenario, the results were simulated for 5 other scenarios. In each scenario, genotype was improved regarding daily growth potential, carcass lean meat content, or the parameters of the Gompertz growth curve (maturing rate [], adult weight of protein [α], and adult weight of lipid mass []). The change in each parameter was equal to approximately 1 SD genetic improvement (ceteris paribus). Increasing , , daily growth potential, or carcass lean meat content increased the return on pig space unit by €12.60, €7.60, €4.10, or €2.90 per year, respectively, whereas an increase in decreased the return by €3.10. The genetic improvement in and resulted in the highest decrease in nitrogen excretion calculated in total or per kilogram of carcass gain but only under the optimal feeding pattern. Simulated changes in the Gompertz growth function parameters imply greater changes in ADG and lean meat content than changes in scenarios focusing on improving ADG and lean meat content directly. The economic value of genetic improvements as well as the quantity of nitrogen excreted during the fattening

  2. A genetic algorithm-based approach to flexible flow-line scheduling with variable lot sizes.

    Science.gov (United States)

    Lee, I; Sikora, R; Shaw, M J

    1997-01-01

    Genetic algorithms (GAs) have been used widely for such combinatorial optimization problems as the traveling salesman problem (TSP), the quadratic assignment problem (QAP), and job shop scheduling. In all of these problems there is usually a well defined representation which GA's use to solve the problem. We present a novel approach for solving two related problems-lot sizing and sequencing-concurrently using GAs. The essence of our approach lies in the concept of using a unified representation for the information about both the lot sizes and the sequence and enabling GAs to evolve the chromosome by replacing primitive genes with good building blocks. In addition, a simulated annealing procedure is incorporated to further improve the performance. We evaluate the performance of applying the above approach to flexible flow line scheduling with variable lot sizes for an actual manufacturing facility, comparing it to such alternative approaches as pair wise exchange improvement, tabu search, and simulated annealing procedures. The results show the efficacy of this approach for flexible flow line scheduling. PMID:18255838

  3. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    Directory of Open Access Journals (Sweden)

    Cesar GAITAN-FONSECA

    2013-01-01

    Full Text Available Objective This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS. Material and Methods An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angle measurement (WCA. The effectiveness of the modification of hydrophobicity was verified by the fluid permeability test (FPT. Results and Conclusions Statistically significant differences were found in the values of WCA and FPT between the two groups. After silanization, the hydrophobic intraradicular dentin surface exhibited in vitro properties that limit fluid penetration into the sealed root canal. This chemical treatment is a new approach for improving the sealing of the root canal system.

  4. An Approach to Self-Assembling Swarm Robots Using Multitree Genetic Programming

    Directory of Open Access Journals (Sweden)

    Jong-Hyun Lee

    2013-01-01

    Full Text Available In recent days, self-assembling swarm robots have been studied by a number of researchers due to their advantages such as high efficiency, stability, and scalability. However, there are still critical issues in applying them to practical problems in the real world. The main objective of this study is to develop a novel self-assembling swarm robot algorithm that overcomes the limitations of existing approaches. To this end, multitree genetic programming is newly designed to efficiently discover a set of patterns necessary to carry out the mission of the self-assembling swarm robots. The obtained patterns are then incorporated into their corresponding robot modules. The computational experiments prove the effectiveness of the proposed approach.

  5. An optimized chemical kinetic mechanism for HCCI combustion of PRFs using multi-zone model and genetic algorithm

    International Nuclear Information System (INIS)

    Highlights: • A new chemical kinetic mechanism for PRFs HCCI combustion is developed. • New mechanism optimization is performed using genetic algorithm and multi-zone model. • Engine-related combustion and performance parameters are predicted accurately. • Engine unburned HC and CO emissions are predicted by the model properly. - Abstract: Development of comprehensive chemical kinetic mechanisms is required for HCCI combustion and emissions prediction to be used in engine development. The main purpose of this study is development of a new chemical kinetic mechanism for primary reference fuels (PRFs) HCCI combustion, which can be applied to combustion models to predict in-cylinder pressure and exhaust CO and UHC emissions, accurately. Hence, a multi-zone model is developed for HCCI engine simulation. Two semi-detailed chemical kinetic mechanisms those are suitable for premixed combustion are used for n-heptane and iso-octane HCCI combustion simulation. The iso-octane mechanism contains 84 species and 484 reactions and the n-heptane mechanism contains 57 species and 296 reactions. A simple interaction between iso-octane and n-heptane is considered in new mechanism. The multi-zone model is validated using experimental data for pure n-heptane and iso-octane. A new mechanism is prepared by combination of these two mechanisms for n-heptane and iso-octane blended fuel, which includes 101 species and 594 reactions. New mechanism optimization is performed using genetic algorithm and multi-zone model. Mechanism contains low temperature heat release region, which decreases with increasing octane number. The results showed that the optimized chemical kinetic mechanism is capable of predicting engine-related combustion and performance parameters. Also after implementing the optimized mechanism, engine unburned HC and CO emissions predicted by the model are in good agreement with the corresponding experimental data

  6. Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

    Science.gov (United States)

    Kruijver, Maarten

    2016-07-01

    Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. PMID:27128695

  7. A Novel Approach for Discovery Quantitative Fuzzy Multi-Level Association Rules Mining Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Saad M. Darwish

    2016-10-01

    Full Text Available Quantitative multilevel association rules mining is a central field to realize motivating associations among data components with multiple levels abstractions. The problem of expanding procedures to handle quantitative data has been attracting the attention of many researchers. The algorithms regularly discretize the attribute fields into sharp intervals, and then implement uncomplicated algorithms established for Boolean attributes. Fuzzy association rules mining approaches are intended to defeat such shortcomings based on the fuzzy set theory. Furthermore, most of the current algorithms in the direction of this topic are based on very tiring search methods to govern the ideal support and confidence thresholds that agonize from risky computational cost in searching association rules. To accelerate quantitative multilevel association rules searching and escape the extreme computation, in this paper, we propose a new genetic-based method with significant innovation to determine threshold values for frequent item sets. In this approach, a sophisticated coding method is settled, and the qualified confidence is employed as the fitness function. With the genetic algorithm, a comprehensive search can be achieved and system automation is applied, because our model does not need the user-specified threshold of minimum support. Experiment results indicate that the recommended algorithm can powerfully generate non-redundant fuzzy multilevel association rules.

  8. A Parallel Approach To Optimum Actuator Selection With a Genetic Algorithm

    Science.gov (United States)

    Rogers, James L.

    2000-01-01

    Recent discoveries in smart technologies have created a variety of aerodynamic actuators which have great potential to enable entirely new approaches to aerospace vehicle flight control. For a revolutionary concept such as a seamless aircraft with no moving control surfaces, there is a large set of candidate locations for placing actuators, resulting in a substantially larger number of combinations to examine in order to find an optimum placement satisfying the mission requirements. The placement of actuators on a wing determines the control effectiveness of the airplane. One approach to placement Maximizes the moments about the pitch, roll, and yaw axes, while minimizing the coupling. Genetic algorithms have been instrumental in achieving good solutions to discrete optimization problems, such as the actuator placement problem. As a proof of concept, a genetic has been developed to find the minimum number of actuators required to provide uncoupled pitch, roll, and yaw control for a simplified, untapered, unswept wing model. To find the optimum placement by searching all possible combinations would require 1,100 hours. Formulating the problem and as a multi-objective problem and modifying it to take advantage of the parallel processing capabilities of a multi-processor computer, reduces the optimization time to 22 hours.

  9. Dynamic phosphoregulation of the cortical actin cytoskeleton and endocytic machinery revealed by real-time chemical genetic analysis

    OpenAIRE

    Sekiya-Kawasaki, Mariko; Groen, Aaron Chris; Cope, M. Jamie T.V.; Kaksonen, Marko; Watson, Hadiya A.; Zhang, Chao; Shokat, Kevan M.; Wendland, Beverly; McDonald, Kent L.; McCaffery, J. Michael; Drubin, David G.

    2003-01-01

    We used chemical genetics to control the activity of budding yeast Prk1p, which is a protein kinase that is related to mammalian GAK and AAK1, and which targets several actin regulatory proteins implicated in endocytosis. In vivo Prk1p inhibition blocked pheromone receptor endocytosis, and caused cortical actin patches to rapidly aggregate into large clumps that contained Abp1p, Sla2p, Pan1p, Sla1p, and Ent1p. Clump formation depended on Arp2p, suggesting that this phenotype might result from...

  10. Supervised extensions of chemography approaches: case studies of chemical liabilities assessment.

    Science.gov (United States)

    Ovchinnikova, Svetlana I; Bykov, Arseniy A; Tsivadze, Aslan Yu; Dyachkov, Evgeny P; Kireeva, Natalia V

    2014-01-01

    Chemical liabilities, such as adverse effects and toxicity, play a significant role in modern drug discovery process. In silico assessment of chemical liabilities is an important step aimed to reduce costs and animal testing by complementing or replacing in vitro and in vivo experiments. Herein, we propose an approach combining several classification and chemography methods to be able to predict chemical liabilities and to interpret obtained results in the context of impact of structural changes of compounds on their pharmacological profile. To our knowledge for the first time, the supervised extension of Generative Topographic Mapping is proposed as an effective new chemography method. New approach for mapping new data using supervised Isomap without re-building models from the scratch has been proposed. Two approaches for estimation of model's applicability domain are used in our study to our knowledge for the first time in chemoinformatics. The structural alerts responsible for the negative characteristics of pharmacological profile of chemical compounds has been found as a result of model interpretation. PMID:24868246

  11. Anabolic implant effects on visceral organ mass, chemical body composition, and estimated energetic efficiency in cloned (genetically identical) beef steers.

    Science.gov (United States)

    Hutcheson, J P; Johnson, D E; Gerken, C L; Morgan, J B; Tatum, J D

    1997-10-01

    Six sets of four genetically identical Brangus steers (n = 24; X BW 409 kg) were used to determine the effect of different anabolic implants on visceral organ mass, chemical body composition, estimated tissue deposition, and energetic efficiency. Steers within a clone set were randomly assigned to one of the following implant treatments: C, no implant; E, estrogenic; A, androgenic, or AE, androgenic + estrogenic. Steers were slaughtered 112 d after implanting; visceral organs were weighed and final body composition determined by mechanical grinding and chemical analysis of the empty body. Mass of the empty gastrointestinal tract (GIT) was reduced approximately 9% (P .10) the efficiency of ME utilization. In general, estrogenic implants decreased GIT, androgenic implants increased liver, and all implants increased hide mass. Steers implanted with an AE combination had additive effects on protein deposition compared with either implant alone. The NEg requirements for body gain are estimated to be reduced 19% by estrogenic or combination implants. PMID:9331863

  12. On a group-theoretical approach to the periodic table of chemical elements

    OpenAIRE

    Kibler, Maurice

    2004-01-01

    This paper is concerned with the application of the group SO(4,2)xSU(2) to the periodic table of chemical elements. It is shown how the Madelung rule of the atomic shell model can be used for setting up a periodic table that can be further rationalized via the group SO(4,2)xSU(2) and some of its subgroups. Qualitative results are obtained from the table and the general lines of a programme for a quantitative approach to the properties of chemical elements are developed on the basis of the gro...

  13. Design of tailor-made chemical blend using a decomposition-based computer-aided approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Gernaey, Krist; Manan, Z.A.;

    2011-01-01

    design methodology for blended liquid products that identifies a set of feasible chemical blends. The blend design problem is formulated as a Mixed Integer Nonlinear Programming (MINLP) model where the objective is to find the optimal blended gasoline or diesel product subject to types of chemicals and...... selection. The application of this systematic and computer-aided approach is illustrated through a case study involving the design of blends of gasoline with oxygenated compounds resulting from degradation and fermentation of biomass for use in internal combustion engines. Emphasis is given here on the...

  14. A nuclear reload optimization approach using a real coded genetic algorithm with random keys

    International Nuclear Information System (INIS)

    The fuel reload of a Pressurized Water Reactor is made whenever the burn up of the fuel assemblies in the nucleus of the reactor reaches a certain value such that it is not more possible to maintain a critical reactor producing energy at nominal power. The problem of fuel reload optimization consists on determining the positioning of the fuel assemblies within the nucleus of the reactor in an optimized way to minimize the cost benefit relationship of fuel assemblies cost per maximum burn up, and also satisfying symmetry and safety restrictions. The fuel reload optimization problem difficulty grows exponentially with the number of fuel assemblies in the nucleus of the reactor. During decades the fuel reload optimization problem was solved manually by experts that used their knowledge and experience to build configurations of the reactor nucleus, and testing them to verify if safety restrictions of the plant are satisfied. To reduce this burden, several optimization techniques have been used, included the binary code genetic algorithm. In this work we show the use of a real valued coded approach of the genetic algorithm, with different recombination methods, together with a transformation mechanism called random keys, to transform the real values of the genes of each chromosome in a combination of discrete fuel assemblies for evaluation of the reload optimization. Four different recombination methods were tested: discrete recombination, intermediate recombination, linear recombination and extended linear recombination. For each of the 4 recombination methods 10 different tests using different seeds for the random number generator were conducted 10 generating, totaling 40 tests. The results of the application of the genetic algorithm are shown with formulation of real numbers for the problem of the nuclear reload of the plant Angra 1 type PWR. Since the best results in the literature for this problem were found by the parallel PSO we will it use for comparison

  15. A genetic algorithm approach to optimization for the radiological worker allocation problem

    International Nuclear Information System (INIS)

    The worker allocation optimization problem in radiological facilities inevitably involves various types of requirements and constraints relevant to radiological protection and labor management. Some of these goals and constraints are not amenable to a rigorous mathematical formulation. Conventional methods for this problem rely heavily on sophisticated algebraic or numerical algorithms, which cause difficulties in the search for optimal solutions in the search space of worker allocation optimization problems. Genetic algorithms (GAB) are stochastic search algorithms introduced by J. Holland in the 1970s based on ideas and techniques from genetic and evolutionary theories. The most striking characteristic of GAs is the large flexibility allowed in the formulation of the optimal problem and the process of the search for the optimal solution. In the formulation, it is not necessary to define the optimal problem in rigorous mathematical terms, as required in the conventional methods. Furthermore, by designing a model of evolution for the optimal search problem, the optimal solution can be sought efficiently with computational simple manipulations without highly complex mathematical algorithms. We reported a GA approach to the worker allocation problem in radiological facilities in the previous study. In this study, two types of hard constraints were employed to reduce the huge search space, where the optimal solution is sought in such a way as to satisfy as many of soft constraints as possible. It was demonstrated that the proposed evolutionary method could provide the optimal solution efficiently compared with conventional methods. However, although the employed hard constraints could localize the search space into a very small region, it brought some complexities in the designed genetic operators and demanded additional computational burdens. In this paper, we propose a simplified evolutionary model with less restrictive hard constraints and make comparisons between

  16. A chemical-genetic strategy reveals distinct temporal requirements for SAD-1 kinase in neuronal polarization and synapse formation

    Directory of Open Access Journals (Sweden)

    Shokat Kevan M

    2008-09-01

    Full Text Available Abstract Background Neurons assemble into a functional network through a sequence of developmental processes including neuronal polarization and synapse formation. In Caenorhabditis elegans, the serine/threonine SAD-1 kinase is essential for proper neuronal polarity and synaptic organization. To determine if SAD-1 activity regulates the establishment or maintenance of these neuronal structures, we examined its temporal requirements using a chemical-genetic method that allows for selective and reversible inactivation of its kinase activity in vivo. Results We generated a PP1 analog-sensitive variant of SAD-1. Through temporal inhibition of SAD-1 kinase activity we show that its activity is required for the establishment of both neuronal polarity and synaptic organization. However, while SAD-1 activity is needed strictly when neurons are polarizing, the temporal requirement for SAD-1 is less stringent in synaptic organization, which can also be re-established during maintenance. Conclusion This study reports the first temporal analysis of a neural kinase activity using the chemical-genetic system. It reveals that neuronal polarity and synaptic organization have distinct temporal requirements for SAD-1.

  17. Childhood adversity and psychosis: examinig whether the association is due to genetic confounding using a monozygotic twin differences approach

    OpenAIRE

    Alemany Sierra, Silvia; Goldberg, Ximena; Winkel, R; Gastó Ferrer, Cristóbal; V. Peralta; Fañanás Saura, Lourdes

    2013-01-01

    Purpose: To test whether the association between childhood adversity and positive and negative psychotic experiences is due to genetic confounding. Method: Childhood adversity and psychotic experiences were assessed in a sample of 226 twins from the general population. A monozygotic (MZ) twin differences approach was used to assess possible genetic confounding. Results: In the whole sample, childhood adversity was significantly associated with positive (β =.45; SE=.16; p=.008) and negative ps...

  18. A systems engineering approach to manage the complexity in sustainable chemical product-process design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    This paper provides a perspective on model-data based solution approaches for chemical product-process design, which consists of finding the identity of the candidate chemical product, designing the process that can sustainably manufacture it and verifying the performance of the product during...... application. The chemical product tree is potentially very large and a wide range of options exist for selecting the product to make, the raw material to use as well as the processing route to employ. It is shown that systematic computer-aided methods and tools integrated within a model-data based design...... framework can manage the complexity associated with product-process problems very efficiently. Three specific computer-aided tools (ICAS, Sustain-Pro and VPPDLab) have been presented and their applications to product-process design, highlighted....

  19. Universal Electrochemical/Chemical Simulator Based on an Exponentially Expanding Grid Network Approach

    Institute of Scientific and Technical Information of China (English)

    DENG,Zhao-Xiang(邓兆祥); LIN,Xiang-Qin(林祥钦); TONG,Zhong-Hua(童中华)

    2004-01-01

    A universal simulator capable of simulating virtually any user-defined electrochemical/chemical problems in one-dimensional diffusion geometry was developed based on an exponentially expanding grid modification of the existing network approach. Some generalized reaction-diffusion governing equations of an arbitrary electrochemical/chemical process were derived, and program controlled automatic generation of the corresponding PSPICE netlist file was realized. On the basis of the above techniques, a universal simulator package was realized, which is capable of dealing with arbitrarily complex electrochemical/chemical problems with one-dimensional diffusion geometry such as planar diffusion, spherical diffusion, cylindrical diffusion and rotational disk diffusion-convection processes. The building of such a simulator is easy and thus it would be very convenient to have it updated for simulations of newly raised electrochemical problems.

  20. From exposure to effect: a comparison of modeling approaches to chemical carcinogenesis.

    Science.gov (United States)

    van Leeuwen, I M; Zonneveld, C

    2001-10-01

    Standardized long-term carcinogenicity tests aim to reveal the relationship between exposure to a chemical and occurrence of a carcinogenic response. The analysis of such tests may be facilitated by the use of mathematical models. To what extent current models actually achieve this purpose is difficult to evaluate. Various aspects of chemically induced carcinogenesis are treated by different modeling approaches, which proceed very much in isolation of each other. With this paper we aim to provide for the non-mathematician a comprehensive and critical overview of models dealing with processes involved in chemical carcinogenesis. We cover the entire process of carcinogenesis, from exposure to effect. We succinctly summarize the biology underlying the models and emphasize the relationship between model assumptions and model formulations. The use of mathematics is restricted as far as possible with some additional information relegated to boxes. PMID:11673088

  1. An approach in building a chemical compound search engine in oracle database.

    Science.gov (United States)

    Wang, H; Volarath, P; Harrison, R

    2005-01-01

    A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework. PMID:17282834

  2. Design of tailor-made chemical blend using a decomposition-based computer-aided approach

    DEFF Research Database (Denmark)

    Yunus, Nor Alafiza; Gernaey, Krist; Manan, Z.A.; Woodley, John; Gani, Rafiqul

    2011-01-01

    Computer aided techniques form an efficient approach to solve chemical product design problems such as the design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product...... attributes (properties).The systematic computer-aided technique first establishes the search space, and then narrows it down in subsequent steps until a small number of feasible and promising candidates remain. At this point, experimental work may be conducted to verify if any or all the candidates satisfy...... the desired product attributes. Alternatively, rigorous modeling could also be used in this final step. In other words, the candidates are quickly generated and screened until a small number is left for final selection and evaluation by experiments and/or rigorous modeling. This paper presents a...

  3. Pollen Sterility—A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    Directory of Open Access Journals (Sweden)

    Albert P. Kausch

    2012-10-01

    Full Text Available Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of transgenes from GM crops. One approach for preventing and/or mitigating transgene flow is the production of trait linked pollen sterility. To evaluate the feasibility of generating pollen sterility lines for gene confinement and breeding purposes we tested the utility of a promoter (Zm13Pro from a maize pollen-specific gene (Zm13 for driving expression of the reporter gene GUS and the cytotoxic gene barnase in transgenic rice (Oryza sativa ssp. Japonica cv. Nipponbare as a monocot proxy for bioenergy grasses. This study demonstrates that the Zm13 promoter can drive pollen-specific expression in stably transformed rice and may be useful for gametophytic transgene confinement and breeding strategies by pollen sterility in food and bioenergy crops.

  4. A Tool to Develop Arabic Handwriting Recognition System Using Genetic Approach

    Directory of Open Access Journals (Sweden)

    Hanan Aljuaid

    2010-01-01

    Full Text Available Problem statement: Significant movement has been made in handwriting recognition technology over the last few years. Up until now, Arabic handwriting recognition systems have been limited to small and medium vocabulary applications, since most of them often rely on a database during the recognition process. The facility of dealing with large database, however, opens up many more applications. Approach: This study presented a complete system to recognize off-line Arabic handwriting image and Arabic handwriting and printed text database AHPD-UTM that used to implement and test the system. That system start from preprocessing and segmentation phases that deepened on thinning the image and found the V and H projection profile until recognition phase by genetic algorithm. Results: The genetic algorithm stand on feature extraction algorithm that defined six feature for each segment beak. The system can be recognized Arabic handwriting with 87% accuracy. The confusion and rejection rates are 8.4, those causes for several problems like characters with broken loops and character segmentation problem. Conclusion: Peak connection solved some of the segmentation problems and helped to provide better accuracy.

  5. Chemical Variation in a Dominant Tree Species: Population Divergence, Selection and Genetic Stability across Environments

    OpenAIRE

    Julianne M O'Reilly-Wapstra; Miller, Alison M.; Hamilton, Matthew G.; Dean Williams; Naomi Glancy-Dean; Potts, Brad M.

    2013-01-01

    Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E). We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs) in a dominant tree species, Eu...

  6. A Modified Genetic Algorithm for Product Family Optimization with Platform Specified by Information Theoretical Approach

    Institute of Scientific and Technical Information of China (English)

    CHEN Chun-bao; WANG Li-ya

    2008-01-01

    Many existing product family design methods assume a given platform, However, it is not an in-tuitive task to select the platform and unique variable within a product family. Meanwhile, most approachesare single-platform methods, in which design variables are either shared across all product variants or not atall. While in multiple-platform design, platform variables can have special value with regard to a subset ofproduct variants within the product family, and offer opportunities for superior overall design. An informationtheoretical approach incorporating fuzzy clustering and Shannon's entropy was proposed for platform variablesselection in multiple-platform product family. A 2-level chromosome genetic algorithm (2LCGA) was proposedand developed for optimizing the corresponding product family in a single stage, simultaneously determiningthe optimal settings for the product platform and unique variables. The single-stage approach can yield im-provements in the overall performance of the product family compared with two-stage approaches, in which thefirst stage involves determining the best settings for the platform and values of unique variables are found foreach product in the second stage. An example of design of a family of universal motors was used to verify theproposed method.

  7. An Interval-Valued Approach to Business Process Simulation Based on Genetic Algorithms and the BPMN

    Directory of Open Access Journals (Sweden)

    Mario G.C.A. Cimino

    2014-05-01

    Full Text Available Simulating organizational processes characterized by interacting human activities, resources, business rules and constraints, is a challenging task, because of the inherent uncertainty, inaccuracy, variability and dynamicity. With regard to this problem, currently available business process simulation (BPS methods and tools are unable to efficiently capture the process behavior along its lifecycle. In this paper, a novel approach of BPS is presented. To build and manage simulation models according to the proposed approach, a simulation system is designed, developed and tested on pilot scenarios, as well as on real-world processes. The proposed approach exploits interval-valued data to represent model parameters, in place of conventional single-valued or probability-valued parameters. Indeed, an interval-valued parameter is comprehensive; it is the easiest to understand and express and the simplest to process, among multi-valued representations. In order to compute the interval-valued output of the system, a genetic algorithm is used. The resulting process model allows forming mappings at different levels of detail and, therefore, at different model resolutions. The system has been developed as an extension of a publicly available simulation engine, based on the Business Process Model and Notation (BPMN standard.

  8. A HYBRID GENETIC ALGORITHM-NEURAL NETWORK APPROACH FOR PRICING CORES AND REMANUFACTURED CORES

    Directory of Open Access Journals (Sweden)

    M. Seidi

    2012-01-01

    Full Text Available

    ENGLISH ABSTRACT:Sustainability has become a major issue in most economies, causing many leading companies to focus on product recovery and reverse logistics. Remanufacturing is an industrial process that makes used products reusable. One of the important aspects in both reverse logistics and remanufacturing is the pricing of returned and remanufactured products (called cores. In this paper, we focus on pricing the cores and remanufactured cores. First we present a mathematical model for this purpose. Since this model does not satisfy our requirements, we propose a simulation optimisation approach. This approach consists of a hybrid genetic algorithm based on a neural network employed as the fitness function. We use automata learning theory to obtain the learning rate required for training the neural network. Numerical results demonstrate that the optimal value of the acquisition price of cores and price of remanufactured cores is obtained by this approach.

    AFRIKAANSE OPSOMMING: Volhoubaarheid het ‘n belangrike saak geword in die meeste ekonomieë, wat verskeie maatskappye genoop het om produkherwinning en omgekeerde logistiek te onder oë te neem. Hervervaardiging is ‘n industriële proses wat gebruikte produkte weer bruikbaar maak. Een van die belangrike aspekte in beide omgekeerde logistiek en hervervaardiging is die prysbepaling van herwinne en hervervaardigde produkte. Hierdie artikel fokus op die prysbepalingsaspekte by wyse van ‘n wiskundige model.

  9. Identification of a thienopyrimidine derivatives target by a kinome and chemical biology approach.

    Science.gov (United States)

    Lee, Chulho; Yang, Jee Sun; Han, Gyoonhee

    2015-09-01

    Target identification through chemical biology has been considered one of the most efficient approaches for drug discovery. Thienopyrimidine derivatives were designed to discover potent IκB kinase β (IKKβ) inhibitors based on a known IKKβ inhibitor library. Most of the thienopyrimidine derivatives inhibited nitric oxide and tumor necrosis factor alpha, which are downstream of the NF-κB signaling pathway, but not IKKβ. To identify the appropriate targets of thienopyrimidine analogues, chemical biology approaches, including text mining and a subsequent kinase panel assay from the kinome profiling were used. Based on the results, Fms-like tyrosine kinase 3 was found to be the target for thienopyrimidine derivatives, and was confirmed to be a potent inhibitor for acute myeloid leukemia. PMID:26186885

  10. Strategies and chemical design approaches to reduce the potential for formation of reactive metabolic species.

    Science.gov (United States)

    Argikar, Upendra A; Mangold, James B; Harriman, Shawn P

    2011-01-01

    Metabolic activation of new chemical entities to reactive intermediates is routinely monitored in drug discovery and development. Reactive intermediates may bind to cellular macromolecules such as proteins, DNA and may eventually lead to cell death via necrosis, apoptosis or oxidative stress. The evidence that the ultimate outcome of metabolic activation is an adverse drug reaction manifested as in vivo toxicity, is at best circumstantial. However, understanding the process of bioactivation of structural alerts by trapping the reactive intermediates is critical to guide medicinal chemistry efforts in quest for safer and potent molecules. This commentary provides a brief introduction to adverse drug reactions and mechanisms of reactive intermediate formation for various functional groups, followed by a review of chemical design approaches, examples of such strategies, possible isosteric replacements for structural alerts and rationalization of laboratory approaches to determine reactive intermediates, as a guide to today's medicinal chemist. PMID:21320068

  11. Comparison of Pyrolysis Mass Spectrometry and Near Infrared Spectroscopy for Genetic Analysis of Lignocellulose Chemical Composition in Populus

    Directory of Open Access Journals (Sweden)

    Jianxing Zhang

    2014-03-01

    Full Text Available Genetic analysis of wood chemical composition is often limited by the cost and throughput of direct analytical methods. The speed and low cost of Fourier transform near infrared (FT-NIR overcomes many of these limitations, but it is an indirect method relying on calibration models that are typically developed and validated with small sample sets. In this study, we used >1500 young greenhouse grown trees from a clonally propagated single Populus family, grown at low and high nitrogen, and compared FT-NIR calibration sample sizes of 150, 250, 500 and 750 on calibration and prediction model statistics, and heritability estimates developed with pyrolysis molecular beam mass spectrometry (pyMBMS wood chemical composition. As calibration sample size increased from 150 to 750, predictive model statistics improved slightly. Overall, stronger calibration and prediction statistics were obtained with lignin, S-lignin, S/G ratio, and m/z 144 (an ion from cellulose, than with C5 and C6 carbohydrates, and m/z 114 (an ion from xylan. Although small differences in model statistics were observed between the 250 and 500 sample calibration sets, when predicted values were used for calculating genetic control, the 500 sample set gave substantially more similar results to those obtained with the pyMBMS data. With the 500 sample calibration models, genetic correlations obtained with FT-NIR and pyMBMS methods were similar. Quantitative trait loci (QTL analysis with pyMBMS and FT-NIR predictions identified only three common loci for lignin traits. FT-NIR identified four QTLs that were not found with pyMBMS data, and these QTLs were for the less well predicted carbohydrate traits.

  12. A ``partitioned leaping'' approach for multiscale modeling of chemical reaction dynamics

    Science.gov (United States)

    Harris, Leonard A.; Clancy, Paulette

    2006-10-01

    We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single partitioned leaping algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters, and is particularly well suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation, and demonstrate the utility of the method via illustrative examples.

  13. Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases.

    Science.gov (United States)

    Hu, Johnny H; Davis, Kevin M; Liu, David R

    2016-01-21

    Programmable DNA nucleases have provided scientists with the unprecedented ability to probe, regulate, and manipulate the human genome. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat-Cas9 system (CRISPR-Cas9) represent a powerful array of tools that can bind to and cleave a specified DNA sequence. In their canonical forms, these nucleases induce double-strand breaks at a DNA locus of interest that can trigger cellular DNA repair processes that disrupt or replace genes. The fusion of these programmable nucleases with a variety of other protein domains has led to a rapidly growing suite of tools for activating, repressing, visualizing, and modifying loci of interest. Maximizing the usefulness and therapeutic relevance of these tools, however, requires precisely controlling their activity and specificity to minimize potentially toxic side effects arising from off-target activities. This need has motivated the application of chemical biology principles and methods to genome-editing proteins, including the engineering of variants of these proteins with improved or altered specificities, and the development of genetic, chemical, optical, and protein delivery methods that control the activity of these agents in cells. Advancing the capabilities, safety, effectiveness, and therapeutic relevance of genome-engineering proteins will continue to rely on chemical biology strategies that manipulate their activity, specificity, and localization. PMID:26933736

  14. Optimization of Electrical System for Offshore Wind Farms via a Genetic Algorithm Approach

    DEFF Research Database (Denmark)

    Zhao, Menghua

    , and the LTC limitation of transformers, the power generation limits and the voltage operation range are considered as the constraints. The optimization method combined with probabilistic analysis is used to obtain the capacity of a given wind farm site. The OES-OWF is approached by Genetic Algorithm (GA...... losses and power generation. This work proposes a serial AC-DC integrated load flow algorithm for variable speed offshore wind farms (VSOWF). The model of DC/DC converters is proposed and integrated into the basic DC load flow algorithm by modifying the Jacobian matrix. Two iterative methods are proposed...... to respectively take into account the control strategy and power losses of PWM converters. A reliability index, Loss of Generation Ratio Probability (LOGRP), is proposed to evaluate the electrical system of OWF. The LOGRP doesn't depend on the load demand and has weaker correlation with wind speed. Based...

  15. A GENETIC ALGORITHM APPROACH FOR SOLVING THE TRIM LOSS OPTIMIZATION PROBLEM IN PAPER MANUFACTURING INDUSTRIES

    Directory of Open Access Journals (Sweden)

    BINITHA S

    2012-05-01

    Full Text Available Minimizing the trim loss is one of the most common issues arising in the paper manufacturing industries and recently has been considered as one among the important research topics in industrial engineering. In the trim loss optimization problem, the machine will turn up with jumbos of constant size over which it is required to satisfy rolls of variable size and variable quantity as per customer requirement. Hence an optimal cutting plan has to be made so as to minimize the wastage or trim loss. This paper addresses the trim loss optimizationproblem by having a genetic algorithm approach. Numerical examples illustrate the efficiency and practicality of the proposed method. The objective is to produce a set of paper rolls from jumbo such that the trim loss is minimized. This can be considered as a cost minimization or as a profit maximization problem.

  16. Plant responses to UV and blue light: biochemical and genetic approaches

    International Nuclear Information System (INIS)

    UV and blue light control many aspects of plant growth and development. It is evident that several different photoreceptors mediate responses to UV and blue light, and there are reports of the functional and biochemical characterisation of a putative photoreceptor for phototropism and of the functional and molecular characterisation of the CRY1 photoreceptor, encoded by the Arabidopsis HY4 gene. The CRY1 photoreceptor mediates extension growth and gene expression responses to UV-A/blue light presumably through different or branching signal transduction pathways. Progress has been made in cell physiological and biochemical studies of UV/blue light signal transduction, but much remains to be done to relate candidate UV/blue signal transduction events to particular photoreceptors and responses. The application of a genetic approach in Arabidopsis has been responsible for many advances in understanding UV/blue responses, but further UV-B, UV-A and blue light response mutants need to be isolated. (author)

  17. NOVEL APPROACH FOR ROBOT PATH PLANNING BASED ON NUMERICAL ARTIFICIAL POTENTIAL FIELD AND GENETIC ALGORITHM

    Institute of Scientific and Technical Information of China (English)

    WANG Weizhong; ZHAO Jie; GAO Yongsheng; CAI Hegao

    2006-01-01

    A novel approach for collision-free path planning of a multiple degree-of-freedom (DOF)articulated robot in a complex environment is proposed. Firstly, based on visual neighbor point (VNP), a numerical artificial potential field is constructed in Cartesian space, which provides the heuristic information, effective distance to the goal and the motion direction for the motion of the robot joints. Secondly, a genetic algorithm, combined with the heuristic rules, is used in joint space to determine a series of contiguous configurations piecewise fiom initial configuration until the goal configuration is attained. A simulation shows that the method can not only handle issues on path planning of the articulated robots in environment with complex obstacles, but also improve the efficiency and quality of path planning.

  18. Beyond the pseudo-time-dependent approach: chemical models of dense core precursors

    OpenAIRE

    Hassel, G. E.; Herbst, E.; Bergin, E. A.

    2010-01-01

    Context: Chemical models of dense cloud cores often utilize the so-called pseudo-time-dependent approximation, in which the physical conditions are held fixed and uniform as the chemistry occurs. In this approximation, the initial abundances chosen, which are totally atomic in nature except for molecular hydrogen, are artificial. A more detailed approach to the chemistry of dense cold cores should include the physical evolution during their early stages of formation. Aims: Our major goal is t...

  19. A Group-Theoretical Approach to the Periodic Table of Chemical Elements: Old and New Developments

    OpenAIRE

    Kibler, M. R.

    2005-01-01

    This paper is a companion article to the review paper by the present author devoted to the classification of matter constituents (chemical elements and particles) and published in the first part of the proceedings of The Second Harry Wiener International Memorial Conference (see quant-ph/0310155). It is mainly concerned with a group-theoretical approach to the Periodic Table of the neutral elements based on the noncompact group SO(4,2)xSU(2).

  20. Bin packing approach for solving VLSI circuit partitioning problem using Genetic algorithm

    Directory of Open Access Journals (Sweden)

    Prof. Sharadindu Roy

    2012-12-01

    Full Text Available In this paper,the circuit partitioning using genetic algorithm with bin packing concept has been attempted. In    this practical paper solution is easy and we can easily apply genetic operator in this type of problem. The bin packing problem is to find the minimum number of bins needed to pack a given set of objects of known sizes so they do not exceed the capacity of each bin. Complexity is both time in space, provided size of problem an as integer (count is infinite.This problem is known NP-hard. The technique of our approach is to be design module trick. We can be realizing with self standard IC chip. Obviously we have taken into account minimum power conjunction. The solution of a circuit partitioning problem is global optimum. Like circuit partitioning is the more critical step in the physical design of various circuit in VLSI.In the partitioning main objective is to minimize the number of cuts.This chapter addresses the problem of partitioning and particular the use of the genetic algorithms for circuit partitioning.The object to be partitioned in VLSI design are typically logic gates or instances of standard cell. Circuit partitioning is one of the important parts in chip designing. We let, the number of bins will be needed equal to be number of genes divided by number of bins. At first the genes will be insert in first bin until the bin is not full, when bin is full then insert second bin and so on. Our method calculates the fitness value and discards solution with low fitness value. The increase in number of crossover point does not necessarily increase the fitness, as the fitness achieved depends on crossover as well as mutation probability. Especially in the paper find minimum cut size. If we get, cut size is same on generation than change the crossover boundary. This paper shows bin packing approach for the circuit partitioning using genetic algorithm . Genetic algorithm is an evolutionary optimization technique based on Darwinian

  1. On the Predictability of Risk Box Approach by Genetic Programming Method for Bankruptcy Prediction

    Directory of Open Access Journals (Sweden)

    Alireza Bahiraie

    2009-01-01

    Full Text Available Problem statement: Theoretical based data representation is an important tool for model selection and interpretations in bankruptcy analysis since the numerical representation are much less transparent. Some methodological problems concerning financial ratios such as non-proportionality, non-asymetricity, non-scalicity are solved in this study and we presented a complementary technique for empirical analysis of financial ratios and bankruptcy risk. Approach: This study presented new geometric technique for empirical analysis of bankruptcy risk using financial ratios. Within this framework, we proposed the use of a new ratio representation which named Risk Box measure (RB. We demonstrated the application of this geometric approach for variable representation, data visualization and financial ratios at different stages of corporate bankruptcy prediction models based on financial balance sheet ratios. These stages were the selection of variables (predictors, accuracy of each estimation model and the representation of each model for transformed and common ratios. Results: We provided evidence of extent to which changes in values of this index were associated with changes in each axis values and how this may alter our economic interpretation of changes in the patterns and direction of risk components. Results of Genetic Programming (GP models were compared as different classification models and results showed the classifiers outperform by modified ratios. Conclusion/Recommendations: In this study, a new dimension to risk measurement and data representation with the advent of the Share Risk method (SR was proposed. Genetic programming method is substantially superior to the traditional methods such as MDA or Logistic method. It was strongly suggested the use of SR methodology for ratio analysis, which provided a conceptual and complimentary methodological solution to many problems associated with the use of ratios. Respectively, GP will provide

  2. [Genetics and genetic counseling].

    Science.gov (United States)

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  3. A genetic predictive model for canine hip dysplasia: integration of Genome Wide Association Study (GWAS and candidate gene approaches.

    Directory of Open Access Journals (Sweden)

    Nerea Bartolomé

    Full Text Available Canine hip dysplasia is one of the most prevalent developmental orthopedic diseases in dogs worldwide. Unfortunately, the success of eradication programs against this disease based on radiographic diagnosis is low. Adding the use of diagnostic genetic tools to the current phenotype-based approach might be beneficial. The aim of this study was to develop a genetic prognostic test for early diagnosis of hip dysplasia in Labrador Retrievers. To develop our DNA test, 775 Labrador Retrievers were recruited. For each dog, a blood sample and a ventrodorsal hip radiograph were taken. Dogs were divided into two groups according to their FCI hip score: control (A/B and case (D/E. C dogs were not included in the sample. Genetic characterization combining a GWAS and a candidate gene strategy using SNPs allowed a case-control population association study. A mathematical model which included 7 SNPs was developed using logistic regression. The model showed a good accuracy (Area under the ROC curve = 0.85 and was validated in an independent population of 114 dogs. This prognostic genetic test represents a useful tool for choosing the most appropriate therapeutic approach once genetic predisposition to hip dysplasia is known. Therefore, it allows a more individualized management of the disease. It is also applicable during genetic selection processes, since breeders can benefit from the information given by this test as soon as a blood sample can be collected, and act accordingly. In the authors' opinion, a shift towards genomic screening might importantly contribute to reducing canine hip dysplasia in the future. In conclusion, based on genetic and radiographic information from Labrador Retrievers with hip dysplasia, we developed an accurate predictive genetic test for early diagnosis of hip dysplasia in Labrador Retrievers. However, further research is warranted in order to evaluate the validity of this genetic test in other dog breeds.

  4. A Genetic Predictive Model for Canine Hip Dysplasia: Integration of Genome Wide Association Study (GWAS) and Candidate Gene Approaches

    Science.gov (United States)

    Bartolomé, Nerea; Segarra, Sergi; Artieda, Marta; Francino, Olga; Sánchez, Elisenda; Szczypiorska, Magdalena; Casellas, Joaquim; Tejedor, Diego; Cerdeira, Joaquín; Martínez, Antonio; Velasco, Alfonso; Sánchez, Armand

    2015-01-01

    Canine hip dysplasia is one of the most prevalent developmental orthopedic diseases in dogs worldwide. Unfortunately, the success of eradication programs against this disease based on radiographic diagnosis is low. Adding the use of diagnostic genetic tools to the current phenotype-based approach might be beneficial. The aim of this study was to develop a genetic prognostic test for early diagnosis of hip dysplasia in Labrador Retrievers. To develop our DNA test, 775 Labrador Retrievers were recruited. For each dog, a blood sample and a ventrodorsal hip radiograph were taken. Dogs were divided into two groups according to their FCI hip score: control (A/B) and case (D/E). C dogs were not included in the sample. Genetic characterization combining a GWAS and a candidate gene strategy using SNPs allowed a case-control population association study. A mathematical model which included 7 SNPs was developed using logistic regression. The model showed a good accuracy (Area under the ROC curve = 0.85) and was validated in an independent population of 114 dogs. This prognostic genetic test represents a useful tool for choosing the most appropriate therapeutic approach once genetic predisposition to hip dysplasia is known. Therefore, it allows a more individualized management of the disease. It is also applicable during genetic selection processes, since breeders can benefit from the information given by this test as soon as a blood sample can be collected, and act accordingly. In the authors’ opinion, a shift towards genomic screening might importantly contribute to reducing canine hip dysplasia in the future. In conclusion, based on genetic and radiographic information from Labrador Retrievers with hip dysplasia, we developed an accurate predictive genetic test for early diagnosis of hip dysplasia in Labrador Retrievers. However, further research is warranted in order to evaluate the validity of this genetic test in other dog breeds. PMID:25874693

  5. A genetic predictive model for canine hip dysplasia: integration of Genome Wide Association Study (GWAS) and candidate gene approaches.

    Science.gov (United States)

    Bartolomé, Nerea; Segarra, Sergi; Artieda, Marta; Francino, Olga; Sánchez, Elisenda; Szczypiorska, Magdalena; Casellas, Joaquim; Tejedor, Diego; Cerdeira, Joaquín; Martínez, Antonio; Velasco, Alfonso; Sánchez, Armand

    2015-01-01

    Canine hip dysplasia is one of the most prevalent developmental orthopedic diseases in dogs worldwide. Unfortunately, the success of eradication programs against this disease based on radiographic diagnosis is low. Adding the use of diagnostic genetic tools to the current phenotype-based approach might be beneficial. The aim of this study was to develop a genetic prognostic test for early diagnosis of hip dysplasia in Labrador Retrievers. To develop our DNA test, 775 Labrador Retrievers were recruited. For each dog, a blood sample and a ventrodorsal hip radiograph were taken. Dogs were divided into two groups according to their FCI hip score: control (A/B) and case (D/E). C dogs were not included in the sample. Genetic characterization combining a GWAS and a candidate gene strategy using SNPs allowed a case-control population association study. A mathematical model which included 7 SNPs was developed using logistic regression. The model showed a good accuracy (Area under the ROC curve = 0.85) and was validated in an independent population of 114 dogs. This prognostic genetic test represents a useful tool for choosing the most appropriate therapeutic approach once genetic predisposition to hip dysplasia is known. Therefore, it allows a more individualized management of the disease. It is also applicable during genetic selection processes, since breeders can benefit from the information given by this test as soon as a blood sample can be collected, and act accordingly. In the authors' opinion, a shift towards genomic screening might importantly contribute to reducing canine hip dysplasia in the future. In conclusion, based on genetic and radiographic information from Labrador Retrievers with hip dysplasia, we developed an accurate predictive genetic test for early diagnosis of hip dysplasia in Labrador Retrievers. However, further research is warranted in order to evaluate the validity of this genetic test in other dog breeds. PMID:25874693

  6. A genetic algorithm approach for assessing soil liquefaction potential based on reliability method

    Indian Academy of Sciences (India)

    M H Bagheripour; I Shooshpasha; M Afzalirad

    2012-02-01

    Deterministic approaches are unable to account for the variations in soil’s strength properties, earthquake loads, as well as source of errors in evaluations of liquefaction potential in sandy soils which make them questionable against other reliability concepts. Furthermore, deterministic approaches are incapable of precisely relating the probability of liquefaction and the factor of safety (FS). Therefore, the use of probabilistic approaches and especially, reliability analysis is considered since a complementary solution is needed to reach better engineering decisions. In this study, Advanced First-Order Second-Moment (AFOSM) technique associated with genetic algorithm (GA) and its corresponding sophisticated optimization techniques have been used to calculate the reliability index and the probability of liquefaction. The use of GA provides a reliable mechanism suitable for computer programming and fast convergence. A new relation is developed here, by which the liquefaction potential can be directly calculated based on the estimated probability of liquefaction (), cyclic stress ratio (CSR) and normalized standard penetration test (SPT) blow counts while containing a mean error of less than 10% from the observational data. The validity of the proposed concept is examined through comparison of the results obtained by the new relation and those predicted by other investigators. A further advantage of the proposed relation is that it relates and FS and hence it provides possibility of decision making based on the liquefaction risk and the use of deterministic approaches. This could be beneficial to geotechnical engineers who use the common methods of FS for evaluation of liquefaction. As an application, the city of Babolsar which is located on the southern coasts of Caspian Sea is investigated for liquefaction potential. The investigation is based primarily on in situ tests in which the results of SPT are analysed.

  7. Genetic and Environmental Influences on Sleep Quality: Quantitative and Molecular Genetic Approaches to an Understanding of Individual Differences

    OpenAIRE

    Barclay, Nicola L

    2011-01-01

    There are vast inter-individual differences in sleep quality in the general population – whilst some individuals sleep well with little or no sleep disturbance, others experience frequent sleep disturbances, problems which often manifest into chronic sleep disorders such as insomnia. The aim of this thesis is to explore factors accounting for these observed differences in sleep quality between individuals. Using data from a large-scale twin study this thesis uses behavioural genetic technique...

  8. Epigenetic and genetic factors in the cellular response to radiations and DNA-damaging chemicals

    International Nuclear Information System (INIS)

    DNA-damaging agents are widely used as therapeutic tools for a variety of disease states. Many such agents are considered to produce detrimental side effects. Thus, it is important to evaluate both therapeutic efficacy and potential risk. DNA-damaging agents can be so evaluated by comparison to agents whose therapeutic benefit and potential hazards are better known. We propose a framework for such comparison, demonstrating that a simple transformation of cytotoxicity-dose response patterns permits a facile comparison of variation between cells exposed to a single DNA-damaging agent or to different cytotoxic agents. Further, by transforming data from experiments which compare responses of 2 cell populations to an effects ratio, different patterns for the changes in cytotoxicity produced by epigenetic and genetic factors were compared. Using these transformations, we found that there is a wide variation (a factor of 4) between laboratories for a single agent (UVC) and only a slightly larger variation (factor of 6) between normal cell response for different types of DNA-damaging agents (x-ray, UVC, alkylating agents, crosslinking agents). Epigenetic factors such as repair and recovery appear to be a factor only at higher dose levels. Comparison in the cytotoxic effect of a spectrum of DNA-damaging agents in xeroderma pigmentosum, ataxia telangiectasia, and Fanconi's anemia cells indicates significantly different patterns, implying that the effect, and perhaps the nature, of these genetic conditions are quite different

  9. A Hybrid Improved Genetic Algorithm and Its Application in Dynamic Optimization Problems of Chemical Processes

    Institute of Scientific and Technical Information of China (English)

    SUN Fan; DU Wenli; QI Rongbin; QIAN Feng; ZHONG Weimin

    2013-01-01

    The solutions of dynamic optimization problems are usually very difficult due to their highly nonlinear and multidimensional nature.Genetic algorithm(GA)has been proved to be a feasible method when the gradient is difficult to calculate.Its advantage is that the control profiles at all time stages are optimized simultaneously,but its convergence is very slow in the later period of evolution and it is easily trapped in the local optimum.In this study,a hybrid improved genetic algorithm(HIGA)for solving dynamic optimization problems is proposed to overcome these defects.Simplex method(SM)is used to perform the local search in the neighborhood of the optimal solution.By using SM,the ideal searching direction of global optimal solution could be found as soon as possible and the convergence speed of the algorithm is improved.The hybrid algorithm presents some improvements,such as protecting the best individual,accepting immigrations,as well as employing adaptive crossover and Gaussian mutation operators.The efficiency of the proposed algorithm is demonstrated by solving several dynamic optimization problems.At last,HIGA is applied to the optimal production of secreted protein in a fed batch reactor and the optimal feed-rate found by HIGA is effective and relatively stable.

  10. Agent-Based Modeling in Supply Chain Management:A Genetic Algorithm and Fuzzy Logic Approach

    Directory of Open Access Journals (Sweden)

    Meriem DJENNAS

    2012-09-01

    Full Text Available In today’s global market, reaching a competitive advantage by integrating firms in a supply chain management strategy becomes a key success for any firm seeking to survive in a complex environment. However, as interactions among agents in the supply chain management (SCM remain unpredictable, simulation appears as a powerful tool aiming to predict market behavior and agents’ performance levels. This paper discusses the issues of supply chain management and the requirements for supply chain simulation modeling. It reviews the relationships amongArtificial Intelligence (AI and SCM and concludes that under some conditions, SCM models exhibit some inadequacies that may be enriched by the use of AI tools. This approach aims to test the supply chain activities of nine companies in the crude oil market. The objective is to tackle the issues under which agents can coexist in a competitive environment. Furthermore, we will specify the supply chain management trading interaction amongagents by using an optimization approach based on a Genetic Algorithm (AG, Clustering and Fuzzy Logic (FL.Results support the view that the structured model provides a good tool for modeling the supply chain activities using AI methodology.

  11. A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

    CERN Document Server

    Harris, L A; Clancy, Paulette; Harris, Leonard A.

    2006-01-01

    We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single *partitioned leaping* algorithmic framework. Distinguishing characteristics of the method include automatic, dynamic and theoretically justifiable time step determination and timescale separation procedures that utilize concepts underlying the tau-leap approach [D.T. Gillespie, J. Chem. Phys. 115, 1716 (2001); D.T. Gillespie and L.R. Petzold, J. Chem. Phys. 119, 8229 (2003)] and require the definition of only three model-independent parameters. Both procedures are based on an individual (but not independent) consideration of reactions, a subtle yet significant ideological concept used in the development of previous exact-stochastic simulation methods [D.T. Gillespie, J. Comput. Phys. 22, 403 (1976); M.A. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000)]. The result is a method that correctly accounts for ...

  12. Applying new genetic approaches to improve quality of population assessment of green and loggerhead turtles

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — As the NOAA-Fisheries? National Sea Turtle Genetics Lab, the SWFSC Marine Turtle Genetics Program has the lead responsibility for generating, analyzing and...

  13. Enhancing the Capability of N-Dimension Self-Organizing Petrinet using Neuro-Genetic Approach

    OpenAIRE

    Manuj Darbari; Rishi Asthana; Hasan Ahmed; Neelu Jyoti Ahuja

    2011-01-01

    The paper highlight intelligent Urban Traffic control using Neuro-Genetic Petrinet. The combination of genetic algorithm provides dynamic change of weight for faster learning and converging of Neuro-Petrinet.

  14. Enhancing the Capability of N-Dimension Self-Organizing Petrinet using Neuro-Genetic Approach

    Directory of Open Access Journals (Sweden)

    Manuj Darbari

    2011-05-01

    Full Text Available The paper highlight intelligent Urban Traffic control using Neuro-Genetic Petrinet. The combination of genetic algorithm provides dynamic change of weight for faster learning and converging of Neuro-Petrinet.

  15. Human genetic marker for resistance to radiations and chemicals. 1998 annual progress report

    International Nuclear Information System (INIS)

    'The broad objective of the project is to understand the molecular basis for the response of cells to radiations and chemicals, with the pragmatic goal of being able to identify human subpopulations that are exceptionally sensitive to DNA damaging agents. The project focuses on HRAD9, a human orthologue of the fission yeast Schizosaccharomyces pombe gene rad9. S. pombe rad9::ura4+ mutant cells are highly sensitive to ionizing radiation, UV and many chemicals, such as the DNA synthesis inhibitor hydroxyurea. They also lack the ability to delay cycling transiently in S phase or in G2 following a block in DNA replication or after incurring DNA damage, respectively -i.e., they lack checkpoint controls. The attempt by mutant cells to progress through mitosis in the absence of fully intact DNA accounts at least in part for their sensitivity to DNA damaging agents. Cells bearing rad9::ura4+ also aberrantly regulate UVDE, an enzyme that participates in a secondary DNA excision repair pathway. The key role played by S. pombe rad9 in promoting resistance to chemicals and radiations suggests that the evolutionarily conserved human cognate also has important functions in mammals. The first set of aims in this proposal centers on characterizing the structure and expression of HRAD9, to assess structure/function relationships and potentially link protein activity to a specific tissue. The next set of aims focuses on determining the role of HRAD9 in radio/chemoresponsiveness and cancer.'

  16. An Improved Approach for Materialized View Selection Based on Genetic Algorithm

    OpenAIRE

    Lijuan Zhou; Xiaoxu He; Kang Li

    2012-01-01

    This paper presents an improved genetic algorithm to solve the materialized view selection problem under query cost constraints. The algorithm dynamically changes the crossover probability and mutation probability in the process of genetic. In this way, it can not only maintain the population diversity, but also ensure the convergence of the genetic algorithm. So it effectively improves the optimization ability of genetic algorithm, thus avoiding the "evolutionary stagnation" problems. Meanwh...

  17. Control of bovine spongiform encephalopathy by genetic engineering: Possible approaches and regulatory considerations

    International Nuclear Information System (INIS)

    Full text: Transmissible spongiform encephalopathies (TSE), including bovine spongiform encephalopathy (BSE) and scrapie in sheep, are diseases in which affected animals exhibit abnormal neurological behavior associated with accumulation of prion protein in nervous system tissues. TSEs also occur in humans and include sporadic Creutzfeldt-Jakob disease (CJD), as well as its new variant (nvCJD) believed to be related to consumption of meat from BSE cattle. Since the emergence of BSE, also known as 'mad cow disease' in 1986, significant numbers of BSE cattle have been diagnosed in several countries and there have been more than 100 deaths from definite or probable nvCJD in humans. This paper examines a possible genetic modification that may render cattle resistant to BSE. Prion proteins (PrP), present in both animals and humans, consist of approximately 250 amino acids and play a role in copper transport and regulation in tissues. The conversion of a normal, wild-type PrPC into the pathogenic prion PrPSc, involves a change in protein folding. Presence of aberrantly folded PrPSc stimulates the conversion of PrPC to PrPSc and the accumulation of PrPSc leads to a dysfunction of the central neural system. The aberrant PrPSc is virtually indestructible as it is not digested by proteases, unaffected by sterilization techniques, high doses of gamma irradiation, or incineration. Naturally occurring scrapie resistant sheep that do not convert PrPC to PrPSc, have the 'ARR' genotype, i.e. amino acids alanine, arginine and arginine in PrP positions 136, 154 and 171. Sheep selection for scrapie resistance based on DNA analyses is now in progress. In humans, the presence of lysine instead of glutamine at position 219 of the PrP amino acid chain results in resistance to sporadic CJD. Any publication on existence of a similar resistance to BSE has not been found in available literature. Research with laboratory mice indicated a possible genetic engineering approach to the

  18. A novel landscape genetic approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum).

    Science.gov (United States)

    Ruiz-Lopez, M J; Barelli, C; Rovero, F; Hodges, K; Roos, C; Peterman, W E; Ting, N

    2016-02-01

    A comprehensive understanding of how human disturbance affects tropical forest ecosystems is critical for the mitigation of future losses in global biodiversity. Although many genetic studies of tropical forest fragmentation have been conducted to provide insight into this issue, relatively few have incorporated landscape data to explicitly test the effects of human disturbance on genetic differentiation among populations. In this study, we use a newly developed landscape genetic approach that relies on a genetic algorithm to simultaneously optimize resistance surfaces to investigate the effects of human disturbance in the Udzungwa Mountains of Tanzania, which is an important part of a universally recognized biodiversity hotspot. Our study species is the endangered Udzungwa red colobus monkey (Procolobus gordonorum), which is endemic to the Udzungwa Mountains and a known indicator species that thrives in large and well-protected blocks of old growth forest. Population genetic analyses identified significant population structure among Udzungwa red colobus inhabiting different forest blocks, and Bayesian cluster analyses identified hierarchical structure. Our new method for creating composite landscape resistance models found that the combination of fire density on the landscape and distance to the nearest village best explains the genetic structure observed. These results demonstrate the effects that human activities are having in an area of high global conservation priority and suggest that this ecosystem is in a precarious state. Our study also illustrates the ability of our novel landscape genetic method to detect the impacts of relatively recent landscape features on a long-lived species. PMID:26374237

  19. Molecule-based approach for computing chemical-reaction rates in upper atmosphere hypersonic flows.

    Energy Technology Data Exchange (ETDEWEB)

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert

    2009-08-01

    This report summarizes the work completed during FY2009 for the LDRD project 09-1332 'Molecule-Based Approach for Computing Chemical-Reaction Rates in Upper-Atmosphere Hypersonic Flows'. The goal of this project was to apply a recently proposed approach for the Direct Simulation Monte Carlo (DSMC) method to calculate chemical-reaction rates for high-temperature atmospheric species. The new DSMC model reproduces measured equilibrium reaction rates without using any macroscopic reaction-rate information. Since it uses only molecular properties, the new model is inherently able to predict reaction rates for arbitrary nonequilibrium conditions. DSMC non-equilibrium reaction rates are compared to Park's phenomenological non-equilibrium reaction-rate model, the predominant model for hypersonic-flow-field calculations. For near-equilibrium conditions, Park's model is in good agreement with the DSMC-calculated reaction rates. For far-from-equilibrium conditions, corresponding to a typical shock layer, the difference between the two models can exceed 10 orders of magnitude. The DSMC predictions are also found to be in very good agreement with measured and calculated non-equilibrium reaction rates. Extensions of the model to reactions typically found in combustion flows and ionizing reactions are also found to be in very good agreement with available measurements, offering strong evidence that this is a viable and reliable technique to predict chemical reaction rates.

  20. From animal models to human disease: a genetic approach for personalized medicine in ALS.

    Science.gov (United States)

    Picher-Martel, Vincent; Valdmanis, Paul N; Gould, Peter V; Julien, Jean-Pierre; Dupré, Nicolas

    2016-01-01

    Amyotrophic Lateral Sclerosis (ALS) is the most frequent motor neuron disease in adults. Classical ALS is characterized by the death of upper and lower motor neurons leading to progressive paralysis. Approximately 10 % of ALS patients have familial form of the disease. Numerous different gene mutations have been found in familial cases of ALS, such as mutations in superoxide dismutase 1 (SOD1), TAR DNA-binding protein 43 (TDP-43), fused in sarcoma (FUS), C9ORF72, ubiquilin-2 (UBQLN2), optineurin (OPTN) and others. Multiple animal models were generated to mimic the disease and to test future treatments. However, no animal model fully replicates the spectrum of phenotypes in the human disease and it is difficult to assess how a therapeutic effect in disease models can predict efficacy in humans. Importantly, the genetic and phenotypic heterogeneity of ALS leads to a variety of responses to similar treatment regimens. From this has emerged the concept of personalized medicine (PM), which is a medical scheme that combines study of genetic, environmental and clinical diagnostic testing, including biomarkers, to individualized patient care. In this perspective, we used subgroups of specific ALS-linked gene mutations to go through existing animal models and to provide a comprehensive profile of the differences and similarities between animal models of disease and human disease. Finally, we reviewed application of biomarkers and gene therapies relevant in personalized medicine approach. For instance, this includes viral delivering of antisense oligonucleotide and small interfering RNA in SOD1, TDP-43 and C9orf72 mice models. Promising gene therapies raised possibilities for treating differently the major mutations in familial ALS cases. PMID:27400686

  1. Modeling solar radiation of Mediterranean region in Turkey by using fuzzy genetic approach

    International Nuclear Information System (INIS)

    The study investigates the ability of FG (fuzzy genetic) approach in modeling solar radiation of seven cities from Mediterranean region of Anatolia, Turkey. Latitude, longitude, altitude and month of the year data from the Adana, K. Maras, Mersin, Antalya, Isparta, Burdur and Antakya cities are used as inputs to the FG model to estimate one month ahead solar radiation. FG model is compared with ANNs (artificial neural networks) and ANFIS (adaptive neruro fuzzzy inference system) models with respect to RMSE (root mean square errors), MAE (mean absolute errors) and determination coefficient (R2) statistics. Comparison results indicate that the FG model performs better than the ANN and ANFIS models. It is found that the FG model can be successfully used for estimating solar radiation by using latitude, longitude, altitude and month of the year information. FG model with RMSE = 6.29 MJ/m2, MAE = 4.69 MJ/m2 and R2 = 0.905 in the test stage was found to be superior to the optimal ANN model with RMSE = 7.17 MJ/m2, MAE = 5.29 MJ/m2 and R2 = 0.876 and ANFIS model with RMSE = 6.75 MJ/m2, MAE = 5.10 MJ/m2 and R2 = 0.892 in estimating solar radiation. - Highlights: • SR (Solar radiation) of seven cities from Mediterranean region of Turkey is predicted. • FG (Fuzzy genetic) models are developed for accurately estimation of SR. • The ability of the FG models used in the study is found to be satisfactory. • FG models are compared with commonly used ANNs (artificial neural networks). • FG models are found to perform better than the ANNs models

  2. A genetic algorithm approach to maximize crop yields and sustain soil fertility

    Directory of Open Access Journals (Sweden)

    Oladapo J. Olakulehin

    2014-07-01

    Full Text Available In order to increase crop production both for now and in future, conscious efforts need to be made towards sustaining soil fertility. One of the challenges facing farmers is how to increase crop yield and sustain soil fertility. Due to the multidimensional aspect of the challenge and, as a consequence, the huge set of potential solutions, field experiments are not well-suited for their choice and assessment. The objective of this study is to formulate, simulate and evaluate a genetic algorithm based model to maximize crop yields and sustain soil fertility. This study develops a nonlinear mixed-integer programming model to solve the maximization of crop yield problem with sustaining soil fertility. As it is an NP-hard problem, a genetic algorithms approach is proposed to determine the crop yield maximization while sustaining soil fertility. The soil fertility depends on several interrelated factors which have their respective determinants. Numerical analysis shows the effectiveness of the proposed method to deal with such a kind of complicated problem. The study identifies bio-physical, technical (including managerial factors influencing soil fertility in the course of crop production. The regression result equally shows that for every hundred percent change in soil fertility, holding other factors constant, there is a substantial change in the crop yield. The findings of this study revealed that it is possible to scientifically appropriate all factors on sustainable basis (physical – such as soil nutrients, technical and managerial with maximum crop yield achieved. On the basis of the findings, it is recommended that in order to have optimal utilization of resources on sustainable level, conscious efforts should be made by agricultural extension experts to ensure that farmers adopt management practices required for maximum yield.

  3. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach

    Science.gov (United States)

    Wright, Megan H.; Clough, Barbara; Rackham, Mark D.; Rangachari, Kaveri; Brannigan, James A.; Grainger, Munira; Moss, David K.; Bottrill, Andrew R.; Heal, William P.; Broncel, Malgorzata; Serwa, Remigiusz A.; Brady, Declan; Mann, David J.; Leatherbarrow, Robin J.; Tewari, Rita; Wilkinson, Anthony J.; Holder, Anthony A.; Tate, Edward W.

    2014-02-01

    Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.

  4. Chemical entity recognition in patents by combining dictionary-based and statistical approaches.

    Science.gov (United States)

    Akhondi, Saber A; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F H; Hettne, Kristina M; van Mulligen, Erik M; Kors, Jan A

    2016-01-01

    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small.Database URL: http://biosemantics.org/chemdner-patents. PMID:27141091

  5. Chemical and genetic diversity of Zataria multiflora Boiss. accessions growing wild in Iran.

    Science.gov (United States)

    Hadian, Javad; Ebrahimi, Samad Nejad; Mirjalili, Mohammad Hossein; Azizi, Ali; Ranjbar, Hamid; Friedt, Wolfgang

    2011-01-01

    Zataria multiflora Boiss. is an aromatic shrub belonging to the Lamiaceae family. Its aerial parts are used in the traditional medicine and in the pharmaceutical and food industries. The terpenoid and genetic profiles of 18 accessions of Z. multiflora, collected in different locations in Iran, have been analyzed by GC/FID and GC/MS or by AFLP (amplified fragment length polymorphism) analyses, respectively. Altogether, 56 compounds were identified in the essential oils, with the major constituents being thymol (6.0-54.9%), carvacrol (0.7-50.6%), linalool (1.2-46.8%), and p-cymene (1.6-14.8%). On the basis of the essential-oil composition, the 18 accessions were divided into four groups. The first group was characterized by a high content of carvacrol, thymol, and linalool, the second group was dominated by carvacrol, thymol, and p-cymene, the third group was characterized by a high concentration of thymol and a low content of carvacrol and p-cymene, and the forth group contained linalool and carvacrol as the main components. The AFLP results revealed that the average genetic similarity (GS) between the accessions was 0.61, ranging from 0.40 to 0.77. The UPGMA (unweighted pair-group method with arithmetic mean) cluster analysis divided all accessions into five groups at a similarity level of 0.60. The two clusters generated, the first based on the essential-oil compositions and the second on the AFLP data, showed a different pattern of relationships among the accessions. The knowledge of the Z. multiflora chemotype diversity, illustrated in this study, will allow an improvement of the homogeneity of the plant material for the production of different types of essential oils, depending on the demands of the pharmaceutical and food industries for specific uses. PMID:21259428

  6. A multi target approach to control chemical reactions in their inhomogeneous solvent environment

    Science.gov (United States)

    Keefer, Daniel; Thallmair, Sebastian; Zauleck, Julius P. P.; de Vivie-Riedle, Regina

    2015-12-01

    Shaped laser pulses offer a powerful tool to manipulate molecular quantum systems. Their application to chemical reactions in solution is a promising concept to redesign chemical synthesis. Along this road, theoretical developments to include the solvent surrounding are necessary. An appropriate theoretical treatment is helpful to understand the underlying mechanisms. In our approach we simulate the solvent by randomly selected snapshots from molecular dynamics trajectories. We use multi target optimal control theory to optimize pulses for the various arrangements of explicit solvent molecules simultaneously. This constitutes a major challenge for the control algorithm, as the solvent configurations introduce a large inhomogeneity to the potential surfaces. We investigate how the algorithm handles the new challenges and how well the controllability of the system is preserved with increasing complexity. Additionally, we introduce a way to statistically estimate the efficiency of the optimized laser pulses in the complete thermodynamical ensemble.

  7. Chemical Exposure Assessment Program at Los Alamos National Laboratory: A risk based approach

    International Nuclear Information System (INIS)

    The University of California Contract And DOE Order 5480.10 require that Los Alamos National Laboratory (LANL) perform health hazard assessments/inventories of all employee workplaces. In response to this LANL has developed the Chemical Exposure Assessment Program. This program provides a systematic risk-based approach to anticipation, recognition, evaluation and control of chemical workplace exposures. Program implementation focuses resources on exposures with the highest risks for causing adverse health effects. Implementation guidance includes procedures for basic characterization, qualitative risk assessment, quantitative validation, and recommendations and reevaluation. Each component of the program is described. It is shown how a systematic method of assessment improves documentation, retrieval, and use of generated exposure information

  8. Fungi as chemical industries and genetic engineering for the production of biologically active secondary metabolites

    Institute of Scientific and Technical Information of China (English)

    Abid Ali Khan; Nafees Bacha; Bashir Ahmad; Ghosia Lutfullah; Umar Farooq; Russell John Cox

    2014-01-01

    Fungi is somewhere in between the micro and macro organisms which is a good source of producing biologically active secondary metabolites. Fungi have been used as tool for producing different types of secondary metabolites by providing different nutrients at different laboratory conditions. The fungi have been engineered for the desired secondary metabolites by using different laboratory techniques, for example, homologous and heterologous expressions. This review reported how the fungi are used as chemical industry for the production of secondary metabolites and how they are engineered in laboratory for the production of desirable metabolites;also the biosynthetic pathways of the bio-organic-molecules were reported.

  9. Fungi as chemical industries and genetic engineering for the production of biologically active secondary metabolites

    Institute of Scientific and Technical Information of China (English)

    Abid; Ali; Khan; Nafees; Bacha; Bashir; Ahmad; Ghosia; Lutfullah; Umar; Farooq; Russell; John; Cox

    2014-01-01

    Fungi is somewhere in between the micro and macro organisms which is a good source of producing biologically active secondary metabolites.Fungi have been used as tool for producing different types of secondary metabolites by providing different nutrients at different laboratory conditions.The fungi have been engineered for the desired secondary metabolites by using different laboratory techniques,for example,homologous and heterologous expressions.This review reported how the fungi are used as chemical industry for the production of secondary metabolites and how they are engineered in laboratory for the production of desirable metabolites:also the biosynthetic pathways of the bio-organic-molecules were reported.

  10. Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach

    OpenAIRE

    Rodríguez-Flores, Juan L.; Zhang, Kuixing; Kang, Sun Woo; Wen, Gen; Ghosh, Sajalendu; Friese, Ryan S.; Mahata, Sushil K.; Subramaniam, Shankar; Hamilton, Bruce A.; O’Connor, Daniel T.

    2010-01-01

    The adrenomedullary hormone epinephrine transduces environmental stressors into cardiovascular events (tachycardia and hypertension). Although the epinephrine biosynthetic enzyme PNMT genetic locus displays both linkage and association to such traits, genetic variation underlying these quantitative phenotypes is not established. Using an integrated suite of computational and experimental approaches, we elucidate a functional mechanism for common (minor allele frequencies > 30%) genetic varian...

  11. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  12. Genetic and Epigenetic Approaches for the Possible Detection of Adulteration and Auto-Adulteration in Saffron (Crocus sativus L.) Spice

    OpenAIRE

    Giovanna Soffritti; Matteo Busconi; Rosa Ana Sánchez; Jean-Marie Thiercelin; Moschos Polissiou; Marta Roldán; José Antonio Fernández

    2016-01-01

    Saffron (Crocus sativus L.) is very expensive and, because of this, often subject to adulteration. Modern genetic fingerprinting techniques are an alternative low cost technology to the existing chemical techniques, which are used to control the purity of food products. Buddleja officinalis Maxim, Gardenia jasminoides Ellis, Curcuma longa L., Carthamus tinctorius L. and Calendula officinalis L. are among the most frequently-used adulterants in saffron spice. Three commercial kits were compare...

  13. A thermal and chemical degradation approach to decipher pristane and phytane precursors in sedimentary organic matter

    Science.gov (United States)

    Koopmans, M.P.; Rijpstra, W.I.C.; Klapwijk, M.M.; De Leeuw, J. W.; Lewan, M.D.; Sinninghe, Damste J.S.

    1999-01-01

    A thermal and chemical degradation approach was followed to determine the precursors of pristane (Pr) and phytane (Ph) in samples from the Gessoso-solfifera, Ghareb and Green River Formations. Hydrous pyrolysis of these samples yields large amounts of Pr and Ph carbon skeletons, indicating that their precursors are predominantly sequestered in high-molecular-weight fractions. However, chemical degradation of the polar fraction and the kerogen of the unheated samples generally does not release large amounts of Pr and Ph. Additional information on the precursors of Pr and Ph is obtained from flash pyrolysis analyses of kerogens and residues after hydrous pyrolysis and after chemical degradation. Multiple precursors for Pr and Ph are recognised in these three samples. The main increase of the Pr/Ph ratio with increasing maturation temperature, which is associated with strongly increasing amounts of Pr and Ph, is probably due to the higher amount of precursors of Pr compared to Ph, and not to the different timing of generation of Pr and Ph.A thermal and chemical degradation approach was followed to determine the precursors of pristane (Pr) and phytane (Ph) in samples from the Gessoso-solfifera, Ghareb and Green River Formations. Hydrous pyrolysis of these samples yields large amounts of Pr and Ph carbon skeletons, indicating that their precursors are predominantly sequestered in high-molecular-weight fractions. However, chemical degradation of the polar fraction and the kerogen of the unheated samples generally does not release large amounts of Pr and Ph. Additional information on the precursors of Pr and Ph is obtained from flash pyrolysis analyses of kerogens and residues after hydrous pyrolysis and after chemical degradation. Multiple precursors for Pr and Ph are recognised in these three samples. The main increase of the Pr/Ph ratio with increasing maturation temperature, which is associated with strongly increasing amounts of Pr and Ph, is probably due to the

  14. Physics-based approach to chemical source localization using mobile robotic swarms

    Science.gov (United States)

    Zarzhitsky, Dimitri

    2008-07-01

    Recently, distributed computation has assumed a dominant role in the fields of artificial intelligence and robotics. To improve system performance, engineers are combining multiple cooperating robots into cohesive collectives called swarms. This thesis illustrates the application of basic principles of physicomimetics, or physics-based design, to swarm robotic systems. Such principles include decentralized control, short-range sensing and low power consumption. We show how the application of these principles to robotic swarms results in highly scalable, robust, and adaptive multi-robot systems. The emergence of these valuable properties can be predicted with the help of well-developed theoretical methods. In this research effort, we have designed and constructed a distributed physicomimetics system for locating sources of airborne chemical plumes. This task, called chemical plume tracing (CPT), is receiving a great deal of attention due to persistent homeland security threats. For this thesis, we have created a novel CPT algorithm called fluxotaxis that is based on theoretical principles of fluid dynamics. Analytically, we show that fluxotaxis combines the essence, as well as the strengths, of the two most popular biologically-inspired CPT methods-- chemotaxis and anemotaxis. The chemotaxis strategy consists of navigating in the direction of the chemical density gradient within the plume, while the anemotaxis approach is based on an upwind traversal of the chemical cloud. Rigorous and extensive experimental evaluations have been performed in simulated chemical plume environments. Using a suite of performance metrics that capture the salient aspects of swarm-specific behavior, we have been able to evaluate and compare the three CPT algorithms. We demonstrate the improved performance of our fluxotaxis approach over both chemotaxis and anemotaxis in these realistic simulation environments, which include obstacles. To test our understanding of CPT on actual hardware

  15. A density functional theory-based chemical potential equalisation approach to molecular polarizability

    Indian Academy of Sciences (India)

    Amita Wadehra; Swapan K Ghosh

    2005-09-01

    The electron density changes in molecular systems in the presence of external electric fields are modeled for simplicity in terms of the induced charges and dipole moments at the individual atomic sites. A chemical potential equalisation scheme is proposed for the calculation of these quantities and hence the dipole polarizability within the framework of density functional theory based linear response theory. The resulting polarizability is expressed in terms of the contributions from individual atoms in the molecule. A few illustrative numerical calculations are shown to predict the molecular polarizabilities in good agreement with available results. The usefulness of the approach to the calculation of intermolecular interaction needed for computer simulation is highlighted.

  16. Evaluation of the botanical origin of black cohosh products by genetic and chemical analyses.

    Science.gov (United States)

    Masada-Atsumi, Sayaka; Kumeta, Yukie; Takahashi, Yutaka; Hakamatsuka, Takashi; Goda, Yukihiro

    2014-01-01

    Despite the increasing sales of black cohosh (the dried rhizome and root of Cimicifuga racemosa L.) in the world herbal market, these products have continuous adulteration issues. The botanical authenticity of the black cohosh products is the first important step for ensuring their quality, safety and efficacy. In this study, we genetically identified the botanical sources of 10 black cohosh products and 5 Cimicifuga Rhizome crude drugs of Japanese Pharmacopoeia grade, and analyzed the metabolic profiling of 25 black cohosh products using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Consequently, we found that C. dahurica and possibly C. foetida are misused as sources of the black cohosh products and in some cases, the extracts of black cohosh were adulterated with the plant materials of C. dahurica. We demonstrated that these three species can be distinguished by three marker compounds in a specific mass range. These results must be helpful in establishing regulations for the safe use of the black cohosh products. PMID:24583864

  17. A Tailored Approach to Family-Centered Genetic Counseling for Cystic Fibrosis Newborn Screening: The Wisconsin Model

    Science.gov (United States)

    Tluczek, Audrey; Zaleski, Christina; Stachiw-Hietpas, Dania; Modaff, Peggy; Adamski, Craig R.; Nelson, Megan R.; Reiser, Catherine A.; Ghate, Sumedha; Josephson, Kevin D.

    2010-01-01

    Objective Develop a tailored family-centered approach to genetic counseling following abnormal newborn screening (NBS) for cystic fibrosis (CF). Method A genetic counseling consortium reviewed research literature, selected theoretical frameworks, and incorporated counseling psychology micro skills. Results This innovative intervention integrated theories and empirically validated techniques. Pilot testing and parent feedback confirmed satisfaction with and feasibility of the approach designed to (a) minimize parents’ distress, (b) facilitate parents’ understanding, (c) increase parents’ capacities to use genetic information, and (d) enhance parents’ experiences with genetic counseling. Counselors engage in a highly interactive process of evaluating parents’ needs and tailoring assessments and interventions that include a therapeutic environment, the family’s emotional needs, parents’ informational needs, and a follow-up plan. Conclusion This promising new model is the first to establish a theory-driven, evidence-based standard for genetic counseling in the context of NBS for CF. Additional research will evaluate the model’s efficacy in clinical practice. PMID:20936425

  18. Control of bovine spongiform encephalopathy by genetic engineering: possible approaches and regulatory considerations

    International Nuclear Information System (INIS)

    Transmissible spongiform encephalopathies (TSE) include bovine spongiform encephalopathy (BSE), scrapie in sheep and Creutzfeldt-Jakob disease (CJD) in humans. A new CJD variant (nvCJD) is believed to be related to consumption of meat from BSE cattle. In TSE individuals, prion proteins (PrP) with approximately 250 amino acids convert to the pathogenic prion PrPSc, leading to a dysfunction of the central neural system. Research elsewhere with mice has indicated a possible genetic engineering approach to the introduction of BSE resistance: individuals with amino acid substitutions at positions 167 or 218, inoculated with a pathogenic prion protein, did not support PrPSc replication. This raises the possibility of producing prion-resistant cattle with a single PrP amino acid substitution. Since prion-resistant animals might still harbour acquired prion infectivity, regulatory assessment of the engineered animals would need to ascertain that such possible 'carriers' do not result in a threat to animal and human health. (author)

  19. Molecular genetic approaches to the construction of amylase high producing microbial strains

    International Nuclear Information System (INIS)

    The use of cassava for the production of single cell protein includes two basic approaches: the selection of strains to utilize cassava carbohydrate for their growth and the improvement of these strains using classic mutagenesis and/or gene engineering techniques and tools. This paper describes molecular genetic procedures applied to increase the amylolytic abilities of the strains of Streptomyces and Thermomonospora genera which are efficient producers of a number of enzymes and to utilize cassava as a carbon source. The specific genes coding the production of alpha-amylase were isolated from Streptomyces limosus and Thermomonospora curvata and inserted into wide spectrum, multicopy plasmid vectors of streptomycetes. The increased dosage of these genes led to over production of alpha-amylases in a series of streptomycete recipients. It is intended that another representative of the order Actinomycetales, Corynebacterium manihot isolated from the cassava root, should be used as a recipient of the prepared wide-spectrum recombined plasmids bearing thermosensitive and thermostable genes (for improvement of utilizing the cassava starch). After verification of the suitability of C. manihot, the strain should be mutagenized to obtain mutants producing increased amounts of an essential amino acid which then would increase the nutritional value of the used microorganism. (author). 7 refs

  20. Stem cells, biomarkers and genetic profiling: approaching future challenges in Urology.

    Science.gov (United States)

    Mancini, Mariangela; Zazzara, Michele; Zattoni, Filiberto

    2016-03-01

    Urological research is facing future challenges, the most difficult one is the fast and meaningful transfer of the massive amount of data from research basic to clinical practice. Between the most important issues that research should focus in the next years are targeting of tumor stem cells, clinical application of biomarkers, and wide application of genetic profiling of urological neoplasms. Several clinical implications are expected, from diagnosis to selection of candidates for different treatment modalities, to modulation of sequential treatment plans, to prognosis. A number of clinical trials based on research data from the hottest issues are in the pipeline. In this review, we will focus on new insights from recent work worlwide in urological research, with particular attention to high-risk nonmuscle-invasive and muscle-invasive bladder cancer, prostate cancer, and kidney cancer. Cancer care is moving towards a personalized approach in patient management. The most important issues in urological research point strongly in this direction and show an enormous potential for the rapid landing of Urology in the era of personalized medicine. PMID:26940971

  1. A hybrid genetic algorithm-extreme learning machine approach for accurate significant wave height reconstruction

    Science.gov (United States)

    Alexandre, E.; Cuadra, L.; Nieto-Borge, J. C.; Candil-García, G.; del Pino, M.; Salcedo-Sanz, S.

    2015-08-01

    Wave parameters computed from time series measured by buoys (significant wave height Hs, mean wave period, etc.) play a key role in coastal engineering and in the design and operation of wave energy converters. Storms or navigation accidents can make measuring buoys break down, leading to missing data gaps. In this paper we tackle the problem of locally reconstructing Hs at out-of-operation buoys by using wave parameters from nearby buoys, based on the spatial correlation among values at neighboring buoy locations. The novelty of our approach for its potential application to problems in coastal engineering is twofold. On one hand, we propose a genetic algorithm hybridized with an extreme learning machine that selects, among the available wave parameters from the nearby buoys, a subset FnSP with nSP parameters that minimizes the Hs reconstruction error. On the other hand, we evaluate to what extent the selected parameters in subset FnSP are good enough in assisting other machine learning (ML) regressors (extreme learning machines, support vector machines and gaussian process regression) to reconstruct Hs. The results show that all the ML method explored achieve a good Hs reconstruction in the two different locations studied (Caribbean Sea and West Atlantic).

  2. Molecular genetic approach to human meningioma: loss of genes on chromosome 22

    Energy Technology Data Exchange (ETDEWEB)

    Seizinger, B.R.; De La Monte, S.; Atkins, L.; Gusella, J.F.; Martuza, R.L.

    1987-08-01

    A molecular genetic approach employing polymorphic DNA markers has been used to investigate the role of chromosomal aberrations in meningioma, one of the most common tumors of the human nervous system. Comparison of the alleles detected by DNA markers in tumor DNA versus DNA from normal tissue revealed chromosomal alterations present in primary surgical specimens. In agreement with cytogenetic studies of cultured meningiomas, the most frequent alteration detected was loss of heterozygosity on chromosome 22. Forty of 51 patients were constitutionally heterozygous for at least one chromosome 22 DNA marker. Seventeen of the 40 constitutionally heterozygotic patients (43%) displayed hemizygosity for the corresponding marker in their meningioma tumor tissues. Loss of heterozygosity was also detected at a significantly lower frequency for markers on several other autosomes. In view of the striking association between acoustic neuroma and meningioma in bilateral acoustic neurofibromatosis and the discovery that acoustic neuromas display specific loss of genes on chromosome 22, the authors propose that a common mechanism involving chromosome 22 is operative in the development of both tumor types. Fine-structure mapping to reveal partial deletions in meningiomas may provide the means to clone and characterize a gene (or genes) of importance for tumorigenesis in this and possibly other clinically associated tumors of the human nervous system.

  3. Combined Simulated Annealing and Genetic Algorithm Approach to Bus Network Design

    Science.gov (United States)

    Liu, Li; Olszewski, Piotr; Goh, Pong-Chai

    A new method - combined simulated annealing (SA) and genetic algorithm (GA) approach is proposed to solve the problem of bus route design and frequency setting for a given road network with fixed bus stop locations and fixed travel demand. The method involves two steps: a set of candidate routes is generated first and then the best subset of these routes is selected by the combined SA and GA procedure. SA is the main process to search for a better solution to minimize the total system cost, comprising user and operator costs. GA is used as a sub-process to generate new solutions. Bus demand assignment on two alternative paths is performed at the solution evaluation stage. The method was implemented on four theoretical grid networks of different size and a benchmark network. Several GA operators (crossover and mutation) were utilized and tested for their effectiveness. The results show that the proposed method can efficiently converge to the optimal solution on a small network but computation time increases significantly with network size. The method can also be used for other transport operation management problems.

  4. Agent-Based Modeling in Supply Chain Management:A Genetic Algorithm and Fuzzy Logic Approach

    Directory of Open Access Journals (Sweden)

    Meriem Djennas

    2012-10-01

    Full Text Available In today’s global market, reaching a competitive advantage by integrating firms in a supply chainmanagement strategy becomes a key success for any firm seeking to survive in a complex environment.However, as interactions among agents in the supply chain management (SCM remain unpredictable,simulation appears as a powerful tool aiming to predict market behavior and agents’ performance levels.This paper discusses the issues of supply chain management and the requirements for supply chainsimulation modeling. It reviews the relationships amongArtificial Intelligence (AI and SCM and concludesthat under some conditions, SCM models exhibit some inadequacies that may be enriched by the use of AItools. This approach aims to test the supply chain activities of nine companies in the crude oil market. Theobjective is to tackle the issues under which agents can coexist in a competitive environment. Furthermore,we will specify the supply chain management trading interaction amongagents by using an optimizationapproach based on a Genetic Algorithm (AG, Clustering and Fuzzy Logic (FL.Results support the viewthat the structured model provides a good tool for modeling the supply chain activities using AImethodology.

  5. Identification of novel starch traits in Sorghum bicolor (S.bicolor): A reverse genetics approach

    International Nuclear Information System (INIS)

    Sorghum (Sorghum bicolor L.) is the fifth most important cereal grain crop in the world and reportedly feeds over 500 million people on a daily basis in the developing world providing dietary starch, dietary protein and some vitamins and minerals. In the West, it is predominantly used as an animal feed and is increasingly important for ethanol production. Sorghum has the potential to be increasingly important as drought and global warming impact on cereal production. Mature seeds of Sorghum bicolor L (cultivar MR 43) were bombarded with gamma radiation. Over 1000 individuals were grown to M2; with DNA extracted for PCR and sequencing. The aim of this study is to use a reverse genetics approach to detect DNA base changes in four important starch synthesis genes encoding; soluble starch synthase (SSI and SSIIa), granule bound starch synthase (GBSS) and starch branching enzyme (SBE IIb) in a gamma irradiated mutant sorghum (cv. MR 43) population. Results are presented showing the induced DNA sequence mutations detected in the genes of interest. Whereas mutations, in the form of single nucleotide polymorphisms (SNP) and insertion/deletion (indel) events, predominantly occurred in non-coding introns, some mutations were also found in exons. The latter will induce amino acid variants compared to the parental type plants, and it is possible that the resultant protein changes may be revealed, in subsequent research in this project, to be associated with changes in starch phenotype. (author)

  6. Genetic programming-based approach to elucidate biochemical interaction networks from data.

    Science.gov (United States)

    Kandpal, Manoj; Kalyan, Chakravarthy Mynampati; Samavedham, Lakshminarayanan

    2013-02-01

    Biochemical systems are characterised by cyclic/reversible reciprocal actions, non-linear interactions and a mixed relationship structures (linear and non-linear; static and dynamic). Deciphering the architecture of such systems using measured data to provide quantitative information regarding the nature of relationships that exist between the measured variables is a challenging proposition. Causality detection is one of the methodologies that are applied to elucidate biochemical networks from such data. Autoregressive-based modelling approach such as granger causality, partial directed coherence, directed transfer function and canonical variate analysis have been applied on different systems for deciphering such interactions, but with limited success. In this study, the authors propose a genetic programming-based causality detection (GPCD) methodology which blends evolutionary computation-based procedures along with parameter estimation methods to derive a mathematical model of the system. Application of the GPCD methodology on five data sets that contained the different challenges mentioned above indicated that GPCD performs better than the other methods in uncovering the exact structure with less false positives. On a glycolysis data set, GPCD was able to fill the 'interaction gaps' which were missed by other methods. PMID:23848052

  7. Risk-Based, genetic algorithm approach to optimize outage maintenance schedule

    Energy Technology Data Exchange (ETDEWEB)

    Hadavi, S. Mohammad Hadi [Department of Nuclear Engineering, School of Engineering, Shiraz University, Shiraz (Iran, Islamic Republic of)], E-mail: smhadihadavi@yahoo.com

    2008-04-15

    A huge number of components are typically scheduled for maintenance when a nuclear power plant is shut down for its planned outage. Among these components, a number of them are risk significant so that their operability as well as reliability is of prime concern. Lack of proper maintenance for such components during the outage would impose substantial risk on the nuclear power plant (NPP) operation. In this paper, a new approach based on genetic algorithm (GA) is presented for the optimization of the NPP maintenance schedule during plant outage/overhaul, and an optimizer is developed accordingly. The developed optimizer, coupled with the suggested risk-cost model, compromises the cost in favor of maintaining the risk imposed by each schedule below regulatory/industry set limits. The suggested cost model consists of two elements, one considering the cost incurred by maintenance activities and the other incorporating the loss of revenues if needed, but unscheduled component maintenance causes further plant shutdown. The optimizer is developed in such a way that any risk and/or cost models the user desires can be applied. The performance of the developed GA/optimizer is evaluated by comparing its predictions with Monte Carlo simulation results. It is shown that the GA/optimizer performs significantly better.

  8. Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

    Directory of Open Access Journals (Sweden)

    Weeks Nathan

    2010-03-01

    Full Text Available Abstract Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL on Linkage Group I (LG I of soybean (Glycine max (L. Merrill has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome.

  9. The genetic origins of biosynthesis and light-responsive control of the chemical UV screen of land plants

    International Nuclear Information System (INIS)

    Most land plants possess the capacity to protect themselves from UV light, and do so by producing pigments that absorb efficiently in the UV-A and UV-B regions of the spectrum while allowing transmission of nearly all photosynthetically useful wavelengths. These UV-absorbing pigments are mainly phenylpropanoids and flavonoids. This chapter summarizes current understanding of the mechanism of UV protection in higher land plants, evaluates the information available from lower land plants and their green-algal relatives, and then considers the possible evolutionary origins of this use of chemical filters for selectively screening UV light from solar radiation. It is proposed that photo control over the biosynthesis of UV-absorbing phenylpropanoids and flavonoids may have evolved in concert with the evolution of the high biosynthetic activity necessary for UV protection. The toxicity of phenylpropanoids and flavonoids has been postulated to have been a barrier to the evolution of an effective chemical UV screen, and that some means for sequestering these compounds and/or for controlling their synthesis probably evolved prior to, or in concert with, the evolution of high rates of biosynthesis. The original photoreceptor and signal transduction system is speculated to have been based on photo isomerization of a phenylpropanoid ester and a pre-existing product feedback mechanism for controlling phenylpropanoid biosynthesis. Understanding the original mechanism for photo control of the chemical UV screen of land plants could be valuable for understanding the adaptability of extant land plants to rising levels of solar UV-B radiation and may suggest genetic strategies for engineering improved UV tolerance in crop plants. (author)

  10. A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

    Energy Technology Data Exchange (ETDEWEB)

    Balmain, Allan [University of California, San Francisco; Song, Ihn Young [University of California, San Francisco

    2013-05-15

    The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

  11. A Genetic Algorithms Based Approach for Identification of Escherichia coli Fed-batch Fermentation

    OpenAIRE

    Olympia Roeva; Stoyan Tzonkov; Bernd Hitzmann; Tania Pencheva

    2004-01-01

    This paper presents the use of genetic algorithms for identification of Escherichia coli fed-batch fermentation process. Genetic algorithms are a directed random search technique, based on the mechanics of natural selection and natural genetics, which can find the global optimal solution in complex multidimensional search space. The dynamic behavior of considered process has known nonlinear structure, described with a system of deterministic nonlinear differential equations according to the m...

  12. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    OpenAIRE

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wid...

  13. Genetic mapping of quantitative trait loci in plants - a novel statistical approach.

    OpenAIRE

    Jansen, R.C.

    1995-01-01

    Quantitative variation is a feature of many important traits such as yield, quality and disease resistance in crop plants and farm animals, and diseases in humans. The genetic mapping, understanding and manipulation of quantitative trait loci (QTLs) are therefore of prime importance. Only by using genetically marked chromosomes is it possible to detect and map these QTLs. The recent advent of complete genetic maps of molecular markers for many plant and animal species therefore heralds a new ...

  14. Can we predict top-level sports performance in power vs endurance events? A genetic approach

    OpenAIRE

    Buxens, Amaya; Ruiz, Jonatan R.; Arteta, David; Artieda, Marta; Santiago Dorrego, Catalina; González-Freire, Marta; Martínez, A.; Tejedor, Diego; Lao, José I.; Gómez Gallego, Félix; Lucía Mulas, Alejandro

    2011-01-01

    The goal of our study was to discriminate potential genetic differences between humans who are in both endpoints of the sports performance continuum (i.e. world-class endurance vs power athletes). We used DNA-microarray technology that included 36 genetic variants (within 20 different genes) to compare the genetic profile obtained in two cohorts of world-class endurance (N=100) and power male athletes (N=53) of the same ethnic origin. Stepwise multivariate logistic regression showed that the ...

  15. Correcting the systematic error of the density functional theory calculation: the alternate combination approach of genetic algorithm and neural network

    International Nuclear Information System (INIS)

    The alternate combinational approach of genetic algorithm and neural network (AGANN) has been presented to correct the systematic error of the density functional theory (DFT) calculation. It treats the DFT as a black box and models the error through external statistical information. As a demonstration, the AGANN method has been applied in the correction of the lattice energies from the DFT calculation for 72 metal halides and hydrides. Through the AGANN correction, the mean absolute value of the relative errors of the calculated lattice energies to the experimental values decreases from 4.93% to 1.20% in the testing set. For comparison, the neural network approach reduces the mean value to 2.56%. And for the common combinational approach of genetic algorithm and neural network, the value drops to 2.15%. The multiple linear regression method almost has no correction effect here. (condensed matter: structure, thermal and mechanical properties)

  16. Mitochondrial diseases: an overview of genetics, pathogenesis, clinical features and an approach to diagnosis and treatment.

    Directory of Open Access Journals (Sweden)

    Singhal N

    2000-07-01

    Full Text Available Defects in structures or functions of mitochondria, mainly involving the oxidative phosphorylation, mitochondrial biogenesis and other metabolic pathways have been shown to be associated with a wide spectrum of clinical phenotypes. The ubiquitous nature of mitochondria and their unique genetic features contribute to the clinical, biochemical and genetic heterogenecity of mitochondrial diseases. This article focuses on the recent advances in the field of mitochondrial disorders with respect to the consequences for an advanced clinical and genetic diagnostics. In addition, an overview on recently identified genetic defects and their pathogenic molecular mechanisms are given.

  17. Chemical and genetic characterization of Phlomis species and wild hybrids in Crete.

    Science.gov (United States)

    Georgescu, Luciana; Stefanakis, Michalis K; Kokkini, Stella; Katerinopoulos, Haralambos E; Pirintsos, Stergios A

    2016-02-01

    The genus Phlomis is represented in the island of Crete (Greece, Eastern Mediterranean) by three species Phlomis cretica C. Presl., Phlomis fruticosa L., the island endemic Phlomis lanata Willd. and three hybrids Phlomis x cytherea Rech.f. (P. cretica x P. fruticosa), Phlomis x commixta Rech.f. (P. cretica x P. lanata) and Phlomis x sieberi Vierh. (P. fruticosa x P. lanata). This work describes (a) the profile of hybrids and parental species concerning their volatile compounds, (b) the suitability of ribosomal nuclear (ITS region), chloroplast (trnH-psbA), and AFLP markers to identify hybrids and (c) their competence to characterize the different chemotypes of both hybrids and their parental species. The cluster analysis and PCA constructed from chemical data (volatile oils) suggest that there are three groups of taxa. Group IA includes P. cretica and P. fruticosa, group IB includes P. x cytherea, whereas group II consists of P. x commixta, P. x sieberi and P. lanata. Volatile compounds detected only in the hybrids P. x sieberi and P. x commixta correspond to the 3% of the total compounds, value that is much higher in P. x cytherea (21%). Neighbor-joining, statistical parsimony analysis and the observations drawn from ribotypes spectrum of ITS markers divided Phlomis species in two groups, P. lanata and the complex P. cretica/P. fruticosa. In contrast to the ITS region, the plastid DNA marker follows a geographically related pattern. Neighbor-Net, PCA and Bayesian assignment analysis performed for AFLP markers separated the genotypes into three groups corresponding to populations of P. cretica, P. fruticosa, and P. lanata, respectively, while populations of P. x commixta, P. x cytherea, and P. x sieberi presented admixed ancestry. Most of the P. x cytherea samples were identified as F1 hybrids by Bayesian assignment test, while those of P. x commixta and P. x sieberi were identified as F2 hybrids. Overall, high chemical differentiation is revealed in one of the

  18. Developing a New Teaching Approach for the Chemical Bonding Concept Aligned with Current Scientific and Pedagogical Knowledge

    Science.gov (United States)

    Nahum, Tami Levy; Mamlok-Naaman, Rachel; Hofstein, Avi; Krajcik, Joseph

    2007-01-01

    The traditional pedagogical approach for teaching chemical bonding is often overly simplistic and not aligned with the most up-to-date scientific models. As a result, high-school students around the world lack fundamental understanding of chemical bonding. In order to improve students' understanding of this concept, it was essential to propose a…

  19. Approaches in the risk assessment of genetically modified foods by the Hellenic Food Safety Authority.

    Science.gov (United States)

    Varzakas, Theodoros H; Chryssochoidis, G; Argyropoulos, D

    2007-04-01

    Risk analysis has become important to assess conditions and take decisions on control procedures. In this context it is considered a prerequisite in the evaluation of GM food. Many consumers worldwide worry that food derived from genetically modified organisms (GMOs) may be unhealthy and hence regulations on GMO authorisations and labelling have become more stringent. Nowadays there is a higher demand for non-GM products and these products could be differentiated from GM products using the identity preservation system (IP) that could apply throughout the grain processing system. IP is the creation of a transparent communication system that encompasses HACCP, traceability and related systems in the supply chain. This process guarantees that certain characteristics of the lots of food (non-GM origin) are maintained "from farm to fork". This article examines the steps taken by the Hellenic Food Safety Authority to examine the presence of GMOs in foods. The whole integrated European legislation framework currently in place still needs to be implemented in Greece. Penalties should be enforced to those who import, process GMOs without special licence and do not label those products. Similar penalties should be enforced to those companies that issue false certificates beyond the liabilities taken by the food enterprises for farmers' compensation. We argue that Greece has no serious reasons to choose the use of GMOs due to the fact that the structural and pedologic characteristics of the Greek agriculture favour the biological and integrated cultivation more. Greece is not in favour of the politics behind coexistence of conventional and GM plants and objects to the use of GMOs in the food and the environment because the processor has a big burden in terms of money, time and will suffer a great deal in order to prove that their products are GMO free or that any contamination is adventitious or technically unavoidable. Moreover, Greece owns a large variety of genetic

  20. Genetic toxicity studies of organic chemicals found as contaminants in spacecraft cabin atmospheres

    Science.gov (United States)

    Torres, Joseph, Jr.

    1987-01-01

    Astronauts can be exposed during spaceflight to organic chemical contaminants in the spacecraft cabin atmosphere. Toxic exposures may cause lesions in the cellular DNA which are subsequently expressed as sister-chromatid exchanges (SCE). Analysis of SCE is a sensitive short term assay techinque to detect and quantitate exposures to DNA damaging (mutagenic) substances. The increase in SCE incidence over baseline (control) levels is generally proportional to the concentration of the mutagen and to the duration of exposure. The BHK-21 baby hamster kidney cell line was the in vitro test system used. Test organics were added to the culture media for 18 hrs, in concentrations ranging from one to 20 ppm. Acetaldehyde and carbon disulfide were chosen for this study since they have occurred as atmospheric contaminants in many of the STS flights, and have been reported to have toxic and mutagenic effects in various test systems. Glutaraldehyde was chosen because few data are available on the mutagenicity of this common fixative, which is carried on STS flights for use in biological experiments. Acetaldehyde was a very strong inducer of SCE at concentrations of 2 ppm and above. Glutaraldehyde and carbon disulfide failed to induce SCE.

  1. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris.

    Directory of Open Access Journals (Sweden)

    Filippo Frizzi

    Full Text Available Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships.

  2. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris.

    Science.gov (United States)

    Frizzi, Filippo; Ciofi, Claudio; Dapporto, Leonardo; Natali, Chiara; Chelazzi, Guido; Turillazzi, Stefano; Santini, Giacomo

    2015-01-01

    Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships. PMID:26445245

  3. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. PMID:23764236

  4. A new approach to nuclear reactor design optimization using genetic algorithms and regression analysis

    International Nuclear Information System (INIS)

    Highlights: • This paper presents a new method useful for the optimization of complex dynamic systems. • The method uses the strengths of; genetic algorithms (GA), and regression splines. • The method is applied to the design of a gas cooled fast breeder reactor design. • Tools like Java, R, and codes like MCNP, Matlab are used in this research. - Abstract: A module based optimization method using genetic algorithms (GA), and multivariate regression analysis has been developed to optimize a set of parameters in the design of a nuclear reactor. GA simulates natural evolution to perform optimization, and is widely used in recent times by the scientific community. The GA fits a population of random solutions to the optimized solution of a specific problem. In this work, we have developed a genetic algorithm to determine the values for a set of nuclear reactor parameters to design a gas cooled fast breeder reactor core including a basis thermal–hydraulics analysis, and energy transfer. Multivariate regression is implemented using regression splines (RS). Reactor designs are usually complex and a simulation needs a significantly large amount of time to execute, hence the implementation of GA or any other global optimization techniques is not feasible, therefore we present a new method of using RS in conjunction with GA. Due to using RS, we do not necessarily need to run the neutronics simulation for all the inputs generated from the GA module rather, run the simulations for a predefined set of inputs, build a multivariate regression fit to the input and the output parameters, and then use this fit to predict the output parameters for the inputs generated by GA. The reactor parameters are given by the, radius of a fuel pin cell, isotopic enrichment of the fissile material in the fuel, mass flow rate of the coolant, and temperature of the coolant at the core inlet. And, the optimization objectives for the reactor core are, high breeding of U-233 and Pu-239 in

  5. Evaluation of a non-targeted "omic" approach in the safety assessment of genetically modified plants

    NARCIS (Netherlands)

    Metzdorff, S.B.; Kok, E.J.; Knuthsen, P.; Pedersen, J.

    2006-01-01

    Genetically modified plants must be approved before release in the European Union, and the approval is generally based upon a comparison of various characteristics between the transgenic plant and a conventional counterpart. As a case study, focusing on safety assessment of genetically modified plan

  6. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach.

    Science.gov (United States)

    Saeb, Amr T M; Al-Naqeb, Dhekra

    2016-01-01

    Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases. PMID:27313952

  7. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  8. The Chemical Master Equation Approach to Nonequilibrium Steady-State of Open Biochemical Systems: Linear Single-Molecule Enzyme Kinetics and Nonlinear Biochemical Reaction Networks

    Directory of Open Access Journals (Sweden)

    Lisa M. Bishop

    2010-09-01

    Full Text Available We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a individual biochemical reactions, (b nonlinear network dynamics approaching to attractors, and (c cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a and (c are stochastic while that with (b is dominantly deterministic. Both (b and (c are emergent properties of a dynamic biochemical network; We suggest that the (c is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b in a “punctuated equilibrium” manner.

  9. The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks.

    Science.gov (United States)

    Qian, Hong; Bishop, Lisa M

    2010-01-01

    We develop the stochastic, chemical master equation as a unifying approach to the dynamics of biochemical reaction systems in a mesoscopic volume under a living environment. A living environment provides a continuous chemical energy input that sustains the reaction system in a nonequilibrium steady state with concentration fluctuations. We discuss the linear, unimolecular single-molecule enzyme kinetics, phosphorylation-dephosphorylation cycle (PdPC) with bistability, and network exhibiting oscillations. Emphasis is paid to the comparison between the stochastic dynamics and the prediction based on the traditional approach based on the Law of Mass Action. We introduce the difference between nonlinear bistability and stochastic bistability, the latter has no deterministic counterpart. For systems with nonlinear bistability, there are three different time scales: (a) individual biochemical reactions, (b) nonlinear network dynamics approaching to attractors, and (c) cellular evolution. For mesoscopic systems with size of a living cell, dynamics in (a) and (c) are stochastic while that with (b) is dominantly deterministic. Both (b) and (c) are emergent properties of a dynamic biochemical network; We suggest that the (c) is most relevant to major cellular biochemical processes such as epi-genetic regulation, apoptosis, and cancer immunoediting. The cellular evolution proceeds with transitions among the attractors of (b) in a "punctuated equilibrium" manner. PMID:20957107

  10. Automatic tuning of liver tissue model using simulated annealing and genetic algorithm heuristic approaches

    Science.gov (United States)

    Sulaiman, Salina; Bade, Abdullah; Lee, Rechard; Tanalol, Siti Hasnah

    2014-07-01

    Mass Spring Model (MSM) is a highly efficient model in terms of calculations and easy implementation. Mass, spring stiffness coefficient and damping constant are three major components of MSM. This paper focuses on identifying the coefficients of spring stiffness and damping constant using automated tuning method by optimization in generating human liver model capable of responding quickly. To achieve the objective two heuristic approaches are used, namely Simulated Annealing (SA) and Genetic Algorithm (GA) on the human liver model data set. The properties of the mechanical heart, which are taken into consideration, are anisotropy and viscoelasticity. Optimization results from SA and GA are then implemented into the MSM to model two human hearts, each with its SA or GA construction parameters. These techniques are implemented while making FEM construction parameters as benchmark. Step size response of both models are obtained after MSMs were solved using Fourth Order Runge-Kutta (RK4) to compare the elasticity response of both models. Remodelled time using manual calculation methods was compared against heuristic optimization methods of SA and GA in showing that model with automatic construction is more realistic in terms of realtime interaction response time. Liver models generated using SA and GA optimization techniques are compared with liver model from manual calculation. It shows that the reconstruction time required for 1000 repetitions of SA and GA is faster than the manual method. Meanwhile comparison between construction time of SA and GA model indicates that model SA is faster than GA with varying rates of time 0.110635 seconds/1000 repetitions. Real-time interaction of mechanical properties is dependent on rate of time and speed of remodelling process. Thus, the SA and GA have proven to be suitable in enhancing realism of simulated real-time interaction in liver remodelling.

  11. Genetic programming approach on evaporation losses and its effect on climate change for Vaipar Basin

    Directory of Open Access Journals (Sweden)

    K.S.Kasiviswanathan

    2011-09-01

    Full Text Available Climate change is the major problem that every human being is facing over the world. The rise in fossil fuel usage increases the emission of `greenhouse' gases, particularly carbon dioxide continuously into the earth's atmosphere. This causes a rise in the amount of heat from the sun withheld in the earth's atmosphere that would normally radiated back into space. This increase in heat has led to the greenhouse effect, resulting in climate change and rise in temperature along with other climatological parameters directly affects evaporation losses. Accurate modelling and forecasting of these evaporation losses are important for preventing further effects due to climate change. Evaporation is purely non-linear and varying both spatially and temporally. This needs suitable data driven approach to model and should have the ability to take care of all these non-linear behaviour of the system. As such, though there are many empirical and analytical models suggested in the literature for the estimation of evaporation losses, such models should be used with care and caution. Further, difficulties arise in obtaining all the climatological data used in a given analytical or empirical model. Genetic programming (GP is one such technique applied where the non-linearity exist. GP has the flexible mathematical structure which is capable of identifying the non-linear relationship between input and output data sets. Thus, it is easy to construct 'local' models for estimating evaporation losses. The performance of GP model is compared with Thornthwaite method, and results from the study indicate that the GP model performed better than the Thornthwaite method. Forecasting of meteorological parameters such as temperature, relative humidity and wind velocity has been performed using Markovian chain series analysis subsequently it is used to estimate the future evaporation losses using developed GP model. Finally the effect of possible future climate change on

  12. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach.

    Science.gov (United States)

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-10-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

  13. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach

    Science.gov (United States)

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-01-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

  14. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Science.gov (United States)

    Rosenow, Phil; Tonner, Ralf

    2016-05-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  15. Analysis of genetics and chemical contents relation compared to commonly used Cissus quadrangularis L. and barcode markers of some Thailand Cissus species.

    Science.gov (United States)

    Sudmoon, Runglawan; Chaveerach, Arunrat; Tanee, Tawatchai

    2016-01-01

    Several Cissus species are commonly used as traditional and modified medicines, and their chemical constituents are major point for precise usage. However, C. quadrangularis is the only species for which the usages and the chemical composition have been reported. These data should be investigated for other species in the genus. Eight species namely C. assamica, C. carnosa, C. elongata, C. hastata, C. javana, C. pteroclada, C. quadrangular is and C. repens were evaluated for genetic relationships and chemical composition. Constructed dendrogram shows high-powered efficiency of inter-simple sequence repeat (ISSR) data used which can clearly identify different and identical species. Genetic similarity (S) value of the identical species is 0.86, whereas for different species the value can vary from 0.53 to 0.75. Four highly related species (S=0.64-0.72), C. assamica, C. carnosa, C. hastata and C. repens were selected to undergo chemical study by gas chromatography-mass spectrometry (GC-MS) on the methanol crude extract. Only one compound, β-sitosterol, found in the four species is identical to the compound reported from C. quadrangular is, where there were five identical chemicals found in the selected species. Species-specific barcode with rbcL region was constructed. Nucleotide variation was evaluated indicating genetic distance value of 0.025 to 0.072. PMID:26826840

  16. A Multi-Objective Optimization Approach Using Genetic Algorithms for Quick Response to Effects of Variability in Flow Manufacturing

    Directory of Open Access Journals (Sweden)

    Parminder Singh Kang

    2012-09-01

    Full Text Available This paper exemplifies a framework for development of multi-objective genetic algorithm based job sequencing method by taking account of multiple resource constraints. Along this, Theory of Constraints based Drum-Buffer-Rope methodology has been combined with genetic algorithm to exploit the system constraints. This paper introduces the Drum-Buffer-Rope to exploit the system constraints, which may affect the lead times, throughput and higher inventory holding costs. Multi-Objective genetic algorithm is introduced for job sequence optimization to minimize the lead times and total inventory holding cost, which includes problem encoding, chromosome representation, selection, genetic operators and fitness measurements, where Queuing times and Throughput are used as fitness measures. Along this, paper provides a brief comparison of proposed approach with other optimisation approaches. The algorithm generates a sequence to maximize the throughput and minimize the queuing time on bottleneck/Capacity Constraint Resource (CCR. Finally, Results are analysed to show the improvement by using current research framework.

  17. The Chemical and Genetic Characteristics of Szechuan Pepper (Zanthoxylum bungeanum and Z. armatum) Cultivars and Their Suitable Habitat

    Science.gov (United States)

    Xiang, Li; Liu, Yue; Xie, Caixiang; Li, Xiwen; Yu, Yadong; Ye, Meng; Chen, Shilin

    2016-01-01

    Szechuan peppers, famous for their unique sensation and flavor, are widely used as a food additive and traditional herbal medicine. Zanthoxylum bungeanum and Z. armatum are both commonly recognized as Szechuan peppers, but they have different tastes and effects. The chemical components, genetic characteristics, and suitable habitat of six cultivars were analyzed in this study. The results indicated that Z. armatum contained a larger proportion of volatile oil, whereas Z. bungeanum produced a more non-volatile ether extraction. The average content of volatile oil and non-volatile ether extract of Z. armatum were 11.84 and 11.63%, respectively, and the average content of volatile oil and non-volatile ether extract of Z. bungeanum were 6.46 and 14.23%, respectively. Combined with an internal transcribed spacer 2 (ITS2) sequence characters and chemical PCA results, six cultivars were classified into their own groups, for the two species in particular. The temperature in January and July were the most significant ecological factors influencing the contents of the Z. armatum volatile oil. However, annual precipitation, temperature in January and relevant humidity had a significant positive correlation with the content of non-volatile ether extract in Z. bungeanum. Thus, the most suitable areas for producing Z. bungeanum cultivars ranged from the Hengduan Mountains to the Ta-pa Mountains, and the regions suitable for Z. armatum cultivars were found to be in the Sichuan Basin and Dalou-Wu mountains. The predicted suitable habitat could be used as a preliminary test area for Szechuan pepper cultivar production. PMID:27148298

  18. An experimental design approach to the chemical characterisation of pectin polysaccharides extracted from Cucumis melo Inodorus.

    Science.gov (United States)

    Denman, Laura J; Morris, Gordon A

    2015-03-01

    Extracted pectins have been utilised in a number of applications in both the food and pharmaceutical industries where they are generally used as gelling agents, thickeners and stabilisers, although a number of pectins have been shown to be bioactive. These functional properties will depend upon extraction conditions. A statistical experimental design approach was used to study the effects of extraction conditions pH, time and temperature on pectins extracted from Cucumis melo Inodorus. The results show that the chemical composition is very sensitive to these conditions and that this has a great influence on for example the degree of branching. Higher temperatures, lower pHs and longer extraction times lead to a loss of the more acid labile arabinofuranose residues present on the pectin side chain. The fitting of regression equations relating yield and composition to extraction conditions can therefore lead to tailor-made pectins for specific properties and/or applications. PMID:25498647

  19. Accelerating forward genetics for cell wall deconstruction

    OpenAIRE

    Vidaurre, Danielle; Bonetta, Dario

    2012-01-01

    The elucidation of the genes involved in cell wall synthesis and assembly remains one of the biggest challenges of cell wall biology. Although traditional genetic approaches, using simple yet elegant screens, have identified components of the cell wall, many unknowns remain. Exhausting the genetic toolbox by performing sensitized screens, adopting chemical genetics or combining these with improved cell wall imaging, hold the promise of new gene discovery and function. With the recent introduc...

  20. A New Genetic Algorithm Based Lane-By-Pass Approach for Smooth Traffic Flow on Road Networks

    OpenAIRE

    Shailendra Tahilyani; Manuj Darbari; Praveen Kumar Shukla

    2012-01-01

    Traffic congestion in urban areas is a very critical problem and increasing day-by-day due to increment in number of vehicles and un-expandable traffic infrastructure. Several intelligent control systems have been developed to deal with this issue. In this paper, a new lane bypass algorithm has been developed for route diversion resulting in smooth traffic flow on the urban road networks. Genetic algorithms are utilized for the parameter optimization in this approach. Finally, the results of ...

  1. On the Heritability of Consumer Decision Making: An Exploratory Approach for Studying Genetic Effects on Judgment and Choice

    OpenAIRE

    Itamar Simonson; Aner Sela

    2011-01-01

    While constructed preferences have received a great deal of attention, there has been virtually no research regarding the genetic basis of consumer judgment and choice. In this research, we examine a wide range of previously unexplored heritable effects on consumer choices and judgments. Moreover, whereas prior research on heritable traits has typically employed a piecemeal approach, demonstrating each heritable trait separately, we propose an alternative way to simultaneously explore common ...

  2. A Hybrid Approach for DICOM Image Feature Extraction, Feature Selection Using Fuzzy Rough set and Genetic Algorithm

    OpenAIRE

    J. Umamaheswari; DR. G. RADHAMANI

    2011-01-01

    The proposed hybrid approach for feature extraction, feature reduction and feature selection of Medical images based on Rough set and Genetic Algorithm (GA). A Gray Level Co-occurrence Matrix (GLCM) and Histogram based texture feature set is derived. The optimal texture features are extracted from normal and infected Digital Imaging and Communications in Medicine (DICOM) images by using GLCM and histogram based features. The inputs of these features are taken for the feature selection process...

  3. Adaptation of Mamdani Fuzzy Inference System Using Neuro - Genetic Approach for Tactical Air Combat Decision Support System

    OpenAIRE

    Tran, Cong; Jain, Lakhmi; Abraham, Ajith

    2004-01-01

    Normally a decision support system is build to solve problem where multi-criteria decisions are involved. The knowledge base is the vital part of the decision support containing the information or data that is used in decision-making process. This is the field where engineers and scientists have applied several intelligent techniques and heuristics to obtain optimal decisions from imprecise information. In this paper, we present a hybrid neuro-genetic learning approach for the adaptation a Ma...

  4. A new approach for the column apparatuses modeling in chemical and power engineering

    Directory of Open Access Journals (Sweden)

    Doichinova Maria

    2015-01-01

    Full Text Available The column apparatuses are main devices for solution of technological and ecological problems in chemical and power engineering. A new approach of the column apparatuses modeling on the base of the physical approximations of the mechanics of continua, using two steps models: convection-diffusion type of model (for qualitative analysis and average concentration model (for quantitative analysis, is presented. The convection-diffusion type of models describe chemical and mass transfer processes in column apparatuses in the cases of one, two ore three phases systems, where the solid phase is reagent, catalytic or packed bad. A qualitative analysis of these models, using generalized (dimensionless variables, where the characteristic (inherent scales are the maximal or average values of the variables, is presented. The using of the convection-diffusion type of models for quantitative analysis of the processes in column apparatuses is not possible because the velocity function in the convection-diffusion equation is unknown. The problem can be avoided if the average values of the velocity and concentration over the cross-sectional area of the column are used. The average concentration models permit to analyze the effect of the radial nonuniformities of the velocity and the concentration on the process efficiency in the column and to solve the scale-up problem. The convection-diffusion type of models are presented as a base for to be created convection and diffusion type of models.

  5. An Approach for Prioritizing “Down-the-Drain” Chemicals Used in the Household

    Directory of Open Access Journals (Sweden)

    Marina Rotsidou

    2015-01-01

    Full Text Available Many chemicals are present in cleaning and personal care products, which after use are washed down the drain and find their way into water bodies, where they may impact the environment. This study surveyed individuals to determine what products were used most in the home, in an attempt to prioritize which compounds may be of most concern. The survey resulted in the identification of 14 categories of products consisting of 315 specific brands. The survey estimated that individuals each discharge almost 33 L of products per year down the drain. Dishwashing liquids and hand wash gels, which accounted for 40% of this volume, were selected for identification of specific ingredients. Ingredients were classified as surfactants, preservatives, fragrances or miscellaneous, with hand wash gels having a wider range of ingredients than dishwashing liquids. A review of the literature suggested that preservatives, which are designed to be toxic, and fragrances, where data on toxicity are limited, should be prioritized. The approach undertaken has successfully estimated use and provisionally identified some classes of chemicals which may be of most concern when used in cleaning and personal care products.

  6. Beyond the pseudo-time-dependent approach: chemical models of dense core precursors

    CERN Document Server

    Hassel, G E; Bergin, E A

    2010-01-01

    Context: Chemical models of dense cloud cores often utilize the so-called pseudo-time-dependent approximation, in which the physical conditions are held fixed and uniform as the chemistry occurs. In this approximation, the initial abundances chosen, which are totally atomic in nature except for molecular hydrogen, are artificial. A more detailed approach to the chemistry of dense cold cores should include the physical evolution during their early stages of formation. Aims: Our major goal is to investigate the initial synthesis of molecular ices and gas-phase molecules as cold molecular gas begins to form behind a shock in the diffuse interstellar medium. The abundances calculated as the conditions evolve can then be utilized as reasonable initial conditions for a theory of the chemistry of dense cores. Methods: Hydrodynamic shock-wave simulations of the early stages of cold core formation are used to determine the time-dependent physical conditions for a gas-grain chemical network. We follow the cold post-sho...

  7. Immune System and Genetics: A Different Approach to the Diversity of Antibodies

    International Nuclear Information System (INIS)

    It is common to find in immunology or genetic books a chapter entitled immune system and genetics; this association focuses on how the generation of antibodies broke the paradigm one gene, one protein, since in this case one gene generates millions of proteins. However, the immune system has many more links to genetics and heredity. For example, any substance or compound that an organism produces is a potential antigen, when it is recognized as foreign by the immune system of another organism from the same or different species. The proteins that are potentially antigenic are encoded by the individual's genotype. The ability of the immune system to respond to antigenic proteins, as well as the type and intensity of that response, are also correlated with the organism's genotype. In addition, deficiencies in the immune response may be associated with mutations or genetic polymorphisms, which result in susceptibility to infection diseases.

  8. Hereditary Cancer: Example of a Public Health Approach to Ensure Population Health Benefits of Genetic Medicine

    Science.gov (United States)

    Cragun, Deborah; Lewis, Courtney; Camperlengo, Lucia; Pal, Tuya

    2016-01-01

    This article introduces the identification, prevention, and treatment of hereditary cancer as an important public health concern. Hereditary cancer research and educational outreach activities are used to illustrate how public health functions can help to achieve health benefits of genetic and genomic medicine. First, we evaluate genetic service delivery through triangulating patient and provider survey results which reveal variability among providers in hereditary cancer knowledge and genetic service provision. Second, we describe efforts we have made to assure competency among healthcare providers and to inform, educate and empower patients with regard to the rapidly evolving field of genomics and hereditary cancer. Lastly, key policy-issues raised by our experiences are discussed in the context of how they may help us to more effectively translate future genomic technologies into practice in order to attain population health benefits from genetic and genomic medicine.

  9. A Genetic Algorithms Based Approach for Identification of Escherichia coli Fed-batch Fermentation

    Directory of Open Access Journals (Sweden)

    Olympia Roeva

    2004-10-01

    Full Text Available This paper presents the use of genetic algorithms for identification of Escherichia coli fed-batch fermentation process. Genetic algorithms are a directed random search technique, based on the mechanics of natural selection and natural genetics, which can find the global optimal solution in complex multidimensional search space. The dynamic behavior of considered process has known nonlinear structure, described with a system of deterministic nonlinear differential equations according to the mass balance. The parameters of the model are estimated using genetic algorithms. Simulation examples for demonstration of the effectiveness and robustness of the proposed identification scheme are included. As a result, the model accurately predicts the process of cultivation of E. coli.

  10. Protein structure prediction as a hard optimization problem the genetic algorithm approach

    CERN Document Server

    Khimasia, M M; Khimasia, Mehul M.; Coveney, Peter V.

    1997-01-01

    Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory, robust search algorithm, such as a genetic algorithm (GA), is required. The dynamics of GAs tend to be complicated and problem-specific. However, their empirical success warrants their further study. In this paper, guidelines for the design of genetic algorithms for protein structure prediction are determined. To accomplish this, the performance of the simplest genetic algorithm is investigated for simple lattice-based protein structure prediction models (which is extendible to real-space), using energy minimization. The study has led us to two important conclusions for `protein-structure-prediction-genetic-algorithms'. Firstly, they require high resolution building blocks attainable by multi-point crossovers and secondly they require a local dynamics operator to `fine tun...

  11. Pollen Sterility—A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    OpenAIRE

    Joel P. Hague; Dellaporta, Stephen L.; Moreno, Maria A.; Chip Longo; Kimberly Nelson; Albert P. Kausch

    2012-01-01

    Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM) crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of tr...

  12. A possibilistic approach for transient identification with 'don't know' response capability optimized by genetic algorithm

    International Nuclear Information System (INIS)

    This work describes a possibilistic approach for transient identification based on the minimum centroids set method, proposed in previous work, optimized by genetic algorithm. The idea behind this method is to split the complex classification problem into small and simple ones, so that the performance in the classification can be increased. In order to accomplish that, a genetic algorithm is used to learn, from realistic simulated data, the optimized time partitions, which the robustness and correctness in the classification are maximized. The use of a possibilistic classification approach propitiates natural and consistent classification rules, leading naturally to a good heuristic to handle the 'don't know 'response, in case of unrecognized transient, which is fairly desirable in transient classification systems where safety is critical. Application of the proposed approach to a nuclear transient indentification problem reveals good capability of the genetic algorithm in learning optimized possibilistic classification rules for efficient diagnosis including 'don't know' response. Obtained results are shown and commented. (author)

  13. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci.

    Science.gov (United States)

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo. PMID:26870082

  14. A new approach of cascade utilization of the chemical energy of fuel

    Institute of Scientific and Technical Information of China (English)

    HAN Wei; JIN Hongguang; LIN Rumou

    2006-01-01

    The indirect release of chemical energy of fuel is investigated, and a new mechanism is proposed to identify the cascade utilization of chemical energy of fuel more clearly. Based on the concept of energy level, the internal phenomenon of the indirect chemical energy release is disclosed, and the equations of energy level describing the utilization of chemical energy and thermal energy during the indirect chemical energy release process are obtained. From theoretical analysis, we find that the superiority of the indirect chemical energy release of fuel comes from the cascade utilization of the fuel's chemical energy. Moreover, the cascade utilization of chemical energy is verified by the investigation of CRGT (chemically recuperated gas turbine). As a result, the thermal exergy obtained from the chemical energy release of fuel increases by 2 % -3 %. The results obtained here may help a deeper understanding of indirect chemical energy release of fuel and provide a theoretical basis for the synthesis of innovative energy systems.

  15. Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

    International Nuclear Information System (INIS)

    Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

  16. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  17. New approaches to evaluating the genetic effects of the atomic bombs

    International Nuclear Information System (INIS)

    In the aftermath of the atomic bombings of Hiroshima and Nagasaki fifty years ago, one of the compelling biomedical questions that arose concerned the genetic effects of this exposure. More recently, revelations of the extent of industrial or accidental exposures in the former Soviet Union and charges that employment in the Sellafield Nuclear Reprocessing Plant in West Cumbria, England has resulted in a gene-mediated increase in children of plant employees have served to keep in the public mind the issue of the genetic risks of exposure to ionizing radiation. The study of the genetic effects of the atomic bombs has moved from the gross morphological level of congenital malformations to the examination of DNA. However, were the need for such genetic studies to arise in the foreseeable future, despite this impressive progress in DNA-oriented systems, the documentation of congenital defect, genetic disease and child survival would still be an essential component of any future study. Whatever the geneticists may think, the phenotypic well-being and survival of children are still the primary indicators on which the public, who ultimately supports these studies, will base its judgement of risk. 28 refs

  18. Stress-sensitive neurosignalling in depression: an integrated network biology approach to candidate gene selection for genetic association analysis

    Directory of Open Access Journals (Sweden)

    J. Anke M. van Eekelen

    2012-07-01

    Full Text Available Genetic risk for depressive disorders is poorly understood despite consistent suggestions of a high heritable component. Most genetic studies have focused on risk associated with single variants, a strategy which has so far only yielded small (often non-replicable risks for depressive disorders. In this paper we argue that more substantial risks are likely to emerge from genetic variants acting in synergy within and across larger neurobiological systems (polygenic risk factors. We show how knowledge of major integrated neurobiological systems provides a robust basis for defining and testing theoretically defensible polygenic risk factors. We do this by describing the architecture of the overall stress response. Maladaptation via impaired stress responsiveness is central to the aetiology of depression and anxiety and provides a framework for a systems biology approach to candidate gene selection. We propose principles for identifying genes and gene networks within the neurosystems involved in the stress response and for defining polygenic risk factors based on the neurobiology of stress-related behaviour. We conclude that knowledge of the neurobiology of the stress response system is likely to play a central role in future efforts to improve genetic prediction of depression and related disorders.

  19. A Genetic Algorithm Approach to the Optimization of a Radioactive Waste Treatment System

    International Nuclear Information System (INIS)

    This study is concerned with the applications of goal programming and genetic algorithm techniques to the analysis of management and operational problems in the radioactive waste treatment system (RWTS). A typical RWTS is modeled and solved by goal program and genetic algorithm to study and resolve the effects of conflicting objectives such as cost, limitation of released radioactivity to the environment, equipment utilization and total treatable radioactive waste volume before discharge and disposal. The developed model is validated and verified using actual data obtained from the RWTS at Kyoto University in Japan. The solution by goal programming and genetic algorithm would show the optimal operation point which is to maximize the total treatable radioactive waste volume and minimize the released radioactivity of liquid waste even under the restricted resources. The comparison of two methods shows very similar results. (author)

  20. Genetic shifting: a novel approach for controlling vector-borne diseases.

    Science.gov (United States)

    Powell, Jeffrey R; Tabachnick, Walter J

    2014-06-01

    Rendering populations of vectors of diseases incapable of transmitting pathogens through genetic methods has long been a goal of vector geneticists. We outline a method to achieve this goal that does not involve the introduction of any new genetic variants to the target population. Rather we propose that shifting the frequencies of naturally occurring alleles that confer refractoriness to transmission can reduce transmission below a sustainable level. The program employs methods successfully used in plant and animal breeding. Because no artificially constructed genetically modified organisms (GMOs) are introduced into the environment, the method is minimally controversial. We use Aedes aegypti and dengue virus (DENV) for illustrative purposes but point out that the proposed program is generally applicable to vector-borne disease control. PMID:24794113

  1. The equidosimetric approach to comparing the action of radioactive and chemical pollutions on natural populations of hydrobionts

    International Nuclear Information System (INIS)

    For the equidosimetric assessment of ionizing radiation and chemical pollutants, it is proposed to compare effects in mutagenically equivalent doses (i.e., those inducing the equal number of cells with chromosome aberrations) by using such criteria as the distribution of chromosome aberrations in cells and the number of aberrations per aberrant cell. On the basis of this approach, the equidosimetric assessment of radioactive and chemical pollution in two water bodies from the ChNPP zone is made

  2. Autism and genetics: Clinical approach and association study with two markers of HRAS gene

    Energy Technology Data Exchange (ETDEWEB)

    Herault, J.; Petit, E.; Cherpi, C. [Laboratoire de Biochimie Medicale, Tours (France)] [and others

    1995-08-14

    Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

  3. Molecular biological approach to study genetic architecture of the genus Ipomoea

    International Nuclear Information System (INIS)

    The most significant obstacles in sweet potato breeding are the self- and cross-incompatibilities. It has made cross breeding and genetic analysis very difficult, besides the problems of polyploidy. Recent development of molecular analysis techniques made some of the genetic analyses possible. In this paper, (1) the phylogenetic relations of sweet potato cultivars and their wild relatives are clarified by the use of RFLP analysis and (2) the nature of a cDNA clone specific for pollen and stigma are reported. (author). 16 refs, 7 figs, 2 tabs

  4. A Systems Approach to Identify Genetic and Environmental Regulators of Metabolism

    OpenAIRE

    Williams, Evan Graehl

    2014-01-01

    For more than a century, it has been recognized that our genetic inheritance and our environment interact to shape who we are and how we act (nature vs. nurture€), and the study of genetics has allowed us to explain why traits can vary dramatically between individuals (i.e. trait variance), and yet often be strongly shared within families (i.e. trait heritability). Scientists, statisticians, and physicians can calculate heritability, and can observe how both genes and environment influence h...

  5. An information-gain approach to detecting three-way epistatic interactions in genetic association studies

    DEFF Research Database (Denmark)

    Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W;

    2013-01-01

    Background Epistasis has been historically used to describe the phenomenon that the effect of a given gene on a phenotype can be dependent on one or more other genes, and is an essential element for understanding the association between genetic and phenotypic variations. Quantifying epistasis of...... tuberculosis data, we found a statistically significant pure three-way epistatic interaction effect that was stronger than any lower-order associations. Conclusion Our study provides a methodological basis for detecting and characterizing high-order gene-gene interactions in genetic association studies....

  6. Determination of contact maps in proteins: A combination of structural and chemical approaches

    International Nuclear Information System (INIS)

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles

  7. Novel Approach for Evaluating Secondary Organic Aerosol from Aromatic Hydrocarbons: SOA Yield and Chemical Composition

    Science.gov (United States)

    Li, Lijie; Tang, Ping; Nakao, Shunsuke; Qi, Li; Kacarab, Mary; Cocker, David

    2016-04-01

    Aromatic hydrocarbons account for 20%-30% of urban atmospheric VOCs and are major contributors to anthropogenic secondary organic aerosol (SOA). However, prediction of SOA from aromatic hydrocarbons as a function of structure, NOx concentration, and OH radical levels remains elusive. Innovative SOA yield and chemical composition evaluation approaches are developed here to investigate SOA formation from aromatic hydrocarbons. SOA yield is redefined in this work by adjusting the molecular weight of all aromatic precursors to the molecular weight of benzene (Yield'= Yieldi×(MWi/MWBenzene); i: aromatic hydrocarbon precursor). Further, SOA elemental ratio is calculated on an aromatic ring basis rather than the classic mole basis. Unified and unique characteristics in SOA formed from aromatic hydrocarbons with different alkyl groups (varying in carbon number and location on aromatic ring) are explored by revisiting fifteen years of UC Riverside/CE-CERT environmental chamber data on 129 experiments from 17 aromatic precursors at urban region relevant low NOx conditions (HC:NO 11.1-171 ppbC:ppb). Traditionally, SOA mass yield of benzene is much greater than that of other aromatic species. However, when adjusting for molecular weight, a similar yield is found across the 17 different aromatic precursors. More importantly, four oxygens per aromatic ring are observed in the resulting SOA regardless of the alkyl substitutes attached to the ring, which majorly affect H/C ratio in SOA. Therefore, resulting SOA bulk composition from aromatic hydrocarbons can be predicted as C6+nH6+2nO4 (n: alkyl substitute carbon number). Further, the dominating role of the aromatic ring carbons is confirmed by studying the chemical composition of SOA formed from the photooxidation of an aromatic hydrocarbon with a 13C isotopically labeled alkyl carbon. Overall, this study unveils the similarity in SOA formation from aromatic hydrocarbons enhancing the understanding of SOA formation from

  8. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  9. Beyond the pseudo-time-dependent approach: chemical models of dense core precursors

    Science.gov (United States)

    Hassel, G. E.; Herbst, E.; Bergin, E. A.

    2010-06-01

    Context. Chemical models of dense cloud cores often utilize the so-called pseudo-time-dependent approximation, in which the physical conditions are held fixed and uniform as the chemistry occurs. In this approximation, the initial abundances chosen, which are totally atomic in nature except for molecular hydrogen, are artificial. A more detailed approach to the chemistry of dense cold cores should include the physical evolution during their early stages of formation. Aims: Our major goal is to investigate the initial synthesis of molecular ices and gas-phase molecules as cold molecular gas begins to form behind a shock in the diffuse interstellar medium. The abundances calculated as the conditions evolve can then be utilized as reasonable initial conditions for a theory of the chemistry of dense cores. Methods: Hydrodynamic shock-wave simulations of the early stages of cold core formation are used to determine the time-dependent physical conditions for a gas-grain chemical network. We follow the cold post-shock molecular evolution of ices and gas-phase molecules as the visual extinction increases with time to AV ≈ 3. (Note that instead of an equal sign, the approximately equal sign should remain.) At higher extinction, self-gravity becomes important. Results: As the newly condensed gas enters its cool post-shock phase, a large amount of CO is produced in the gas. As the CO forms, water ice is produced on grains, while accretion of CO produces CO ice. The production of CO2 ice from CO occurs via several surface mechanisms, while the production of CH4 ice is slowed by gas-phase conversion of C into CO.

  10. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Science.gov (United States)

    Wołek, Karol; Gómez-Sicilia, Àngel; Cieplak, Marek

    2015-12-01

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  11. Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets

    Science.gov (United States)

    Mann, Paul A.; Müller, Anna; Wolff, Kerstin A.; Fischmann, Thierry; Wang, Hao; Reed, Patricia; Hou, Yan; Li, Wenjin; Müller, Christa E.; Xiao, Jianying; Murgolo, Nicholas; Sher, Xinwei; Mayhood, Todd; Sheth, Payal R.; Mirza, Asra; Labroli, Marc; Xiao, Li; McCoy, Mark; Gill, Charles J.; Pinho, Mariana G.; Schneider, Tanja; Roemer, Terry

    2016-01-01

    Here we describe a chemical biology strategy performed in Staphylococcus aureus and Staphylococcus epidermidis to identify MnaA, a 2-epimerase that we demonstrate interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA wall teichoic acid (WTA) biosynthesis enzymes. Genetic inactivation of mnaA results in complete loss of WTA and dramatic in vitro β-lactam hypersensitivity in methicillin-resistant S. aureus (MRSA) and S. epidermidis (MRSE). Likewise, the β-lactam antibiotic imipenem exhibits restored bactericidal activity against mnaA mutants in vitro and concomitant efficacy against 2-epimerase defective strains in a mouse thigh model of MRSA and MRSE infection. Interestingly, whereas MnaA serves as the sole 2-epimerase required for WTA biosynthesis in S. epidermidis, MnaA and Cap5P provide compensatory WTA functional roles in S. aureus. We also demonstrate that MnaA and other enzymes of WTA biosynthesis are required for biofilm formation in MRSA and MRSE. We further determine the 1.9Å crystal structure of S. aureus MnaA and identify critical residues for enzymatic dimerization, stability, and substrate binding. Finally, the natural product antibiotic tunicamycin is shown to physically bind MnaA and Cap5P and inhibit 2-epimerase activity, demonstrating that it inhibits a previously unanticipated step in WTA biosynthesis. In summary, MnaA serves as a new Staphylococcal antibiotic target with cognate inhibitors predicted to possess dual therapeutic benefit: as combination agents to restore β-lactam efficacy against MRSA and MRSE and as non-bioactive prophylactic agents to prevent Staphylococcal biofilm formation. PMID:27144276

  12. Characterization of pellicle inhibition in Gluconacetobacter xylinus 53582 by a small molecule, pellicin, identified by a chemical genetics screen.

    Directory of Open Access Journals (Sweden)

    Janice L Strap

    Full Text Available Pellicin ([2E]-3-phenyl-1-[2,3,4,5-tetrahydro-1,6-benzodioxocin-8-yl]prop-2-en-1-one was identified in a chemical genetics screen of 10,000 small molecules for its ability to completely abolish pellicle production in Gluconacetobacter xylinus. Cells grown in the presence of pellicin grew 1.5 times faster than untreated cells. Interestingly, growth in pellicin also caused G. xylinus cells to elongate. Measurement of cellulose synthesis in vitro showed that cellulose synthase activity was not directly inhibited by pellicin. Rather, when cellulose synthase activity was measured in cells that were pre-treated with the compound, the rate of cellulose synthesis increased eight-fold over that observed for untreated cells. This phenomenon was also apparent in the rapid production of cellulose when cells grown in the presence of pellicin were washed and transferred to media lacking the inhibitor. The rate at which cellulose was produced could not be accounted for by growth of the organism. Pellicin was not detected when intracellular contents were analyzed. Furthermore, it was found that pellicin exerts its effect extracellularly by interfering with the crystallization of pre-cellulosic tactoidal aggregates. This interference of the crystallization process resulted in enhanced production of cellulose II as evidenced by the ratio of acid insoluble to acid soluble product in in vitro assays and confirmed in vivo by scanning electron microscopy and powder X-ray diffraction. The relative crystallinity index, RCI, of pellicle produced by untreated G. xylinus cultures was 70% while pellicin-grown cultures had RCI of 38%. Mercerized pellicle of untreated cells had RCI of 42%, which further confirms the mechanism of action of pellicin as an inhibitor of the cellulose I crystallization process. Pellicin is a useful tool for the study of cellulose biosynthesis in G. xylinus.

  13. A generalised chemical precipitation modelling approach in wastewater treatment applied to calcite.

    Science.gov (United States)

    Mbamba, Christian Kazadi; Batstone, Damien J; Flores-Alsina, Xavier; Tait, Stephan

    2015-01-01

    Process simulation models used across the wastewater industry have inherent limitations due to over-simplistic descriptions of important physico–chemical reactions, especially for mineral solids precipitation. As part of the efforts towards a larger Generalized Physicochemical Modelling Framework, the present study aims to identify a broadly applicable precipitation modelling approach. The study uses two experimental platforms applied to calcite precipitating from synthetic aqueous solutions to identify and validate the model approach. Firstly, dynamic pH titration tests are performed to define the baseline model approach. Constant Composition Method (CCM) experiments are then used to examine influence of environmental factors on the baseline approach. Results show that the baseline model should include precipitation kinetics (not be quasi-equilibrium), should include a 1st order effect of the mineral particulate state (Xcryst) and, for calcite, have a 2nd order dependency (exponent n = 2.05 ± 0.29) on thermodynamic supersaturation (σ). Parameter analysis indicated that the model was more tolerant to a fast kinetic coefficient (kcryst) and so, in general, it is recommended that a large kcryst value be nominally selected where insufficient process data is available. Zero seed (self nucleating) conditions were effectively represented by including arbitrarily small amounts of mineral phase in the initial conditions. Both of these aspects are important for wastewater modelling, where knowledge of kinetic coefficients is usually not available, and it is typically uncertain which precipitates are actually present. The CCM experiments confirmed the baseline model, particularly the dependency on supersaturation. Temperature was also identified as an influential factor that should be corrected for via an Arrhenius-style correction of kcryst. The influence of magnesium (a common and representative added impurity) on kcryst was found to be significant but was considered

  14. An Approach to Calculate Mineralś Bulk Moduli KS from Chemical Composition and Density ρ

    Science.gov (United States)

    Breuer, S.; Schilling, F. R.; Mueller, B.; Drüppel, K.

    2015-12-01

    The elastic properties of minerals are fundamental parameters for technical and geotechnical applications and an important research topic towards a better understanding of the Eart&hacute;s interior. Published elastic properties, chemical composition, and density data of 86 minerals (total of 258 data including properties of minerals at various p, T conditions) were collected into a database. It was used to test different hypotheses about relationships between these properties (e.g. water content in minerals and their Poisson's ratio). Furthermore, a scheme to model the average elastic properties, i.e. the bulk modulus KS, based on mineral density and composition was developed. Birc&hacute;s law, a linearity between density ρ and wave velocity (e.g. vp.), is frequently used in seismic and seismology to derive density of the Eart&hacute;s interior from seismic velocities. Applying the compiled mineral data contradicts the use of a simple velocity-density relation (e.g. Gardneŕs relation, 1974). The presented model-approach to estimate the mineralś bulk moduli Ks (as Voigt-Reuss-Hill average) is based on the idea of pressure-temperature (p-T) dependent ionś bulk moduli. Using a multi-exponential regression to ascertain the ionś bulk moduli and by applying an exponential scaling with density ρ, their bulk moduli could be modelled. As a result, > 88 % of the 258 bulk moduli data are predicted with an uncertainty of < 20 % compared to published values. Compared to other models (e.g. Anderson et al. 1970 and Anderson & Nafe 1965), the here presented approach to model the bulk moduli only requires the density ρ and chemical composition of the mineral and is not limited to a specific group of minerals, composition, or structure. In addition to this, by using the pressure and temperature dependent density ρ(p, T), it is possible to predict bulk moduli for varying p-T conditions. References:Gardner, G.H.F, Gardner, L.W. and Gregory, A.R. (1974). Geophysics, 39, No. 6

  15. BARC 2006 station report for NC-1004 national project on Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork

    Science.gov (United States)

    The NC-1004 national project assesses “Genetic and Functional Genomic Approaches to Improve Production and Quality of Pork.” This final NC-1004 station report summarizes the BARC lab’s recent research progress on the second objective: Discover genetic mechanisms controlling animal health in pork pro...

  16. A Molecular Genetic Approach to Evaluate a Novel Seedless Phenotype Found in Tango, a New Variety of Mandarin Developed From Gamma-Irradiated W. Murcott

    OpenAIRE

    Crowley, Jennifer Robyn

    2011-01-01

    ABSTRACT OF THE DISSERTATIONA Molecular Genetic Approach to Evaluate a Novel Seedless Phenotype Found in Tango, a New Variety of Mandarin Developed From Gamma-Irradiated W. Murcott by Jennifer Robyn CrowleyDoctor of Philosophy, Graduate Program in Genetics, Genomics, Bioinformatics University of California, Riverside, December 2011 Dr. Mikeal Ro...

  17. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    Directory of Open Access Journals (Sweden)

    Li Hai-Long

    2011-06-01

    Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  18. Genetic, Genomic, and Breeding Approaches to Further Explore Kernel Composition Traits and Grain Yield in Maize

    Science.gov (United States)

    Da Silva, Helena Sofia Pereira

    2009-01-01

    Maize ("Zea mays L.") is a model species well suited for the dissection of complex traits which are often of commercial value. The purpose of this research was to gain a deeper understanding of the genetic control of maize kernel composition traits starch, protein, and oil concentration, and also kernel weight and grain yield. Germplasm with…

  19. A latent class approach to investigating demand for genetically modified banana in Uganda

    NARCIS (Netherlands)

    Kikulwe, E.M.; Birol, E.; Wesseler, J.H.H.; Falck-Zepeda, J.

    2011-01-01

    This study explores consumer acceptance and valuation of a genetically modified (GM) staple food crop in a developing country prior to its commercialization. We focus on the hypothetical introduction of a disease-resistant GM banana variety in Uganda, where bananas are among the most important stapl

  20. Workshop overview : Approaches to the assessment of the allergenic potential of food from genetically modified crops

    NARCIS (Netherlands)

    Ladics, G.S.; Holsapple, M.P.; Astwood, J.D.; Kimber, I.; Knippels, L.M.J.; Helm, R.M.; Dong, W.

    2003-01-01

    There is a need to assess the safety of foods deriving from genetically modified (GM) crops, including the allergenic potential of novel gene products. Presently, there is no single in vitro or in vivo model that has been validated for the identification or characterization of potential food allerge

  1. GENETIC ALGORITHM BASED APPROACH FOR THE SELECTION OF PROJECTS IN PUBLIC R&D INSTITUTIONS

    OpenAIRE

    MANILAL P; Sanjay, S.; Pradeep, S; MANIKANTA V; KUMARA S.S; HARSHA P

    2011-01-01

    Identification and selection of new project concepts are one of the crucial steps in the project selection process in research establishments. It is essential to ensure that objectives of proposed projects are evaluated for duplicity and redundancy against databases. In this context, implementation of a genetic algorithm (GA) basedapproach is described.

  2. High-throughput approaches for characterization and efficient use of plant genetic resources

    Czech Academy of Sciences Publication Activity Database

    Ovesná, J.; Janská, A.; Zelenková, S.; Maršík, Petr

    New York : CRC Press, 2011 - (Benkeblia, N.), s. 23-39 ISBN 978-1-4398-2504-4. - (Advances in Agroecology ) Institutional support: RVO:61389030 Keywords : genomics * proteomics * plant genetic resource Subject RIV: GE - Plant Breeding http://www.crcpress.com/product/isbn/9781439825044

  3. Students' Understanding of Genetics Concepts: The Effect of Reasoning Ability and Learning Approaches

    Science.gov (United States)

    Kiliç, Didem; Saglam, Necdet

    2014-01-01

    Students tend to learn genetics by rote and may not realise the interrelationships in daily life. Because reasoning abilities are necessary to construct relationships between concepts and rote learning impedes the students' sound understanding, it was predicted that having high level of formal reasoning and adopting meaningful learning…

  4. A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets

    DEFF Research Database (Denmark)

    Taneera, Jalal; Lang, Stefan; Sharma, Amitabh;

    2012-01-01

    Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified...

  5. Bacterial Conjugation in Soil and Water: An Experimental Approach to Environmental Genetics.

    Science.gov (United States)

    Trevors, J. T.

    1989-01-01

    Described is a laboratory experiment that can be used to investigate bacterial survival in soil or water as well as the study of genetic transfer via conjugation. Discussed are materials, laboratory procedures, typical results, and a list of six references. (CW)

  6. A multi-objective genetic approach to domestic load scheduling in an energy management system

    International Nuclear Information System (INIS)

    In this paper a multi-objective genetic algorithm is used to solve a multi-objective model to optimize the time allocation of domestic loads within a planning period of 36 h, in a smart grid context. The management of controllable domestic loads is aimed at minimizing the electricity bill and the end-user’s dissatisfaction concerning two different aspects: the preferred time slots for load operation and the risk of interruption of the energy supply. The genetic algorithm is similar to the Elitist NSGA-II (Nondominated Sorting Genetic Algorithm II), in which some changes have been introduced to adapt it to the physical characteristics of the load scheduling problem and improve usability of results. The mathematical model explicitly considers economical, technical, quality of service and comfort aspects. Illustrative results are presented and the characteristics of different solutions are analyzed. - Highlights: • A genetic algorithm similar to the NSGA-II is used to solve a multi-objective model. • The optimized time allocation of domestic loads in a smart grid context is achieved. • A variable preference profile for the operation of the managed loads is included. • A safety margin is used to account for the quality of the energy services provided. • A non-dominated front with the solutions in the two-objective space is obtained

  7. Novel genomic approaches unravel genetic architecture of complex traits in apple.

    NARCIS (Netherlands)

    Kumar, S.; Garrick, D.J.; Bink, M.C.A.M.; Whitworth, C.; Chagné, D.

    2013-01-01

    BACKGROUND: Understanding the genetic architecture of quantitative traits is important for developing genome-based crop improvement methods. Genome-wide association study (GWAS) is a powerful technique for mining novel functional variants. Using a family-based design involving 1,200 apple (Malus × d

  8. Molecular and genetics approaches for investigation of phospholipase D role in plant cells

    Directory of Open Access Journals (Sweden)

    Volotovsky I. D.

    2010-04-01

    Full Text Available The review is devoted to the analysis of publications ñoncerning the role of phospholipase D (PLD in regulation of metabolism in plant cells. Analysis of molecular and genetic studies suggest that PLD is an important component of various hormonal and stress signaling pathways

  9. Two-edge disjoint survivable network design problem with relays: a hybrid genetic algorithm and Lagrangian heuristic approach

    Science.gov (United States)

    Konak, Abdullah

    2014-01-01

    This article presents a network design problem with relays considering the two-edge network connectivity. The problem arises in telecommunications and logistic networks where a constraint is imposed on the distance that a commodity can travel on a route without being processed by a relay, and the survivability of the network is critical in case of a component failure. The network design problem involves selecting two-edge disjoint paths between source and destination node pairs and determining the location of relays to minimize the network design cost. The formulated problem is solved by a hybrid approach of a genetic algorithm (GA) and a Lagrangian heuristic such that the GA searches for two-edge disjoint paths for each commodity, and the Lagrangian heuristic is used to determine relays on these paths. The performance of the proposed hybrid approach is compared to the previous approaches from the literature, with promising results.

  10. Quantitative genetics of taura syndrome resistance in pacific white shrimp (penaeus vannamei: a cure model approach

    Directory of Open Access Journals (Sweden)

    Meuwissen Theo HE

    2011-03-01

    Full Text Available Abstract Background In aquaculture breeding, resistance against infectious diseases is commonly assessed as time until death under exposure to a pathogen. For some diseases, a fraction of the individuals may appear as "cured" (non-susceptible, and the resulting survival time may thus be a result of two confounded underlying traits, i.e., endurance (individual hazard and susceptibility (whether at risk or not, which may be accounted for by fitting a cure survival model. We applied a cure model to survival data of Pacific white shrimp (Penaeus vannamei challenged with the Taura syndrome virus, which is one of the major pathogens of Panaeid shrimp species. Methods In total, 15,261 individuals of 513 full-sib families from three generations were challenge-tested in 21 separate tests (tanks. All challenge-tests were run until mortality naturally ceased. Time-until-event data were analyzed with a mixed cure survival model using Gibbs sampling, treating susceptibility and endurance as separate genetic traits. Results Overall mortality at the end of test was 28%, while 38% of the population was considered susceptible to the disease. The estimated underlying heritability was high for susceptibility (0.41 ± 0.07, but low for endurance (0.07 ± 0.03. Furthermore, endurance and susceptibility were distinct genetic traits (rg = 0.22 ± 0.25. Estimated breeding values for endurance and susceptibility were only moderately correlated (0.50, while estimated breeding values from classical models for analysis of challenge-test survival (ignoring the cured fraction were closely correlated with estimated breeding values for susceptibility, but less correlated with estimated breeding values for endurance. Conclusions For Taura syndrome resistance, endurance and susceptibility are apparently distinct genetic traits. However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure

  11. A novel genetic score approach using instruments to investigate interactions between pathways and environment: application to air pollution.

    Directory of Open Access Journals (Sweden)

    Marie-Abele Bind

    Full Text Available 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 (p(interaction = 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 (p(interaction = 0.12, CRP (p(interaction = 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.

  12. Variable approaches to genetic counseling for microarray regions of homozygosity associated with parental relatedness.

    Science.gov (United States)

    Grote, Lauren; Myers, Melanie; Lovell, Anne; Saal, Howard; Sund, Kristen Lipscomb

    2014-01-01

    SNP microarrays are capable of detecting regions of homozygosity (ROH) which can suggest parental relatedness. This study was designed to describe pre- and post-test counseling practices of genetics professionals regarding ROH, explore perceived comfort and ethical concerns in the follow-up of such results, demonstrate awareness of laws surrounding duty to report consanguinity and incest, and allow respondents to share their personal experiences with results suggesting a parental relationship. A 35 question survey was administered to 240 genetic counselors and geneticists who had ordered or counseled for SNP microarray. The results are presented using descriptive statistics. There was variation in both pre- and post-test counseling practices of genetics professionals. Twenty-five percent of respondents reported pre-test counseling that ROH can indicate parental relatedness. The most commonly reported ethical concern was disclosure of findings suggesting parental relatedness to parents of the patient; only 48.4% reported disclosing parental relatedness when indicated. Fifty-seven percent felt comfortable receiving results suggesting parental consanguinity while 17% felt comfortable receiving results suggesting parental incest. Twenty percent of respondents were extremely/moderately familiar with the laws about duty to report incest. Personal experiences in post-test counseling included both parental acknowledgement and denial of relatedness. This study highlights the differences in genetics professionals' pre- and post-test counseling practices, comfort, and experiences surrounding parental relatedness suggested by SNP microarray results. It identifies a need for professional organizations to offer guidance to genetics professionals about how to respond to and counsel for molecular results suggesting parental consanguinity or incest. PMID:24243712

  13. MODELING A MIXTURE: PBPK/PD APPROACHES FOR PREDICTING CHEMICAL INTERACTIONS.

    Science.gov (United States)

    Since environmental chemical exposures generally involve multiple chemicals, there are both regulatory and scientific drivers to develop methods to predict outcomes of these exposures. Even using efficient statistical and experimental designs, it is not possible to test in vivo a...

  14. An approach to modeling coupled thermal-hydraulic-chemical processes in geothermal systems

    Science.gov (United States)

    Palguta, Jennifer; Williams, Colin F.; Ingebritsen, Steven E.; Hickman, Stephen H.; Sonnenthal, Eric

    2011-01-01

    Interactions between hydrothermal fluids and rock alter mineralogy, leading to the formation of secondary minerals and potentially significant physical and chemical property changes. Reactive transport simulations are essential for evaluating the coupled processes controlling the geochemical, thermal and hydrological evolution of geothermal systems. The objective of this preliminary investigation is to successfully replicate observations from a series of hydrothermal laboratory experiments [Morrow et al., 2001] using the code TOUGHREACT. The laboratory experiments carried out by Morrow et al. [2001] measure permeability reduction in fractured and intact Westerly granite due to high-temperature fluid flow through core samples. Initial permeability and temperature values used in our simulations reflect these experimental conditions and range from 6.13 × 10−20 to 1.5 × 10−17 m2 and 150 to 300 °C, respectively. The primary mineralogy of the model rock is plagioclase (40 vol.%), K-feldspar (20 vol.%), quartz (30 vol.%), and biotite (10 vol.%). The simulations are constrained by the requirement that permeability, relative mineral abundances, and fluid chemistry agree with experimental observations. In the models, the granite core samples are represented as one-dimensional reaction domains. We find that the mineral abundances, solute concentrations, and permeability evolutions predicted by the models are consistent with those observed in the experiments carried out by Morrow et al. [2001] only if the mineral reactive surface areas decrease with increasing clay mineral abundance. This modeling approach suggests the importance of explicitly incorporating changing mineral surface areas into reactive transport models.

  15. Acute toxicity testing of chemicals-Opportunities to avoid redundant testing and use alternative approaches.

    Science.gov (United States)

    Creton, Stuart; Dewhurst, Ian C; Earl, Lesley K; Gehen, Sean C; Guest, Robert L; Hotchkiss, Jon A; Indans, Ian; Woolhiser, Michael R; Billington, Richard

    2010-01-01

    Assessment of the acute systemic oral, dermal, and inhalation toxicities, skin and eye irritancy, and skin sensitisation potential of chemicals is required under regulatory schemes worldwide. In vivo studies conducted to assess these endpoints can sometimes be associated with substantial adverse effects in the test animals, and their use should always be scientifically justified. It has been argued that while information obtained from such acute tests provides data needed to meet classification and labelling regulations, it is of limited value for hazard and risk assessments. Inconsistent application of in vitro replacements, protocol requirements across regions, and bridging principles also contribute to unnecessary and redundant animal testing. Assessment of data from acute oral and dermal toxicity testing demonstrates that acute dermal testing rarely provides value for hazard assessment purposes when an acute oral study has been conducted. Options to waive requirements for acute oral and inhalation toxicity testing should be employed to avoid unnecessary in vivo studies. In vitro irritation models should receive wider adoption and be used to meet regulatory needs. Global requirements for sensitisation testing need continued harmonisation for both substance and mixture assessments. This paper highlights where alternative approaches or elimination of tests can reduce and refine animal use for acute toxicity requirements. PMID:20144136

  16. Chemical and Enzymatic Approaches to Carbohydrate-Derived Spiroketals: Di-D-Fructose Dianhydrides (DFAs

    Directory of Open Access Journals (Sweden)

    José M. García Fernández

    2008-08-01

    Full Text Available Di-D-fructose dianhydrides (DFAs comprise a unique family of stereoisomeric spiro-tricyclic disaccharides formed upon thermal and/or acidic activation of sucroseand/ or D-fructose-rich materials. The recent discovery of the presence of DFAs in food products and their remarkable nutritional features has attracted considerable interest from the food industry. DFAs behave as low-caloric sweeteners and have proven to exert beneficial prebiotic nutritional functions, favouring the growth of Bifidobacterium spp. In the era of functional foods, investigation of the beneficial properties of DFAs has become an important issue. However, the complexity of the DFA mixtures formed during caramelization or roasting of carbohydrates by traditional procedures (up to 14 diastereomeric spiroketal cores makes evaluation of their individual properties a difficult challenge. Great effort has gone into the development of efficient procedures to obtain DFAs in pure form at laboratory and industrial scale. This paper is devoted to review the recent advances in the stereoselective synthesis of DFAs by means of chemical and enzymatic approaches, their scope, limitations, and complementarities.

  17. An approach to develop chemical intuition for atomistic electron transport calculations using basis set rotations.

    Science.gov (United States)

    Borges, A; Solomon, G C

    2016-05-21

    Single molecule conductance measurements are often interpreted through computational modeling, but the complexity of these calculations makes it difficult to directly link them to simpler concepts and models. Previous work has attempted to make this connection using maximally localized Wannier functions and symmetry adapted basis sets, but their use can be ambiguous and non-trivial. Starting from a Hamiltonian and overlap matrix written in a hydrogen-like basis set, we demonstrate a simple approach to obtain a new basis set that is chemically more intuitive and allows interpretation in terms of simple concepts and models. By diagonalizing the Hamiltonians corresponding to each atom in the molecule, we obtain a basis set that can be partitioned into pseudo-σ and -π and allows partitioning of the Landuaer-Büttiker transmission as well as create simple Hückel models that reproduce the key features of the full calculation. This method provides a link between complex calculations and simple concepts and models to provide intuition or extract parameters for more complex model systems. PMID:27208940

  18. Consequences of New Approach to Chemical Stability Tests to Active Pharmaceutical Ingredients.

    Science.gov (United States)

    Jamrógiewicz, Marzena

    2016-01-01

    There is a great need of broaden look on stability tests of active pharmaceutical ingredients (APIs) in comparison with current requirements contained in pharmacopeia. By usage of many modern analytical methods the conception of monitoring the changes of APIs during initial stage of their exposure to harmful factors has been developed. New knowledge must be acquired in terms of identification of each degradation products, especially volatile ones. Further research as toxicology prediction during in silico studies of determined and identified degradation products is necessary. In silico methods are known as computational toxicology or computer-assisted technologies which are used for predicting toxicology of pharmaceutical substances such as impurities or degradation products. This is a specialized software and databases intended to calculate probability of genotoxicity or mutagenicity of these substances through a chemical structure-based screening process and algorithm specific to a given software program. Applying of new analytical approach is proposed as the usage of PAT tools, XRD, HS-SPME GC-MS/MS, LC-MS/MS for stability testing. Described improvements should be taken into account in case of each drug existing already in the market as well as being implemented as new one. PMID:26955356

  19. A Chemical Biology Approach to Reveal Sirt6-targeted Histone H3 Sites in Nucleosomes.

    Science.gov (United States)

    Wang, Wesley Wei; Zeng, Yu; Wu, Bo; Deiters, Alexander; Liu, Wenshe R

    2016-07-15

    As a member of a highly conserved family of NAD(+)-dependent histone deacetylases, Sirt6 is a key regulator of mammalian genome stability, metabolism, and life span. Previous studies indicated that Sirt6 is hardwired to remove histone acetylation at H3K9 and H3K56. However, how Sirt6 recognizes its nucleosome substrates has been elusive due to the difficulty of accessing homogeneous acetyl-nucleosomes and the low activity of Sirt6 toward peptide substrates. Based on the fact that Sirt6 has an enhanced activity to remove long chain fatty acylation from lysine, we developed an approach to recombinantly synthesize histone H3 with a fatty acylated lysine, N(ε)-(7-octenoyl)-lysine (OcK), installed at a number of lysine sites and used these acyl-H3 proteins to assemble acyl-nucleosomes as active Sirt6 substrates. A chemical biology approach that visualizes OcK in nucleosomes and therefore allows direct sensitization of Sirt6 activities on its acyl-nucleosome substrates was also formulated. By combining these two approaches, we showed that Sirt6 actively removes acylation from H3K9, H3K18, and H3K27; has relatively low activities toward H3K4 and K3K23; but sluggishly removes acylation at H3K14, H3K36, H3K56, and H3K79. Overexpressing Sirt6 in 293T cells led to downregulated acetylation at H3K18 and K3K27, confirming these two novel Sirt6-targeted nucleosome lysine sites in cells. Given that downregulation of H3K18 acetylation is correlated with a poor prognosis of several cancer types and H3K27 acetylation antagonizes repressive gene regulation by di- and trimethylation at H3K27, our current study implies that Sirt6 may serve as a target for cancer intervention and regulatory pathway investigation in cells. PMID:27152839

  20. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    International Nuclear Information System (INIS)

    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N2 flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure

  1. A Case Based Approach to Clinical Genetics of Thoracic Aortic Aneurysm/Dissection

    Directory of Open Access Journals (Sweden)

    Betti Giusti

    2016-01-01

    Full Text Available Thoracic aortic aneurysm/dissection (TAAD is a potential lethal condition with a rising incidence. This condition may occur sporadically; nevertheless, it displays familial clustering in >20% of the cases. Family history confers a six- to twentyfold increased risk of TAAD and has to be considered in the identification and evaluation of patients needing an adequate clinical follow-up. Familial TAAD recognizes a number of potential etiologies with a significant genetic heterogeneity, in either syndromic or nonsyndromic forms of the manifestation. The clinical impact and the management of patients with TAAD differ according to the syndromic and nonsyndromic forms of the manifestation. The clinical management of TAAD patients varies, depending on the different forms. Starting from the description of patient history, in this paper, we summarized the state of the art concerning assessment of clinical/genetic profile and therapeutic management of TAAD patients.

  2. A Case Based Approach to Clinical Genetics of Thoracic Aortic Aneurysm/Dissection.

    Science.gov (United States)

    Giusti, Betti; Nistri, Stefano; Sticchi, Elena; De Cario, Rosina; Abbate, Rosanna; Gensini, Gian Franco; Pepe, Guglielmina

    2016-01-01

    Thoracic aortic aneurysm/dissection (TAAD) is a potential lethal condition with a rising incidence. This condition may occur sporadically; nevertheless, it displays familial clustering in >20% of the cases. Family history confers a six- to twentyfold increased risk of TAAD and has to be considered in the identification and evaluation of patients needing an adequate clinical follow-up. Familial TAAD recognizes a number of potential etiologies with a significant genetic heterogeneity, in either syndromic or nonsyndromic forms of the manifestation. The clinical impact and the management of patients with TAAD differ according to the syndromic and nonsyndromic forms of the manifestation. The clinical management of TAAD patients varies, depending on the different forms. Starting from the description of patient history, in this paper, we summarized the state of the art concerning assessment of clinical/genetic profile and therapeutic management of TAAD patients. PMID:27314043

  3. Exploiting problem structure in a genetic algorithm approach to a nurse rostering problem

    CERN Document Server

    Uwe, Aickelin

    2008-01-01

    There is considerable interest in the use of genetic algorithms to solve problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle the conflict between objectives and constraints that typically occurs in such problems. In order to overcome this, successful implementations frequently make use of problem specific knowledge. This paper is concerned with the development of a GA for a nurse rostering problem at a major UK hospital. The structure of the constraints is used as the basis for a co-evolutionary strategy using co-operating sub-populations. Problem specific knowledge is also used to define a system of incentives and disincentives, and a complementary mutation operator. Empirical results based on 52 weeks of live data show how these features are able to improve an unsuccessful canonical GA to the point where it is able to provide a practical solution to the problem

  4. A Case Based Approach to Clinical Genetics of Thoracic Aortic Aneurysm/Dissection

    Science.gov (United States)

    Giusti, Betti; Nistri, Stefano; Sticchi, Elena; De Cario, Rosina; Abbate, Rosanna; Gensini, Gian Franco; Pepe, Guglielmina

    2016-01-01

    Thoracic aortic aneurysm/dissection (TAAD) is a potential lethal condition with a rising incidence. This condition may occur sporadically; nevertheless, it displays familial clustering in >20% of the cases. Family history confers a six- to twentyfold increased risk of TAAD and has to be considered in the identification and evaluation of patients needing an adequate clinical follow-up. Familial TAAD recognizes a number of potential etiologies with a significant genetic heterogeneity, in either syndromic or nonsyndromic forms of the manifestation. The clinical impact and the management of patients with TAAD differ according to the syndromic and nonsyndromic forms of the manifestation. The clinical management of TAAD patients varies, depending on the different forms. Starting from the description of patient history, in this paper, we summarized the state of the art concerning assessment of clinical/genetic profile and therapeutic management of TAAD patients. PMID:27314043

  5. Patient Electronic Health Records as a Means to Approach Genetic Research in Gastroenterology.

    Science.gov (United States)

    Ananthakrishnan, Ashwin N; Lieberman, David

    2015-10-01

    Electronic health records (EHRs) are being increasingly utilized and form a unique source of extensive data gathered during routine clinical care. Through use of codified and free text concepts identified using clinical informatics tools, disease labels can be assigned with a high degree of accuracy. Analysis linking such EHR-assigned disease labels to a biospecimen repository has demonstrated that genetic associations identified in prospective cohorts can be replicated with adequate statistical power and novel phenotypic associations identified. In addition, genetic discovery research can be performed utilizing clinical, laboratory, and procedure data obtained during care. Challenges with such research include the need to tackle variability in quality and quantity of EHR data and importance of maintaining patient privacy and data security. With appropriate safeguards, this novel and emerging field of research offers considerable promise and potential to further scientific research in gastroenterology efficiently, cost-effectively, and with engagement of patients and communities. PMID:26073373

  6. Biotechnology approach to determination of genetic and epigenetic control in cells

    Directory of Open Access Journals (Sweden)

    Yasuda Kenji

    2004-11-01

    Full Text Available Abstract A series of studies aimed at developing methods and systems for analyzing epigenetic information in cells are presented. The role of the epigenetic information of cells, which is complementary to their genetic information, was inferred by comparing the predictions of genetic information with the cell behaviour observed under conditions chosen to reveal adaptation processes and community effects. Analysis of epigenetic information was developed starting from the twin complementary viewpoints of cells regulation as an 'algebraic' system (emphasis on the temporal aspect and as a 'geometric' system (emphasis on the spatial aspect. The knowlege acquired from this study will lead to the use of cells for fully controlled practical applications like cell-based drug screening and the regeneration of organs.

  7. Approaches to quality management and accreditation in a genetic testing laboratory

    OpenAIRE

    Berwouts, Sarah; Morris, Michael A; Dequeker, Elisabeth

    2010-01-01

    Medical laboratories, and specifically genetic testing laboratories, provide vital medical services to different clients: clinicians requesting a test, patients from whom the sample was collected, public health and medical-legal instances, referral laboratories and authoritative bodies. All expect results that are accurate and obtained in an efficient and effective manner, within a suitable time frame and at acceptable cost. There are different ways of achieving the end results, but complianc...

  8. Why Don't Smart Teens Have Sex? A Behavioral Genetic Approach

    OpenAIRE

    Harden, K. Paige; Mendle, Jane

    2011-01-01

    Academic achievement and cognitive ability have been shown to predict later age at first sexual intercourse. Using a sample of 536 same-sex twin pairs who were followed longitudinally from adolescence to early adulthood, this study tested whether relations between intelligence, academic achievement and age at first sex were due to unmeasured genetic and environmental differences between families. Twins who differed in their intelligence or their academic achievement did not differ in their ag...

  9. Recurrent pneumonia caused by genetic immunodeficiency: a prophylactic and rehabilitative approach

    OpenAIRE

    Renata Cristina de Angelo Calsaverini Leal; Érika Cristina Pavarino Bertelli; Zaida Aurora Sperli Geraldes Soler

    2007-01-01

    Recurrent infections are a consequence of a series of genetic diseases characterized by deficiency in the immunological response. One of these diseases is the agammaglobulinemia, which is characterized by the basic defect in the maturation of lymphocytes B. The carrier of this kind of immunodeficiency, which is linked to the X (XLA) chromosome, has had primary pneumonias that have evolved into secondary pneumonias (chronic lungs with sequelae) after the third or fourth year of life. The clini...

  10. COST EFFECTIVE APPROACH ON FEATURE SELECTION USING GENETIC ALGORITHMS AND FUZZY LOGIC FOR DIABETES DIAGNOSIS

    OpenAIRE

    E.P.Ephzibah

    2011-01-01

    A way to enhance the performance of a model that combines genetic algorithms and fuzzy logic for feature selection and classification is proposed. Early diagnosis of any disease with less cost is preferable. Diabetes is one such disease. Diabetes has become the fourth leading cause of death in developed countries and there is substantial evidence that it is reaching epidemic proportions in many developing and newly industrialized nations. In medical diagnosis, patterns consist of observable s...

  11. Genetic determinism of inulin metabolism in industrial chicory (Cichorium intybus L.) : an association mapping approach

    OpenAIRE

    Raulier, Pierre

    2015-01-01

    Inulin is a fructose polymer extracted from the root of industrial chicory (Cichorium intybus L.). The quality of the root extract is determined by the polymerization degree of inulin molecules and the free fructose concentration. Low autumnal temperatures trigger an inulin degradation phase which decreases the quality of the root extract. Therefore, the objective of this thesis was to understand the genetic determinism of the synthesis and the cold induced degradation of inulin. To do so, we...

  12. Enhanced Genetic Algorithm approach for Solving Dynamic Shortest Path Routing Problems using Immigrants and Memory Schemes

    OpenAIRE

    Nair, T. R. Gopalakrishnan; Sooda, Kavitha; Yashoda, M. B.

    2011-01-01

    In Internet Routing, the static shortest path (SP) problem has been addressed using well known intelligent optimization techniques like artificial neural networks, genetic algorithms (GAs) and particle swarm optimization. Advancement in wireless communication lead more and more mobile wireless networks, such as mobile networks [mobile ad hoc networks (MANETs)] and wireless sensor networks. Dynamic nature of the network is the main characteristic of MANET. Therefore, the SP routing problem in ...

  13. University students' reflections on representations in genetics and stereochemistry revealed by a focus group approach

    OpenAIRE

    Inger Edfors; Susanne Wikman; Brita Johansson Cederblad; Cedric Linder

    2015-01-01

    Genetics and organic chemistry are areas of science that students regard as difficult to learn. Part of this difficulty is derived from the disciplines having representations as part of their discourses. In order to optimally support students’ meaning-making, teachers need to use representations to structure the meaning-making experience in thoughtful ways that consider the variation in students’ prior knowledge. Using a focus group setting, we explored 43 university students’ reasoning on re...

  14. A Genetic Algorithm Approach for the TV Self-Promotion Assignment Problem

    OpenAIRE

    Pereira, Paulo A.; Fontes, Fernando A. C. C.; Fontes, Dalila B. M. M.

    2009-01-01

    We report on the development of a Genetic Algorithm (GA), which has been integrated into a Decision Support System to plan the best assignment of the weekly self-promotion space for a TV station. The problem addressed consists on deciding which shows to advertise and when such that the number of viewers, of an intended group or target, is maximized. The GA proposed incorporates a greedy heuristic to find good initial solutions. These solutions, as well as the solutions later obtai...

  15. A MapReduce Approach for Ridge Regression in Neuroimaging-Genetic Studies

    OpenAIRE

    Da Mota, Benoit; Eickenberg, Michael; Laguitton, Soizic; Frouin, Vincent; Varoquaux, Gaël; Poline, Jean-baptiste; Thirion, Bertrand

    2012-01-01

    In order to understand the large between-subject variability observed in brain organization and assess factor risks of brain diseases, massive efforts have been made in the last few years to acquire high-dimensional neuroimaging and genetic data on large cohorts of subjects. The statistical analysis of such high-dimensional and complex data is carried out with increasingly sophisticated techniques and represents a great computational challenge. To be fully exploited, the concurrent increase of...

  16. Development of genetic sexing strains in Lepidoptera: from traditional to transgenic approaches

    Czech Academy of Sciences Publication Activity Database

    Marec, František; Neven, L. G.; Robinson, A. S.; Vreysen, M.; Goldsmith, M. R.; Nagaraju, J.; Franz, G.

    2005-01-01

    Roč. 98, č. 2 (2005), s. 248-259. ISSN 0022-0493 R&D Projects: GA AV ČR(CZ) IAA6007307 Grant ostatní: IAEA(AT) 12055/R; IAEA(AT) 12619/R Institutional research plan: CEZ:AV0Z50070508 Keywords : Lepidoptera * codling moth * sterile insect technique Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.205, year: 2005

  17. Demodulating the Response of Optical Fibre Long-Period Gratings: Genetic Algorithm Approach

    Institute of Scientific and Technical Information of China (English)

    P. S. André; R. A. Sá. Ferreira; C. M. L. Correia; H. Kalinowshy; XIN Xiang-Jun; J. L. Pinto

    2006-01-01

    @@ The extraction of the physical parameters of long period gratings from the spectral response is not an easy process. We present a demodulation technique to synthesize the physical parameters of a long period grating recorded in an optical fibre. The demodulation is achieved through the implementation of a genetic algorithm.The extracted parameters are in agreement with the typical values known for long period gratings.

  18. Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS

    OpenAIRE

    Panda, Pritam Kumar; Rane, Riya; Ravichandran, Rahul; Singh, Shrinkhla; Panchal, Hetalkumar

    2016-01-01

    Polycystic ovary syndrome (PCOS) is a hormonal imbalance in women, which causes problems during menstrual cycle and in pregnancy that sometimes results in fatality. Though the genetics of PCOS is not fully understood, early diagnosis and treatment can prevent long-term effects. In this study, we have studied the proteins involved in PCOS and the structural aspects of the proteins that are taken into consideration using computational tools. The proteins involved are modeled using Modeller 9v14...

  19. New Approaches for Crop Genetic Adaptation to the Abiotic Stresses Predicted with Climate Change

    OpenAIRE

    Robert Redden

    2013-01-01

    Extreme climatic variation is predicted with climate change this century. In many cropping regions, the crop environment will tend to be warmer with more irregular rainfall and spikes in stress levels will be more severe. The challenge is not only to raise agricultural production for an expanding population, but to achieve this under more adverse environmental conditions. It is now possible to systematically explore the genetic variation in historic local landraces by using GPS locators and w...

  20. The theological and legal approach of prenatal and preimplantation genetic control

    OpenAIRE

    George Katsimigas; Evridiki Kamba

    2012-01-01

    Aim: The investigation of the theological and legal questions derived from the application of prenatal and preimplantation genetic control on human embryos. Moreover, the review of the European and Greek legislation with regard to the prenatal and preimplantation control. Material and Method: A literature review based on both review and research literature, conducted during the period of 1984-2009, derived from MEDLINE, SCOPUS and ΙΑΤΡΟΤΕΚ databases using as key words Prenatal diagnosis , Bio...

  1. Genetic counseling follow-up - a retrospective study with a quantitative approach

    Directory of Open Access Journals (Sweden)

    De Pina-Neto João M.

    1999-01-01

    Full Text Available The impact of genetic counseling (GC was evaluated in families, who were interviewed at least two and half years and at most seven years after GC at the Genetics Service of the University Hospital, Faculty of Medicine of Ribeirão Preto, University of São Paulo (HC, FMRP, USP. The 113 families interviewed in this study were asked 48 questions and all children born after GC were studied clinically. We evaluated the families for spontaneous motivation for GC and understanding of GC information, their reproductive decisions, changes in the family after GC and the health status of new children. The majority of families seen at the Hospital das Clínicas de Ribeirão Preto were not spontaneously motivated to undergo GC. They had a low level of understanding about the information they received during GC. Generally families were using contraceptive methods (even when at low genetic risk with a consequent low rate of pregnancies and children born after GC. These families also had a very low rate of child adoption and divorces when compared to other studies.

  2. A new approach to self-organizing fuzzy polynomial neural networks guided by genetic optimization

    International Nuclear Information System (INIS)

    In this study, we introduce a new topology of Fuzzy Polynomial Neural Networks (FPNN) that is based on a genetically optimized multilayer perceptron with fuzzy polynomial neurons (FPNs) and discuss its comprehensive design methodology. The underlying methodology involves mechanisms of genetic optimization, especially genetic algorithms (GAs). Let us recall that the design of the 'conventional' FPNNs uses an extended Group Method of Data Handling (GMDH) and exploits a fixed fuzzy inference type located at each FPN of the FPNN as well as considers a fixed number of input nodes at FPNs (or nodes) located in each layer. The proposed FPNN gives rise to a structurally optimized structure and comes with a substantial level of flexibility in comparison to the one we encounter in conventional FPNNs. The structural optimization is realized via GAs whereas in the case of the parametric optimization we proceed with a standard least square method based learning. Through the consecutive process of such structural and parametric optimization, an optimized and flexible fuzzy neural network is generated in a dynamic fashion. The performance of the proposed gFPNN is quantified through experimentation that exploits standard data already being used in fuzzy modeling. The results reveal superiority of the proposed networks over the existing fuzzy and neural models

  3. Forensic Science in Support of Wildlife Conservation Efforts - Genetic Approaches (Global Trends).

    Science.gov (United States)

    Linacre, A

    2011-01-01

    Wildlife forensic science is a relatively recent development to meet the increasing need of the criminal justice system where there are investigations in alleged transgressions of either international or national legislation. This application of science draws on conservation genetics and forensic geneticists from mainstream forensic science. This review is a broad overview of the history of forensic wildlife science and some of the recent developments in forensic wildlife genetics with the application of DNA developments to nonhuman samples encountered in a forensic science investigation. The review will move from methods to look at the entire genome, when there is no previous knowledge of the species studied, through methods of species identification, using DNA to determine a possible geographic origin, through to assigning samples to a particular individual or a close genetic relative of this individual. The transfer of research methods into the criminal justice system for the investigation of wildlife crimes has been largely successful as is illustrated in the review. The review concludes with comments on the need for standardization and regulation in wildlife forensic science. PMID:26231165

  4. The glycinergic system in human startle disease: a genetic screening approach

    Directory of Open Access Journals (Sweden)

    Mark I Rees

    2010-03-01

    Full Text Available Human startle disease, also known as hyperekplexia (OMIM 149400, is a paroxysmal neurological disorder caused by defects in glycinergic neurotransmission. Hyperekplexia is characterised by an exaggerated startle reflex in response to tactile or acoustic stimuli which first presents as neonatal hypertonia, followed in some with episodes of life-threatening infantile apnoea. Genetic screening studies have demonstrated that hyperekplexia is genetically heterogeneous with several missense and nonsense mutations in the postsynaptic glycine receptor (GlyR a1 subunit gene (GLRA1 as the primary cause. More recently, missense, nonsense and frameshift mutations have also been identified in the glycine transporter GlyT2 gene, SLC6A5, demonstrating a presynaptic component to this disease. Further mutations, albeit rare, have been identified in the genes encoding the GlyR b subunit (GLRB, collybistin (ARHGEF9 and gephyrin (GPHN – all of which are postsynaptic proteins involved in orchestrating glycinergic neurotransmission. In this review, we describe the clinical ascertainment aspects, phenotypic considerations and the downstream molecular genetic tools utilised to analyse both presynaptic and postsynaptic components of this heterogeneous human neurological disorder. Moreover, we will describe how the ancient startle response is the preserve of glycinergic neurotransmission and how animal models and human hyperekplexia patients have provided synergistic evidence that implicates this inhibitory system in the control of startle reflexes.

  5. Buffering mechanisms in aging: a systems approach toward uncovering the genetic component of aging.

    Directory of Open Access Journals (Sweden)

    Aviv Bergman

    2007-08-01

    Full Text Available An unrealized potential to understand the genetic basis of aging in humans, is to consider the immense survival advantage of the rare individuals who live 100 years or more. The Longevity Gene Study was initiated in 1998 at the Albert Einstein College of Medicine to investigate longevity genes in a selected population: the "oldest old" Ashkenazi Jews, 95 years of age and older, and their children. The study proved the principle that some of these subjects are endowed with longevity-promoting genotypes. Here we reason that some of the favorable genotypes act as mechanisms that buffer the deleterious effect of age-related disease genes. As a result, the frequency of deleterious genotypes may increase among individuals with extreme lifespan because their protective genotype allows disease-related genes to accumulate. Thus, studies of genotypic frequencies among different age groups can elucidate the genetic determinants and pathways responsible for longevity. Borrowing from evolutionary theory, we present arguments regarding the differential survival via buffering mechanisms and their target age-related disease genes in searching for aging and longevity genes. Using more than 1,200 subjects between the sixth and eleventh decades of life (at least 140 subjects in each group, we corroborate our hypotheses experimentally. We study 66 common allelic site polymorphism in 36 candidate genes on the basis of their phenotype. Among them we have identified a candidate-buffering mechanism and its candidate age-related disease gene target. Previously, the beneficial effect of an advantageous cholesteryl ester transfer protein (CETP-VV genotype on lipoprotein particle size in association with decreased metabolic and cardiovascular diseases, as well as with better cognitive function, have been demonstrated. We report an additional advantageous effect of the CETP-VV (favorable genotype in neutralizing the deleterious effects of the lipoprotein(a (LPA gene

  6. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP

    Directory of Open Access Journals (Sweden)

    Davis Trisha N

    2011-06-01

    Full Text Available Abstract Background Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. Results The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1 aminoglycoside phosphotransferase; 2 imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3 hygromycin B phosphotransferase; and 4 the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. Conclusions Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully

  7. Combining genetic and distributional approaches to sourcing introduced species: a case study on the Nile monitor (Varanus niloticus) in Florida.

    Science.gov (United States)

    Dowell, Stephanie A; Wood, Jared P; Campbell, Todd S; Kolokotronis, Sergios-Orestis; Hekkala, Evon R

    2016-04-01

    Three separate breeding populations of the Nile monitor (Varanus niloticus) have been identified in Florida, USA, located in Cape Coral, West Palm Beach and Homestead Air Reserve Base. This large, predatory lizard could have negative effects on Florida's native wildlife. Here, we infer the source of the introduced populations using genetic and statistical approaches, as well as estimate the potential non-native distribution of V. niloticus in North America. We collected genetic data from 25 Florida individuals as well as utilized genetic datasets from reference individuals spanning the full native distribution throughout sub-Saharan Africa. Using occurrence data from the inferred source population and the full species range, we built ecological niche models (ENMs) and projected them onto North America to determine regions with suitable climate. Our results indicated that the introduced populations resulted from three separate introduction events, and all originated from the southern coastal region of West Africa. The ENM built from the West African source population predicted only the southernmost portions of North America to be suitable. Conversely, the model derived from the full species' range predicted suitable climates across a large portion of the United States. This information can be used to focus management and eradication efforts. PMID:27152204

  8. Genetic transformation of the tomato pathogen Pyrenochaeta lycopersici allowed gene knockout using a split-marker approach.

    Science.gov (United States)

    Aragona, Maria; Valente, Maria Teresa

    2015-05-01

    Pyrenochaeta lycopersici, as other soil-transmitted fungal pathogens, generally received little attention compared to the pathogens affecting the aerial parts of the plants, although causing stunt and important fruit yield reduction of agronomic relevant crops. The scope of this study was to develop a system allowing to investigate the functional role of P. lycopersici genes putatively involved in the corky root rot of tomato. A genetic transformation system based on a split-marker approach was developed and tested to knock out a P. lycopersici gene encoding for a lytic polysaccharide monooxygenase (Plegl1) induced during the disease development. The regions flanking Plegl1 gene were fused with the overlapping parts of hygromycin marker gene, to favour homologous recombination. We were able to obtain four mutants not expressing the Plegl1 gene though, when tested on a susceptible tomato cultivar, Plegl1 mutants showed unaltered virulence, compared with the wild-type strain. The strategy illustrated in the present work demonstrated for the first time that homologous recombination occurs in P. lycopersici. Moreover, a transformation system mediated by Agrobacterium tumefaciens was established and stable genetic transformants have been obtained. The transformation systems developed represent important tools for investigating both the role of genes putatively involved in P. lycopersici interaction with host plant and the function of other physiological traits which emerged to be genetically expanded from the recent genome sequencing of this fungus. PMID:25413737

  9. Chemical treatment of the intra-canal dentin surface: a new approach to modify dentin hydrophobicity

    OpenAIRE

    GAITAN-FONSECA, Cesar; COLLART-DUTILLEUL, Pierre-Yves; SEMETEY, Vincent; Olivier ROMIEU; Roel CRUZ; Flores, Hector; Frederic CUISINIER; Elias PEREZ; POZOS-GUILLEN, Amaury

    2013-01-01

    Objective This study evaluated the hydrophobicity of dentin surfaces that were modified through chemical silanization with octadecyltrichlorosilane (OTS). Material and Methods An in vitro experimental study was performed using 40 human permanent incisors that were divided into the following two groups: non-silanized and silanized. The specimens were pretreated and chemically modified with OTS. After the chemical modification, the dentin hydrophobicity was examined using a water contact angl...

  10. Extraction of Phthalic Acid from Aqueous Solution by Using Ionic Liquids: A Quantum Chemical Approach

    OpenAIRE

    Pilli, S; Mohanty, Kaustubha; Banerjee, Tamal

    2014-01-01

    Phthalic acid is an industrial chemical and it comes under the domain of endocrine disrupting chemicals (EDCs). Green solvents such as ionic liquids (ILs) posses good extractable capabilities for EDCs. COSMO–RS methodology is a widely accepted method for the design or selection of ionic liquids. COSMO–RS is a quantum chemical based method based on COSMO polarization charge densities. In this work the model has been used to screen the potential ionic liquids for the removal of phthalic acid fr...

  11. The potential of computer-based quantitative structure activity approaches for predicting acute toxicity of chemicals

    OpenAIRE

    Zvinavashe, E.

    2008-01-01

    Within the EU, the management of the risks of chemicals currently falls under a new legislation called Registration, Evaluation, and Authorization of Chemicals (REACH). Within the next 10 years, existing (eco)toxicological data gaps for the more than 100 000 chemicals on the European Inventory of Existing Commercial Substances (EINECS) should be filled. The challenge is to provide this toxicity information in a fast, cost effective manner, avoiding the use of experimental animals as much as p...

  12. Metabolomics of Genetically Modified Crops

    OpenAIRE

    Carolina Simó; Clara Ibáez; Alberto Valdés; Alejandro Cifuentes; Virginia García-Cañas

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resul...

  13. A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.

    Science.gov (United States)

    Basnet, Ram Kumar; Del Carpio, Dunia Pino; Xiao, Dong; Bucher, Johan; Jin, Mina; Boyle, Kerry; Fobert, Pierre; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

    2016-01-01

    Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTLs for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL) hotspots were found at major fatty acid QTLs on linkage groups A03, A04, A05, and A09. An eQTL-guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTLs with fatty acid QTLs, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed. PMID:26518343

  14. Unintended Changes in Genetically Modified Rice Expressing the Lysine-Rich Fusion Protein Gene Revealed by a Proteomics Approach

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiang-xiang; TANG Tang; LIU Fu-xia; LU Chang-li; HU Xiao-lan; JI Li-lian; LIU Qiao-quan

    2013-01-01

    Development of new technologies for evaluating genetically modiifed (GM) crops has revealed that there are unintended insertions and expression changes in GM crops. Proifling techniques are non-targeted approaches and are capable of detecting more unintended changes in GM crops. Here, we report the application of a comparative proteomic approach to investigate the protein proifle differences between a GM rice line, which has a lysine-rich protein gene, and its non-transgenic parental line. Proteome analysis by two-dimensional gel electrophoresis (2-DE) and mass spectrum analysis of the seeds identiifed 22 differentially expressed protein spots. Apart from a number of glutelins that were detected as targeted proteins in the GM line, the majority of the other changed proteins were involved in carbohydrate metabolism, protein synthesis and stress responses. These results indicated that the altered proteins were not associated with plant allergens or toxicity.

  15. AGROBACTERIUM-MEDIATED GENETIC TRANSFORMATION OF SORGHUM USING TISSUE CULTURE-BASED AND POLLEN-MEDIATED APPROACHES

    Directory of Open Access Journals (Sweden)

    Elkonin L.A.

    2012-08-01

    Full Text Available Genetic transformation is a powerful tool for genetic improvement of arable crops. Genetic engineering approaches are especially important for modification of starch and protein contents, vitamin and micronutrient concentration, improvement of nutritive value of protein fractions, and increase tolerance to environmental stresses. Application of transgenic technologies for genetic improvement of sorghum, a highly productive heat tolerant and drought resistant crop, is extremely important since climate aridization in many regions all over the globe hampers sustainable production of traditional cereals, such as wheat, maize and barley. However, sorghum, in spite of great number of investigations, is one of the most recalcitrant crop species to genetic modification. The most frequently reported problems are a low frequency of transformation and silencing of transgenes. Using the A. tumefaciens strain AGL0/p35SGIB with the bar and gus-intron genes under the nos and CaMV35S promoters, respectively, we studied different methods of Agrobacterium-mediated genetic transformation of the grain sorghum: in vitro culture-based techniques, by inoculation of immature embryos or embryo-derived calli, and pollen-mediated approach, by inoculation of flowering panicles. Four lines of grain sorghum – Milo-10, [9E] Milo-10 (CMS-line, KVV-114, and KVV-45 – were used. In both approaches, for activation of vir-genes agrobacterial cell suspension was grown in the AB or modified AB media with acetosyringone at room temperature. In vitro culture approach was effective for obtaining transgenic plants in the lines Milo-10 and KVV-45, which were able to produce embryogenic callus from immature embryos after their co-cultivation with agrobacterial cell suspension. Callus cultures tolerant to glufosinate ammonium (GA and capable to plant regeneration were obtained. The frequency of immature embryos producing PCR-positive transgenic plants varied in different experiments

  16. Metabolomics of genetically modified crops.

    Science.gov (United States)

    Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

    2014-01-01

    Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade. PMID:25334064

  17. Metabolomics of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Carolina Simó

    2014-10-01

    Full Text Available Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade.

  18. An Efficient Approach of Creating New Genetic Resources in Hybrid Rice Breeding

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@It is more and more important to create new genetic resources in hybrid rice breedding by using the tertiary and the forth gene pool through biotechnologic methods after the success of the utilization of inter-subspecific heterosis. We have established a simple procedure which is modified from that of Pena to transfer exogenous DAN into rice. When the recipient plant has undergone meiosis, exogenous DNA is injected into the upermost internode of a stem, the position just under the panicle base. In the next generation (D1), variants are found at a rate from 10-3to 10-1.

  19. A Genetic Algorithm-based Approach to Scheduling of Batch Production with Maximum Profit

    Institute of Scientific and Technical Information of China (English)

    伍联营; 胡仰栋; 徐冬梅; 华贲

    2005-01-01

    The optimal scheduling of multi-product batch process is studied and a new mathematics model targeting the maximum profit is proposed, which can be solved by the modified genetic algorithm (MGA) with mixed coding (sequence coding and decimal coding) developed by us. In which, the partially matched cross over (PMX) and reverse mutation are used for the sequence coding, whereas the arithmetic crossover and heteropic mutation are used for the decimal coding. In axidition, the relationship between production scale and production cost is analyzed and the maximum profit is always a trade-off of the production scale and production cost. Two examples are solved to demonstrate the effectiveness of the method.

  20. The Genetic Basis of Quality of Life in Healthy Swedish Women: A Candidate Gene Approach

    OpenAIRE

    Dounya Schoormans; Jingmei Li; Hatef Darabi; Yvonne Brandberg; Sprangers, Mirjam A. G.; Mikael Eriksson; Zwinderman, Koos H.; Per Hall

    2015-01-01

    Background Quality of life (QoL) is an increasingly important parameter in clinical practice as it predicts mortality and poor health outcomes. It is hypothesized that one may have a genetic predisposition for QoL. We therefore related 139 candidate genes, selected through a literature search, to QoL in healthy females. Methods In 5,142 healthy females, background characteristics (i.e. demographic, clinical, lifestyle, and psychological factors) were assessed. QoL was measured by the EORTC QL...