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Sample records for qrr genes varies

  1. The phosphotransferase VanU represses expression of four qrr genes antagonizing VanO-mediated quorum-sensing regulation in Vibrio anguillarum.

    Science.gov (United States)

    Weber, Barbara; Lindell, Kristoffer; El Qaidi, Samir; Hjerde, Erik; Willassen, Nils-Peder; Milton, Debra L

    2011-12-01

    Vibrio anguillarum utilizes quorum sensing to regulate stress responses required for survival in the aquatic environment. Like other Vibrio species, V. anguillarum contains the gene qrr1, which encodes the ancestral quorum regulatory RNA Qrr1, and phosphorelay quorum-sensing systems that modulate the expression of small regulatory RNAs (sRNAs) that destabilize mRNA encoding the transcriptional regulator VanT. In this study, three additional Qrr sRNAs were identified. All four sRNAs were positively regulated by σ(54) and the σ(54)-dependent response regulator VanO, and showed a redundant activity. The Qrr sRNAs, together with the RNA chaperone Hfq, destabilized vanT mRNA and modulated expression of VanT-regulated genes. Unexpectedly, expression of all four qrr genes peaked at high cell density, and exogenously added N-acylhomoserine lactone molecules induced expression of the qrr genes at low cell density. The phosphotransferase VanU, which phosphorylates and activates VanO, repressed expression of the Qrr sRNAs and stabilized vanT mRNA. A model is presented proposing that VanU acts as a branch point, aiding cross-regulation between two independent phosphorelay systems that activate or repress expression of the Qrr sRNAs, giving flexibility and precision in modulating VanT expression and inducing a quorum-sensing response to stresses found in a constantly changing aquatic environment.

  2. Main: 1QRR [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available Molecule: Sulfolipid Biosynthesis (Sqd1) Protein; Chain: A; Engineered: Yes Isomerase A.M.Mulichak, M.J.Thei...IASIHDRISRWKALTGKSIELYVGDICDFEFLAESFKSFEPDSVVHFGEQRSAPYSMIDRSRAVYTQHNNVIGTLNVLFAIKEFGEECHLVKLGTMGEYGTPNIDIEE...LNRFCVQAAVGHPLTVYGKGGQTRGYLDIRDTVQCVEIAIANPAKAGEFRVFNQFTEQFSVNELASLVTKAGSKLGLDVKKMTVPNPRVEAEEHYYNAKHTKLMELGLEPHYLSDSLLDSLLNFAVQFKDRVDTKQIMPSVSWKKIGVKTKSMTT arabi_1QRR.jpg ...

  3. A qrr noncoding RNA deploys four different regulatory mechanisms to optimize quorum-sensing dynamics.

    Science.gov (United States)

    Feng, Lihui; Rutherford, Steven T; Papenfort, Kai; Bagert, John D; van Kessel, Julia C; Tirrell, David A; Wingreen, Ned S; Bassler, Bonnie L

    2015-01-15

    Quorum sensing is a cell-cell communication process that bacteria use to transition between individual and social lifestyles. In vibrios, homologous small RNAs called the Qrr sRNAs function at the center of quorum-sensing pathways. The Qrr sRNAs regulate multiple mRNA targets including those encoding the quorum-sensing regulatory components luxR, luxO, luxM, and aphA. We show that a representative Qrr, Qrr3, uses four distinct mechanisms to control its particular targets: the Qrr3 sRNA represses luxR through catalytic degradation, represses luxM through coupled degradation, represses luxO through sequestration, and activates aphA by revealing the ribosome binding site while the sRNA itself is degraded. Qrr3 forms different base-pairing interactions with each mRNA target, and the particular pairing strategy determines which regulatory mechanism occurs. Combined mathematical modeling and experiments show that the specific Qrr regulatory mechanism employed governs the potency, dynamics, and competition of target mRNA regulation, which in turn, defines the overall quorum-sensing response. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Gene dosage compensation calibrates four regulatory RNAs to control Vibrio cholerae quorum sensing

    DEFF Research Database (Denmark)

    Svenningsen, Sine L; Tu, Kimberly C; Bassler, Bonnie L

    2009-01-01

    the quorum regulatory RNAs 1-4 (Qrr1-4). The four Qrr sRNAs are functionally redundant. That is, expression of any one of them is sufficient for wild-type quorum-sensing behaviour. Here, we show that the combined action of two feedback loops, one involving the sRNA-activator LuxO and one involving the sRNA......Quorum sensing is a mechanism of cell-to-cell communication that allows bacteria to coordinately regulate gene expression in response to changes in cell-population density. At the core of the Vibrio cholerae quorum-sensing signal transduction pathway reside four homologous small RNAs (sRNAs), named......-target HapR, promotes gene dosage compensation between the four qrr genes. Gene dosage compensation adjusts the total Qrr1-4 sRNA pool and provides the molecular mechanism underlying sRNA redundancy. The dosage compensation mechanism is exquisitely sensitive to small perturbations in Qrr levels. Precisely...

  5. Inferring time-varying network topologies from gene expression data.

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    Rao, Arvind; Hero, Alfred O; States, David J; Engel, James Douglas

    2007-01-01

    Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has been a need to infer and represent networks in a dynamic, that is, time-varying fashion, in order to account for different cellular states affecting the interactions amongst genes. In this work, we present an approach, regime-SSM, to understand gene regulatory networks within such a dynamic setting. The approach uses a clustering method based on these underlying dynamics, followed by system identification using a state-space model for each learnt cluster--to infer a network adjacency matrix. We finally indicate our results on the mouse embryonic kidney dataset as well as the T-cell activation-based expression dataset and demonstrate conformity with reported experimental evidence.

  6. Pharmacogenomics genes show varying perceptibility to microRNA regulation

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Vinther, Jeppe; Shomron, Noam

    2011-01-01

    The aim of pharmacogenomics is to identify individual differences in genome and transcriptome composition and their effect on drug efficacy. MicroRNAs (miRNAs) are short noncoding RNAs that negatively regulate expression of the majority of animal genes, including many genes involved in drug...

  7. Dietary adaptation of FADS genes in Europe varied across time and geography.

    Science.gov (United States)

    Ye, Kaixiong; Gao, Feng; Wang, David; Bar-Yosef, Ofer; Keinan, Alon

    2017-05-26

    Fatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long-chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFA-poor diets (for example, plant-based). Positive selection on FADS genes has been reported in multiple populations, but its cause and pattern in Europeans remain unknown. Here we demonstrate, using ancient and modern DNA, that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite (that is, alternative) alleles. Recent selection in farmers also varied geographically, with the strongest signal in southern Europe. These varying selection patterns concur with anthropological evidence of varying diets, and with the association of farming-adaptive alleles with higher FADS1 expression and thus enhanced LCPUFA biosynthesis. Genome-wide association studies reveal that farming-adaptive alleles not only increase LCPUFAs, but also affect other lipid levels and protect against several inflammatory diseases.

  8. Does the endometrial gene expression of fertile women vary within and between cycles?

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    Evans, Gloria E; Phillipson, Gregory T M; Sykes, Peter H; McNoe, Les A; Print, Cristin G; Evans, John J

    2018-01-23

    Does gene expression of putative endometrial implantation markers vary in expression between menstrual cycles? In fertile women the expression of certain genes exhibits a pattern of stable regulation.which is not affected even when sampled twice in one cycle. Successful implantation occurs in a minority of IVF embryo transfers. In contrast to knowledge regarding the ovulatory process, there is a sparse understanding of endometrial genes critical to implantation. This lack of knowledge hinders progress in this field. Endometrial pipelle samples were collected based on blood endocrinological markers at 2 and 7 days post initial LH surge. Five samples were collected over four cycles where the interval between collections ranged from sequential months to three years. Six fertile women attending an IVF clinic for male factor infertility, had samples collected. Global gene expression profiles were obtained from laser-microdissected, endometrial glands and stroma. Nineteen potential proliferation, cytokine and adhesion markers based on previous validated reports were studied. There was a significant modification between LH+2 and LH+7 of expression for 23 genes-11 in 8 in glands and stroma, 4 in stroma only and 3 in glands only suggesting stable, controlled regulation. Nevertheless, genes exhibited individual characteristics, e.g MKI67 exhibited lower expression at LH+7 than LH+2 and CCL4 higher, whereas TRO expressed limited difference in both cell types. Stability between cycles was demonstrated for gene expression at both LH+2-more than 60% of genes had cycles for each participant permitted the aim of obtaining information on intercycle and intracycle variability to be achieved. Our results support the feasibility of a clinical means of identification of a functional receptive endometrium. The robustness of data from individual women suggests that samples from one cycle can generally be applied to subsequent cycles. Funding was granted from the Tertiary Education

  9. Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.

    Science.gov (United States)

    Zhu, Li-Ping; Yue, Xin-Jing; Han, Kui; Li, Zhi-Feng; Zheng, Lian-Shuai; Yi, Xiu-Nan; Wang, Hai-Long; Zhang, You-Ming; Li, Yue-Zhong

    2015-07-22

    Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes.

  10. A Kalman-filter based approach to identification of time-varying gene regulatory networks.

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    Jie Xiong

    Full Text Available MOTIVATION: Conventional identification methods for gene regulatory networks (GRNs have overwhelmingly adopted static topology models, which remains unchanged over time to represent the underlying molecular interactions of a biological system. However, GRNs are dynamic in response to physiological and environmental changes. Although there is a rich literature in modeling static or temporally invariant networks, how to systematically recover these temporally changing networks remains a major and significant pressing challenge. The purpose of this study is to suggest a two-step strategy that recovers time-varying GRNs. RESULTS: It is suggested in this paper to utilize a switching auto-regressive model to describe the dynamics of time-varying GRNs, and a two-step strategy is proposed to recover the structure of time-varying GRNs. In the first step, the change points are detected by a Kalman-filter based method. The observed time series are divided into several segments using these detection results; and each time series segment belonging to two successive demarcating change points is associated with an individual static regulatory network. In the second step, conditional network structure identification methods are used to reconstruct the topology for each time interval. This two-step strategy efficiently decouples the change point detection problem and the topology inference problem. Simulation results show that the proposed strategy can detect the change points precisely and recover each individual topology structure effectively. Moreover, computation results with the developmental data of Drosophila Melanogaster show that the proposed change point detection procedure is also able to work effectively in real world applications and the change point estimation accuracy exceeds other existing approaches, which means the suggested strategy may also be helpful in solving actual GRN reconstruction problem.

  11. Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline

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    Seyfried, Erin E.; Newton, Ryan J.; Rubert, Kennedy F.; Pedersen, Joel A.; McMahon, Katherine D.

    2014-01-01

    The contribution of human activities to environmental reservoirs of antibiotic resistance is poorly understood. The purpose of this study was to determine if oxytetracycline (OTC) use in aquaculture facilities increased the detection frequency (i.e. prevalence) of tetracycline resistance genes relative to facilities with no recent OTC treatment. We used PCR to screen water and sediment from four non-commercial fish farms in northwestern Wisconsin for the presence of ten tetracycline resistance determinants (tetR): tet(A), tet(B), tet(D), tet(E), tet(G), tet(M), tet(O), tet(Q), tet(S) and tet(W). Water from farms with recent OTC use had significantly higher tetR detection frequencies than did water from farms without recent OTC use, with prevalence in raceways and rearing ponds of farms with recent OTC use exceeded by more than two-fold that of farms not using OTC. Effluent from all farms, regardless of treatment regime, had higher tetR detection frequencies than their corresponding influent for all genes, but the specific combinations of tetR genes detected in a sample were not different from their corresponding influent. Although OTC use was associated with the increased occurrence and diversity of tetR genes in water samples, it was not found to relate to tetR gene occurrence in sediment samples. Sediment samples from facilities with no recent OTC use had significantly higher frequencies of tetR gene detection than did samples from facilities with recent OTC use. All of the tetR genes were detected in both the medicated and non-medicated feed samples analyzed in this study. These findings suggest that both OTC treatment in aquaculture facilities, and the farms themselves, may be sources of tetR gene introduction to the environment. To our knowledge, this is the first study to use genotypic and cultivation-independent methods to examine tetR gene occurrence associated with OTC use in aquaculture. PMID:20217406

  12. Excretion of Antibiotic Resistance Genes by Dairy Calves Fed Milk Replacers with Varying Doses of Antibiotics

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    Thames, Callie H.; Pruden, Amy; James, Robert E.; Ray, Partha P.; Knowlton, Katharine F.

    2012-01-01

    Elevated levels of antibiotic resistance genes (ARGs) in soil and water have been linked to livestock farms and in some cases feed antibiotics may select for antibiotic resistant gut microbiota. The purpose of this study was to examine the establishment of ARGs in the feces of calves receiving milk replacer containing no antibiotics versus subtherapeutic or therapeutic doses of tetracycline and neomycin. The effect of antibiotics on calf health was also of interest. Twenty-eight male and female dairy calves were assigned to one of the three antibiotic treatment groups at birth and fecal samples were collected at weeks 6, 7 (prior to weaning), and 12 (5 weeks after weaning). ARGs corresponding to the tetracycline (tetC, tetG, tetO, tetW, and tetX), macrolide (ermB, ermF), and sulfonamide (sul1, sul2) classes of antibiotics along with the class I integron gene, intI1, were monitored by quantitative polymerase chain reaction as potential indicators of direct selection, co-selection, or horizontal gene transfer of ARGs. Surprisingly, there was no significant effect of antibiotic treatment on the absolute abundance (gene copies per gram wet manure) of any of the ARGs except ermF, which was lower in the antibiotic-treated calf manure, presumably because a significant portion of host bacterial cells carrying ermF were not resistant to tetracycline or neomycin. However, relative abundance (gene copies normalized to 16S rRNA genes) of tetO was higher in calves fed the highest dose of antibiotic than in the other treatments. All genes, except tetC and intI1, were detectable in feces from 6 weeks onward, and tetW and tetG significantly increased (P calves. Overall, the results provide new insight into the colonization of calf gut flora with ARGs in the early weeks. Although feed antibiotics exerted little effect on the ARGs monitored in this study, the fact that they also provided no health benefit suggests that the greater than conventional nutritional intake applied

  13. Comparative transcriptome and gene co-expression network analysis reveal genes and signaling pathways adaptively responsive to varied adverse stresses in the insect fungal pathogen, Beauveria bassiana.

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    He, Zhangjiang; Zhao, Xin; Lu, Zhuoyue; Wang, Huifang; Liu, Pengfei; Zeng, Fanqin; Zhang, Yongjun

    2018-01-01

    Sensing, responding, and adapting to the surrounding environment are crucial for all living organisms to survive, proliferate, and differentiate in their biological niches. Beauveria bassiana is an economically important insect-pathogenic fungus which is widely used as a biocontrol agent to control a variety of insect pests. The fungal pathogen unavoidably encounters a variety of adverse environmental stresses and defense response from the host insects during application of the fungal agents. However, few are known about the transcription response of the fungus to respond or adapt varied adverse stresses. Here, we comparatively analyzed the transcriptome of B. bassiana in globe genome under the varied stationary-phase stresses including osmotic agent (0.8 M NaCl), high temperature (32 °C), cell wall-perturbing agent (Congo red), and oxidative agents (H 2 O 2 or menadione). Total of 12,412 reads were obtained, and mapped to the 6767 genes of the B. bassiana. All of these stresses caused transcription responses involved in basal metabolism, cell wall construction, stress response or cell rescue/detoxification, signaling transduction and gene transcription regulation, and likely other cellular processes. An array of genes displayed similar transcription patterns in response to at least two of the five stresses, suggesting a shared transcription response to varied adverse stresses. Gene co-expression network analysis revealed that mTOR signaling pathway, but not HOG1 MAP kinase pathway, played a central role in regulation the varied adverse stress responses, which was verified by RNAi-mediated knockdown of TOR1. Our findings provided an insight of transcription response and gene co-expression network of B. bassiana in adaptation to varied environments. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply

    DEFF Research Database (Denmark)

    Azevedo, Herlânder; Azinheiro, Sarah Gaspar; Muñoz-Mérida, Antonio

    2016-01-01

    Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1......]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray...... experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed...

  15. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply

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    Herlânder Azevedo

    2016-03-01

    Full Text Available Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1]. This information should contribute to the development of plant-based solutions with improved nutrient-use-efficiency traits in crops. Previously, the transcription factors bZIP19 and bZIP23 were identified as essential regulators of the response to zinc deficiency in Arabidopsis thaliana [2]. A microarray experiment comparing gene expression between roots of wild-type and the mutant bzip19 bzip23, exposed to zinc deficiency, led to the identification of differentially expressed genes related with zinc homeostasis, namely its transport and plant internal translocation [2]. Here, we provide the detailed methodology, bioinformatics analysis and quality controls related to the microarray gene expression profiling published by Assunção and co-workers [2]. Most significantly, the present dataset comprises new experimental variables, including analysis of shoot tissue, and zinc sufficiency and excess supply. Thus, it expands from 8 to 42 microarrays hybridizations, which have been deposited at the Gene Expression Omnibus (GEO under the accession number GSE77286. Overall, it provides a resource for research on the molecular basis and regulatory events of the plant response to zinc supply, emphasizing the importance of Arabidopsis bZIP19 and bZIP23 transcription factors. Keywords: Microarray, Micronutrient, Zinc deficiency, Arabidopsis, bZIP

  16. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns

    Science.gov (United States)

    2012-01-01

    Background The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. Results Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that

  17. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns

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    Barvkar Vitthal T

    2012-05-01

    Full Text Available Abstract Background The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L. is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. Results Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N. Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST, microarray data and reverse transcription quantitative real time PCR (RT-qPCR. Seventy-three per cent of these genes (100 out of 137 showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot

  18. Interactions between the FTO and GNB3 genes contribute to varied clinical phenotypes in hypertension.

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    Rahul Kumar

    Full Text Available The genes FTO and GNB3 are implicated in essential hypertension but their interaction remains to be explored. This study investigates the role of interaction between the two genes in the pathophysiology of essential hypertension.In a case-control study comprising 750 controls and 550 patients, interaction between the polymorphisms of FTO and GNB3 was examined using multifactor dimensionality reduction (MDR. The influence of interaction on clinical phenotypes like systolic and diastolic blood pressure, mean arterial pressure and body mass index was also investigated. The 3-locus MDR model comprising FTO rs8050136C/A and GNB3 rs1129649T/C and rs5443C/T emerged as the best disease conferring model. Moreover, the interacted-genotypes having either 1, 2, 3, 4 or 5 risk alleles correlated with linearly increasing odds ratios of 1.91 (P = 0.027; 3.93 (P = 2.08E-06; 4.51 (P = 7.63E-07; 7.44 (P = 3.66E-08 and 11.57 (P = 1.18E-05, respectively, when compared with interacted-genotypes devoid of risk alleles. Furthermore, interactions among haplotypes of FTO (H1-9 and GNB3 (Ha-d differed by >1.5-fold for protective-haplotypes, CTGGC+TC [H2+Ha] and CTGAC+TC [H4+Ha] (OR = 0.39, P = 0.003; OR = 0.22, P = 6.86E-05, respectively and risk-haplotypes, AAAGC+CT [H3+Hc] and AAAGC+TT [H3+Hd] (OR = 2.91, P = 9.98E-06; OR = 2.50, P = 0.004, respectively compared to individual haplotypes. Moreover, the effectiveness of gene-gene interaction was further corroborated with a 1.29-, 1.25- and 1.38-fold higher SBP, MAP and BMI, respectively, in patients having risk interacted-haplotype H3+Hc and 2.48-fold higher SBP having risk interacted-haplotype H3+Hd compared to individual haplotypes.Interactions between genetic variants of FTO and GNB3 influence clinical parameters to augment hypertension.

  19. Genus beta human papillomavirus E6 proteins vary in their effects on the transactivation of p53 target genes.

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    White, Elizabeth A; Walther, Johanna; Javanbakht, Hassan; Howley, Peter M

    2014-08-01

    The genus beta human papillomaviruses (beta HPVs) cause cutaneous lesions and are thought to be involved in the initiation of some nonmelanoma skin cancers (NMSCs), particularly in patients with the genetic disorder epidermodysplasia verruciformis (EV). We have previously reported that at least two of the genus beta HPV E6 proteins bind to and/or increase the steady-state levels of p53 in squamous epithelial cells. This is in contrast to a well-characterized ability of the E6 proteins of cancer-associated HPVs of genus alpha HPV, which inactivate p53 by targeting its ubiquitin-mediated proteolysis. In this study, we have investigated the ability of genus beta E6 proteins from eight different HPV types to block the transactivation of p53 target genes following DNA damage. We find that the E6 proteins from diverse beta HPV species and types vary in their capacity to block the induction of MDM2, p21, and proapoptotic genes after genotoxic stress. We conclude that some genus beta HPV E6 proteins inhibit at least some p53 target genes, although perhaps not by the same mechanism or to the same degree as the high-risk genus alpha HPV E6 proteins. This study addresses the ability of various human papillomavirus E6 proteins to block the activation of p53-responsive cellular genes following DNA damage in human keratinocytes, the normal host cell for HPVs. The E6 proteins encoded by the high-risk, cancer-associated HPV types of genus alpha HPV have a well-established activity to target p53 degradation and thereby inhibit the response to DNA damage. In this study, we have investigated the ability of genus beta HPV E6 proteins from eight different HPV types to block the ability of p53 to transactivate downstream genes following DNA damage. We find that some, but not all, genus beta HPV E6 proteins can block the transactivation of some p53 target genes. This differential response to DNA damage furthers the understanding of cutaneous HPV biology and may help to explain the

  20. Ranking of persister genes in the same Escherichia coli genetic background demonstrates varying importance of individual persister genes in tolerance to different antibiotics

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    Nan eWu

    2015-09-01

    Full Text Available Despite the identification of many genes and pathways involved in the persistence phenomenon of bacteria, the relative importance of these genes in a single organism remains unclear. Here, using Escherichia coli as a model, we generated mutants of 21 known candidate persister genes and compared the relative importance of these mutants in persistence to various antibiotics (ampicillin, gentamicin, norfloxacin, and trimethoprim at different times. We found that oxyR, dnaK, sucB, relA, rpoS, clpB, mqsR, and recA were prominent persister genes involved in persistence to multiple antibiotics. These genes map to the following pathways: antioxidative defense pathway (oxyR, global regulators (dnaK, clpB, and rpoS, energy production (sucB, stringent response (relA, toxin–antitoxin (TA module (mqsR, and SOS response (recA. Among the TA modules, the ranking order was mqsR, lon, relE, tisAB, hipA, and dinJ. Intriguingly, rpoS deletion caused a defect in persistence to gentamicin but increased persistence to ampicillin and norfloxacin. Mutants demonstrated dramatic differences in persistence to different antibiotics at different time points: some mutants (oxyR, dnaK, phoU, lon, recA, mqsR, and tisAB displayed defect in persistence from early time points, while other mutants (relE, smpB, glpD, umuD, and tnaA showed defect only at later time points. These results indicate that varying hierarchy and importance of persister genes exist and that persister genes can be divided into those involved in shallow persistence and those involved in deep persistence. Our findings suggest that the persistence phenomenon is a dynamic process with different persister genes playing roles of variable significance at different times. These findings have implications for improved understanding of persistence phenomenon and developing new drugs targeting persisters for more effective cure of persistent infections.

  1. Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture

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    Haack, Sheridan K.; Duris, Joseph W.; Kolpin, Dana W.; Focazio, Michael J.; Meyer, Michael T.; Johnson, Heather E.; Oster, Ryan J.; Foreman, William T.

    2016-01-01

    Animal waste, stream water, and streambed sediment from 19 small (animal agriculture (control, n = 4), or predominantly beef (n = 4), dairy (n = 3), swine (n = 5), or poultry (n = 3) were tested for: 1) cholesterol, coprostanol, estrone, and fecal indicator bacteria (FIB) concentrations, and 2) shiga-toxin producing and enterotoxigenic Escherichia coli, Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci by polymerase chain reaction (PCR) on enrichments, and/or direct quantitative PCR. Pathogen genes were most frequently detected in dairy wastes, followed by beef, swine and poultry wastes in that order; there was only one detection of an animal-source-specific pathogen gene (stx1) in any water or sediment sample in any control watershed. Post-rainfall pathogen gene numbers in stream water were significantly correlated with FIB, cholesterol and coprostanol concentrations, and were most highly correlated in dairy watershed samples collected from 3 different states. Although collected across multiple states and ecoregions, animal-waste gene profiles were distinctive via discriminant analysis. Stream water gene profiles could also be discriminated by the watershed animal type. Although pathogen genes were not abundant in stream water or streambed samples, PCR on enrichments indicated that many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, vancomycin-resistant enterococci) that could potentially affect either human or animal health. Pathogen gene numbers and types in stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the amount of local rainfall, and not by studied watershed soil or physical characteristics. Our results indicated that stream water in small agricultural U.S. watersheds was susceptible to pathogen gene inputs under typical agricultural practices and environmental conditions

  2. Coordinated Regulation of Anthocyanin Biosynthesis Genes Confers Varied Phenotypic and Spatial-Temporal Anthocyanin Accumulation in Radish (Raphanus sativus L.

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    Everlyne M'mbone Muleke

    2017-07-01

    Full Text Available Anthocyanins are natural pigments that have important functions in plant growth and development. Radish taproots are rich in anthocyanins which confer different taproot colors and are potentially beneficial to human health. The crop differentially accumulates anthocyanin during various stages of growth, yet molecular mechanisms underlying this differential anthocyanin accumulation remains unknown. In the present study, transcriptome analysis was used to concisely identify putative genes involved in anthocyanin biosynthesis in radish. Spatial-temporal transcript expressions were then profiled in four color variant radish cultivars. From the total transcript sequences obtained through illumina sequencing, 102 assembled unigenes, and 20 candidate genes were identified to be involved in anthocyanin biosynthesis. Fifteen genomic sequences were isolated and sequenced from radish taproot. The length of these sequences was between 900 and 1,579 bp, and the unigene coverage to all of the corresponding cloned sequences was more than 93%. Gene structure analysis revealed that RsF3′H is intronless and anthocyanin biosynthesis genes (ABGs bear asymmetrical exons, except RsSAM. Anthocyanin accumulation showed a gradual increase in the leaf of the red radish and the taproot of colored cultivars during development, with a rapid increase at 30 days after sowing (DAS, and the highest content at maturity. Spatial-temporal transcriptional analysis of 14 genes revealed detectable expressions of 12 ABGs in various tissues at different growth levels. The investigation of anthocyanin accumulation and gene expression in four color variant radish cultivars, at different stages of development, indicated that total anthocyanin correlated with transcript levels of ABGs, particularly RsUFGT, RsF3H, RsANS, RsCHS3 and RsF3′H1. Our results suggest that these candidate genes play key roles in phenotypic and spatial-temporal anthocyanin accumulation in radish through

  3. Intercoalescence time distribution of incomplete gene genealogies in temporally varying populations, and applications in population genetic inference.

    Science.gov (United States)

    Chen, Hua

    2013-03-01

    Tracing back to a specific time T in the past, the genealogy of a sample of haplotypes may not have reached their common ancestor and may leave m lineages extant. For such an incomplete genealogy truncated at a specific time T in the past, the distribution and expectation of the intercoalescence times conditional on T are derived in an exact form in this paper for populations of deterministically time-varying sizes, specifically, for populations growing exponentially. The derived intercoalescence time distribution can be integrated to the coalescent-based joint allele frequency spectrum (JAFS) theory, and is useful for population genetic inference from large-scale genomic data, without relying on computationally intensive approaches, such as importance sampling and Markov Chain Monte Carlo (MCMC) methods. The inference of several important parameters relying on this derived conditional distribution is demonstrated: quantifying population growth rate and onset time, and estimating the number of ancestral lineages at a specific ancient time. Simulation studies confirm validity of the derivation and statistical efficiency of the methods using the derived intercoalescence time distribution. Two examples of real data are given to show the inference of the population growth rate of a European sample from the NIEHS Environmental Genome Project, and the number of ancient lineages of 31 mitochondrial genomes from Tibetan populations. © 2013 Blackwell Publishing Ltd/University College London.

  4. Removal of antibiotic-resistant bacteria and antibiotic resistance genes affected by varying degrees of fouling on anaerobic microfiltration membranes

    KAUST Repository

    Cheng, Hong; Hong, Pei-Ying

    2017-01-01

    An anaerobic membrane bioreactor was retrofitted with polyvinylidene fluoride (PVDF) microfiltration membrane units, each of which was fouled to a different extent. The membranes with different degrees of fouling were evaluated for their efficiencies in removing three antibiotic-resistant bacteria (ARB), namely, blaNDM-1-positive Escherichia coli PI-7, blaCTX-M-15-positive Klebsiella pneumoniae L7, and blaOXA-48-positive E. coli UPEC-RIY-4, as well as their associated plasmid-borne antibiotic resistance genes (ARGs). The results showed that the log removal values (LRVs) of ARGs correlated positively with the extent of membrane fouling and ranged from 1.9 to 3.9. New membranes with a minimal foulant layer could remove more than 5 log units of ARB. However, as the membranes progressed to subcritical fouling, the LRVs of ARB decreased at increasing operating transmembrane pressures (TMPs). The LRV recovered back to 5 when the membrane was critically fouled, and the achieved LRV remained stable at different operating TMPs. Furthermore, characterization of the surface attributed the removal of both the ARB and ARGs to adsorption, which was facilitated by an increasing hydrophobicity and a decreasing surface ζ potential as the membranes fouled. Our results indicate that both the TMP and the foulant layer synergistically affected ARB removal, but the foulant layer was the main factor that contributed to ARG removal.

  5. Removal of antibiotic-resistant bacteria and antibiotic resistance genes affected by varying degrees of fouling on anaerobic microfiltration membranes

    KAUST Repository

    Cheng, Hong

    2017-09-28

    An anaerobic membrane bioreactor was retrofitted with polyvinylidene fluoride (PVDF) microfiltration membrane units, each of which was fouled to a different extent. The membranes with different degrees of fouling were evaluated for their efficiencies in removing three antibiotic-resistant bacteria (ARB), namely, blaNDM-1-positive Escherichia coli PI-7, blaCTX-M-15-positive Klebsiella pneumoniae L7, and blaOXA-48-positive E. coli UPEC-RIY-4, as well as their associated plasmid-borne antibiotic resistance genes (ARGs). The results showed that the log removal values (LRVs) of ARGs correlated positively with the extent of membrane fouling and ranged from 1.9 to 3.9. New membranes with a minimal foulant layer could remove more than 5 log units of ARB. However, as the membranes progressed to subcritical fouling, the LRVs of ARB decreased at increasing operating transmembrane pressures (TMPs). The LRV recovered back to 5 when the membrane was critically fouled, and the achieved LRV remained stable at different operating TMPs. Furthermore, characterization of the surface attributed the removal of both the ARB and ARGs to adsorption, which was facilitated by an increasing hydrophobicity and a decreasing surface ζ potential as the membranes fouled. Our results indicate that both the TMP and the foulant layer synergistically affected ARB removal, but the foulant layer was the main factor that contributed to ARG removal.

  6. Removal of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes Affected by Varying Degrees of Fouling on Anaerobic Microfiltration Membranes.

    Science.gov (United States)

    Cheng, Hong; Hong, Pei-Ying

    2017-11-07

    An anaerobic membrane bioreactor was retrofitted with polyvinylidene fluoride (PVDF) microfiltration membrane units, each of which was fouled to a different extent. The membranes with different degrees of fouling were evaluated for their efficiencies in removing three antibiotic-resistant bacteria (ARB), namely, bla NDM-1 -positive Escherichia coli PI-7, bla CTX-M-15 -positive Klebsiella pneumoniae L7, and bla OXA-48 -positive E. coli UPEC-RIY-4, as well as their associated plasmid-borne antibiotic resistance genes (ARGs). The results showed that the log removal values (LRVs) of ARGs correlated positively with the extent of membrane fouling and ranged from 1.9 to 3.9. New membranes with a minimal foulant layer could remove more than 5 log units of ARB. However, as the membranes progressed to subcritical fouling, the LRVs of ARB decreased at increasing operating transmembrane pressures (TMPs). The LRV recovered back to 5 when the membrane was critically fouled, and the achieved LRV remained stable at different operating TMPs. Furthermore, characterization of the surface attributed the removal of both the ARB and ARGs to adsorption, which was facilitated by an increasing hydrophobicity and a decreasing surface ζ potential as the membranes fouled. Our results indicate that both the TMP and the foulant layer synergistically affected ARB removal, but the foulant layer was the main factor that contributed to ARG removal.

  7. Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes"

    Directory of Open Access Journals (Sweden)

    Lemos Bernardo

    2010-12-01

    Full Text Available Abstract Background Hybrid male sterility (HMS is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Results Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. Conclusions The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

  8. Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes".

    Science.gov (United States)

    Araripe, Luciana O; Montenegro, Horácio; Lemos, Bernardo; Hartl, Daniel L

    2010-12-14

    Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

  9. Coronary artery disease and the frequencies of MTHFR and PON1 gene polymorphism studies in a varied population of Hyderabad, Telangana region in south India

    Directory of Open Access Journals (Sweden)

    Kavitha Matam

    2015-04-01

    Full Text Available Coronary artery disease (CAD also known as coronary heart disease is one of the leading causes of death and disability worldwide. Genetic and environmental factors play an important role in the pathogenesis and progression of CAD. The aim of this study was to evaluate the combined contribution of 3 gene polymorphisms to the risk of CAD and gene–gene interaction in the south Indian population. In this case-control study, 200 cases of CAD and 200 healthy controls were recruited. We studied 3 well known genetic polymorphisms of MTHFR (C677T; rs1801133, PON1 (Q192R; rs662 and ACE (I/D: rs4646994 in relation to CAD in South Indian population. Polymerase chain reaction (PCR was carried out and followed by the restriction fragment length polymorphism and agarose gel electrophoresis. Genotypes of MTHFR C677T, CT and CT+TT, and PON1 Q192R QR were associated with the risk of CAD (C677T CT+TT vs CC: odds ratio [OR] = 3.3, 95% confidence intervals [CI] = 1.8–6.2; p = 0.00001, (CT vs CC: OR = 3.2, 95%CI = 1.8–5.6; p = 0.00003, and (Q192R QQ vs QR: OR = 2.1, 95%CI = 1.1–3.9; p = 0.03. The allele frequencies for T vs C: OR = 3.1, 95%CI = 1.8–5.3; p = 0.00001 and R vs Q: OR = 1.3, 95% CI = 1.0–1.7 p = 0.03. Multifactor dimensionality reduction (MDR analysis was carried out with the combination of three genes and the results indicate that MDR analysis showed that, PON1 gene polymorphism formed a significant model in predicting the CAD risk in south Indian population.

  10. Relative transcription of Listeria monocytogenes virulence genes in liver pâtés with varying NaCl content

    DEFF Research Database (Denmark)

    Olesen, Inger; Thorsen, Line; Jespersen, Lene

    2010-01-01

    three liver pâtés with reduced NaCl content of which one also has been supplied with organic acids (Ca-acetate and Ca-lactate). The three strains (EGD-e: reference strain; O57: more NaCl sensitive; 6896: more NaCl tolerant) were selected out of twelve strains based on their growth in BHI broth adjusted......B for both O57 and 6896 were significantly higher when the strains were grown in BHI compared to the standard liver pâté. Reducing the NaCl content of the standard liver pâté did not change relative transcription levels of prfA, inlA, sigB or clpC (except for prfA in O57 and sigB in 6896). However......, the presence of Ca-acetate and Ca-lactate induced relative transcription of the stress response gene, clpC, for all three strains. This study demonstrates that relative microbial gene transcription can be measured in complex food matrices and points to the need for designing experimental set-ups in real food...

  11. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  12. Time-varying BRDFs.

    Science.gov (United States)

    Sun, Bo; Sunkavalli, Kalyan; Ramamoorthi, Ravi; Belhumeur, Peter N; Nayar, Shree K

    2007-01-01

    The properties of virtually all real-world materials change with time, causing their bidirectional reflectance distribution functions (BRDFs) to be time varying. However, none of the existing BRDF models and databases take time variation into consideration; they represent the appearance of a material at a single time instance. In this paper, we address the acquisition, analysis, modeling, and rendering of a wide range of time-varying BRDFs (TVBRDFs). We have developed an acquisition system that is capable of sampling a material's BRDF at multiple time instances, with each time sample acquired within 36 sec. We have used this acquisition system to measure the BRDFs of a wide range of time-varying phenomena, which include the drying of various types of paints (watercolor, spray, and oil), the drying of wet rough surfaces (cement, plaster, and fabrics), the accumulation of dusts (household and joint compound) on surfaces, and the melting of materials (chocolate). Analytic BRDF functions are fit to these measurements and the model parameters' variations with time are analyzed. Each category exhibits interesting and sometimes nonintuitive parameter trends. These parameter trends are then used to develop analytic TVBRDF models. The analytic TVBRDF models enable us to apply effects such as paint drying and dust accumulation to arbitrary surfaces and novel materials.

  13. varying elastic parameters distributions

    KAUST Repository

    Moussawi, Ali

    2014-12-01

    The experimental identication of mechanical properties is crucial in mechanics for understanding material behavior and for the development of numerical models. Classical identi cation procedures employ standard shaped specimens, assume that the mechanical elds in the object are homogeneous, and recover global properties. Thus, multiple tests are required for full characterization of a heterogeneous object, leading to a time consuming and costly process. The development of non-contact, full- eld measurement techniques from which complex kinematic elds can be recorded has opened the door to a new way of thinking. From the identi cation point of view, suitable methods can be used to process these complex kinematic elds in order to recover multiple spatially varying parameters through one test or a few tests. The requirement is the development of identi cation techniques that can process these complex experimental data. This thesis introduces a novel identi cation technique called the constitutive compatibility method. The key idea is to de ne stresses as compatible with the observed kinematic eld through the chosen class of constitutive equation, making possible the uncoupling of the identi cation of stress from the identi cation of the material parameters. This uncoupling leads to parametrized solutions in cases where 5 the solution is non-unique (due to unknown traction boundary conditions) as demonstrated on 2D numerical examples. First the theory is outlined and the method is demonstrated in 2D applications. Second, the method is implemented within a domain decomposition framework in order to reduce the cost for processing very large problems. Finally, it is extended to 3D numerical examples. Promising results are shown for 2D and 3D problems.

  14. Levels of potential bioactive compounds including carotenoids, vitamin C and phenolic compounds, and expression of their cognate biosynthetic genes vary significantly in different varieties of potato (Solanum tuberosum L.) grown under uniform cultural conditions.

    Science.gov (United States)

    Valcarcel, Jesus; Reilly, Kim; Gaffney, Michael; O'Brien, Nora M

    2016-02-01

    In addition to their high carbohydrate content, potatoes are also an important dietary source of vitamin C and bioactive secondary metabolites, including phenolic compounds and carotenoids, which have been suggested to play a role in human health. The expression of genes encoding key enzymes involved in the synthesis of these compounds was assessed by reverse transcription-quantitative polymerase chain reaction and compared to the accumulation of the corresponding product in seven potato varieties showing contrasting levels of metabolite accumulation. Strong positive correlations were found between phenolic content in the flesh of tubers and transcript levels of phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS) genes. The expression of PAL and CHS was also related to that of AN1, a transcription factor involved in the synthesis of anthocyanins, suggesting that these genes are regulated in a coordinated manner. No clear relationship was found between transcript levels of phytoene synthase (PSY) or L-galactono-1,4-lactone dehydrogenase (GLDH) genes and total carotenoid or vitamin C accumulation, respectively. Data indicate that levels of total phenolic and flavonoid compounds in potato are controlled primarily by PAL and CHS gene expression. Transcript levels of PSY and GLDH did not control accumulation of carotenoids or vitamin C. © 2015 Society of Chemical Industry.

  15. The prevalence of the duodenal ulcer promoting gene (dupA in Helicobacter pylori isolates varies by ethnic group and is not universally associated with disease development: a case-control study

    Directory of Open Access Journals (Sweden)

    Schmidt Heather-Marie A

    2009-03-01

    /mL for dupA-negative isolates. Conclusion Although dupA is highly conserved when present, we identified no consistent association between dupA and DU or GC development across the ethnic groups investigated, with the dupA prevalence in control groups varying significantly. Our results would suggest that in the clinical isolates investigated dupA is not associated with IL-8 induction in vitro.

  16. The prevalence of the duodenal ulcer promoting gene (dupA) in Helicobacter pylori isolates varies by ethnic group and is not universally associated with disease development: a case-control study.

    Science.gov (United States)

    Schmidt, Heather-Marie A; Andres, Sönke; Kaakoush, Nadeem O; Engstrand, Lars; Eriksson, Lena; Goh, Khean-Lee; Fock, Kwong Ming; Hilmi, Ida; Dhamodaran, Subbiah; Forman, David; Mitchell, Hazel

    2009-03-11

    A is highly conserved when present, we identified no consistent association between dupA and DU or GC development across the ethnic groups investigated, with the dupA prevalence in control groups varying significantly. Our results would suggest that in the clinical isolates investigated dupA is not associated with IL-8 induction in vitro.

  17. Time-varying Crash Risk

    DEFF Research Database (Denmark)

    Christoffersen, Peter; Feunoua, Bruno; Jeon, Yoontae

    We estimate a continuous-time model with stochastic volatility and dynamic crash probability for the S&P 500 index and find that market illiquidity dominates other factors in explaining the stock market crash risk. While the crash probability is time-varying, its dynamic depends only weakly on re...

  18. Eestlased Karlovy Varys / J. R.

    Index Scriptorium Estoniae

    J. R.

    2007-01-01

    Ilmar Raagi mängufilm "Klass" osaleb 42. Karlovy Vary rahvusvahelise filmifestivali võistlusprogrammis "East of the West" ja Asko Kase lühimängufilm "Zen läbi prügi" on valitud festivali kõrvalprogrammi "Forum of Independents"

  19. Esmaklassiline Karlovy Vary / Jaanus Noormets

    Index Scriptorium Estoniae

    Noormets, Jaanus

    2007-01-01

    Ilmar Raagi mängufilm "Klass" võitis 42. Karlovy Vary rahvusvahelise filmifestivalil kaks auhinda - ametliku kõrvalvõistlusprogrammi "East of the West" eripreemia "Special mention" ja Euroopa väärtfilmikinode keti Europa Cinemas preemia. Ka Asko Kase lühifilmi "Zen läbi prügi linastumisest ning teistest auhinnasaajatest ning osalejatest

  20. Optimistlik Karlovy Vary / Jaan Ruus

    Index Scriptorium Estoniae

    Ruus, Jaan, 1938-2017

    2007-01-01

    42. Karlovy Vary rahvusvahelise filmifestivali auhinnatud filmidest (žürii esimees Peter Bart). Kristallgloobuse sai Islandi-Saksamaa "Katseklaasilinn" (režii Baltasar Kormakur), parimaks režissööriks tunnistati norralane Bard Breien ("Negatiivse mõtlemise kunst"). Austraallase Michael James Rowlandi "Hea õnne teekond" sai žürii eripreemia

  1. Genetic polymorphisms in varied environments.

    Science.gov (United States)

    Powell, J R

    1971-12-03

    Thirteen experimenital populationis of Drosophila willistoni were maintained in cages, in some of which the environments were relatively constant and in others varied. After 45 weeks, the populations were assayed by gel electrophoresis for polymorphisms at 22 protein loci. The average heterozygosity per individual and the average unmber of alleles per locus were higher in populations maintained in heterogeneous environments than in populations in more constant enviroments.

  2. Varying Constants, Gravitation and Cosmology

    Directory of Open Access Journals (Sweden)

    Jean-Philippe Uzan

    2011-03-01

    Full Text Available Fundamental constants are a cornerstone of our physical laws. Any constant varying in space and/or time would reflect the existence of an almost massless field that couples to matter. This will induce a violation of the universality of free fall. Thus, it is of utmost importance for our understanding of gravity and of the domain of validity of general relativity to test for their constancy. We detail the relations between the constants, the tests of the local position invariance and of the universality of free fall. We then review the main experimental and observational constraints that have been obtained from atomic clocks, the Oklo phenomenon, solar system observations, meteorite dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic microwave background and big bang nucleosynthesis. At each step we describe the basics of each system, its dependence with respect to the constants, the known systematic effects and the most recent constraints that have been obtained. We then describe the main theoretical frameworks in which the low-energy constants may actually be varying and we focus on the unification mechanisms and the relations between the variation of different constants. To finish, we discuss the more speculative possibility of understanding their numerical values and the apparent fine-tuning that they confront us with.

  3. Weighted approximation with varying weight

    CERN Document Server

    Totik, Vilmos

    1994-01-01

    A new construction is given for approximating a logarithmic potential by a discrete one. This yields a new approach to approximation with weighted polynomials of the form w"n"(" "= uppercase)P"n"(" "= uppercase). The new technique settles several open problems, and it leads to a simple proof for the strong asymptotics on some L p(uppercase) extremal problems on the real line with exponential weights, which, for the case p=2, are equivalent to power- type asymptotics for the leading coefficients of the corresponding orthogonal polynomials. The method is also modified toyield (in a sense) uniformly good approximation on the whole support. This allows one to deduce strong asymptotics in some L p(uppercase) extremal problems with varying weights. Applications are given, relating to fast decreasing polynomials, asymptotic behavior of orthogonal polynomials and multipoint Pade approximation. The approach is potential-theoretic, but the text is self-contained.

  4. Estrelas variáveis

    OpenAIRE

    Viana, Sérgio Manuel de Oliveira

    2001-01-01

    A observação do céu nocturno é uma prática que vem da Antiguidade. Desde então e durante muito tempo pensou-se que as estrelas mantinham o brilho constante. Assim foi até ao século XVI, quando David Fabricius observou uma estrela cujo brilho variava periodicamente. Dois séculos mais tarde, Jonh Goodricke descobriu uma segunda estrela e com o desenvolvimento de instrumentos de observação este conjunto foi muito alargado e hoje inclui o Sol.A variação do brilho das estrelas variáveis permite d...

  5. A mathematical model and quantitative comparison of the small RNA circuit in the Vibrio harveyi and Vibrio cholerae quorum sensing systems

    International Nuclear Information System (INIS)

    Hunter, G A M; Vasquez, F Guevara; Keener, J P

    2013-01-01

    Quorum sensing is the process by which bacteria regulate their gene expression based on the local cell-population density. The quorum sensing systems of Vibrio harveyi and Vibrio cholerae are comprised of a phosphorelay cascade coupled to a small RNA (sRNA) circuit. The sRNA circuit contains multiple quorum regulated small RNA (Qrr) that regulate expression of the homologous master transcriptional regulators LuxR (in V. harveyi) and HapR (in V. cholerae). Their quorum sensing systems are topologically similar and homologous thereby making it difficult to understand why repression of HapR is more robust than LuxR to changes in Qrr. In this work we formulate and parameterize a novel mathematical model of the V. harveyi and V. cholerae sRNA circuit. We parameterize the model by fitting it to a variety of empirical data from both species. We show that we can distinguish all of the parameters and that the parameterizations (one for each species) are robust to errors in the data. We then use our model to propose some experiments to identify and explain kinetic differences between the species. We find that V. cholerae Qrr are more abundant and more sensitive to changes in LuxO than V. harveyi Qrr and argue that this is why expression of HapR is more robust than LuxR to changes in Qrr. (paper)

  6. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  7. A varying-α brane world cosmology

    International Nuclear Information System (INIS)

    Youm, Donam

    2001-08-01

    We study the brane world cosmology in the RS2 model where the electric charge varies with time in the manner described by the varying fine-structure constant theory of Bekenstein. We map such varying electric charge cosmology to the dual variable-speed-of-light cosmology by changing system of units. We comment on cosmological implications for such cosmological models. (author)

  8. VariVis: a visualisation toolkit for variation databases

    Directory of Open Access Journals (Sweden)

    Smith Timothy D

    2008-04-01

    Full Text Available Abstract Background With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in online variation databases and provide important clues to the cause of diseases and potential side effects or resistance to drugs. However, the data presentation techniques employed by most of these databases make them difficult to use and understand. Results Here we present a visualisation toolkit that can be employed by online variation databases to generate graphical models of gene sequence with corresponding variations and their consequences. The VariVis software package can run on any web server capable of executing Perl CGI scripts and can interface with numerous Database Management Systems and "flat-file" data files. VariVis produces two easily understandable graphical depictions of any gene sequence and matches these with variant data. While developed with the goal of improving the utility of human variation databases, the VariVis package can be used in any variation database to enhance utilisation of, and access to, critical information.

  9. Spacetime-varying couplings and Lorentz violation

    International Nuclear Information System (INIS)

    Kostelecky, V. Alan; Lehnert, Ralf; Perry, Malcolm J.

    2003-01-01

    Spacetime-varying coupling constants can be associated with violations of local Lorentz invariance and CPT symmetry. An analytical supergravity cosmology with a time-varying fine-structure constant provides an explicit example. Estimates are made for some experimental constraints

  10. Detection of dynamically varying interaural time differences

    DEFF Research Database (Denmark)

    Kohlrausch, Armin; Le Goff, Nicolas; Breebaart, Jeroen

    2010-01-01

    of fringes surrounding the probe is equal to the addition of the effects of the individual fringes. In this contribution, we present behavioral data for the same experimental condition, called dynamically varying ITD detection, but for a wider range of probe and fringe durations. Probe durations varied...

  11. Eesti film võistleb Karlovy Varys

    Index Scriptorium Estoniae

    2008-01-01

    8. juulil esilinastub Karlovy Vary filmifestivalil Rene Vilbre noortefilm "Mina olin siin", mille aluseks on Sass Henno romaan "Mina olin siin. Esimene arest", stsenaariumi kirjutas Ilmar Raag. Film võistleb võistlusprogrammis "East of the West"

  12. Matching Value Propositions with Varied Customer Needs

    DEFF Research Database (Denmark)

    Heikka, Eija-Liisa; Frandsen, Thomas; Hsuan, Juliana

    2018-01-01

    Organizations seek to manage varied customer segments using varied value propositions. The ability of a knowledge-intensive business service (KIBS) provider to formulate value propositions into attractive offerings to varied customers becomes a competitive advantage. In this specific business based...... on often highly abstract service offerings, this requires the provider to have a clear overview of its knowledge and resources and how these can be configured to obtain the desired customization of services. Hence, the purpose of this paper is to investigate how a KIBS provider can match value propositions...... with varied customer needs utilizing service modularity. To accomplish this purpose, a qualitative multiple case study is organized around 5 projects allowing within-case and cross-case comparisons. Our findings describe how through the configuration of knowledge and resources a sustainable competitive...

  13. Compilation of Instantaneous Source Functions for Varying ...

    African Journals Online (AJOL)

    Compilation of Instantaneous Source Functions for Varying Architecture of a Layered Reservoir with Mixed Boundaries and Horizontal Well Completion Part III: B-Shaped Architecture with Vertical Well in the Upper Layer.

  14. Compilation of Instantaneous Source Functions for Varying ...

    African Journals Online (AJOL)

    Compilation of Instantaneous Source Functions for Varying Architecture of a Layered Reservoir with Mixed Boundaries and Horizontal Well Completion Part IV: Normal and Inverted Letter 'h' and 'H' Architecture.

  15. Varying constants, black holes, and quantum gravity

    International Nuclear Information System (INIS)

    Carlip, S.

    2003-01-01

    Tentative observations and theoretical considerations have recently led to renewed interest in models of fundamental physics in which certain 'constants' vary in time. Assuming fixed black hole mass and the standard form of the Bekenstein-Hawking entropy, Davies, Davis and Lineweaver have argued that the laws of black hole thermodynamics disfavor models in which the fundamental electric charge e changes. I show that with these assumptions, similar considerations severely constrain 'varying speed of light' models, unless we are prepared to abandon cherished assumptions about quantum gravity. Relaxation of these assumptions permits sensible theories of quantum gravity with ''varying constants,'' but also eliminates the thermodynamic constraints, though the black hole mass spectrum may still provide some restrictions on the range of allowable models

  16. "Mina olin siin" esilinastub Karlovy Varys

    Index Scriptorium Estoniae

    2008-01-01

    Karlovy Vary filmifestivalil esilinastub Rene Vilbre noortefilm "Mina olin siin", mille aluseks on Sass Henno romaan "Mina olin siin. Esimene arest", stsenaariumi kirjutas Ilmar Raag. Film võistleb võistlusprogrammis "East of the West". Esitlema sõidavad R. Vilbre, R. Sildos, R. Kaljujärv, T. Tuisk

  17. Tracking time-varying coefficient-functions

    DEFF Research Database (Denmark)

    Nielsen, Henrik Aalborg; Nielsen, Torben Skov; Joensen, Alfred K.

    2000-01-01

    is a combination of recursive least squares with exponential forgetting and local polynomial regression. It is argued, that it is appropriate to let the forgetting factor vary with the value of the external signal which is the argument of the coefficient functions. Some of the key properties of the modified method...... are studied by simulation...

  18. Filmihullu eluvesi voolab Karlovy Varys / Margit Tõnson

    Index Scriptorium Estoniae

    Tõnson, Margit, 1978-

    2010-01-01

    Karlovy Vary rahvusvahelisest filmifestivalist. Filmidest "Mr. Nobody" (rež. Jaco Van Dormaeli), "Kasside ema Teresa" (rež. Pawel Sala) ja "The Arbor" (rež. Clio Barnardi). Nimekiri võitnud töödest ja viimastel aastatel festivalil näidatud Eesti mängufilmidest

  19. Ellipsometry with randomly varying polarization states

    NARCIS (Netherlands)

    Liu, F.; Lee, C. J.; Chen, J. Q.; E. Louis,; van der Slot, P. J. M.; Boller, K. J.; F. Bijkerk,

    2012-01-01

    We show that, under the right conditions, one can make highly accurate polarization-based measurements without knowing the absolute polarization state of the probing light field. It is shown that light, passed through a randomly varying birefringent material has a well-defined orbit on the Poincar

  20. Õunpuu Karlovy Varys edukas

    Index Scriptorium Estoniae

    2010-01-01

    45. Karlovy Vary filmifestivali võistlusprogrammis "East of the West" märgiti ära Veiko Õunpuu film "Püha Tõnu kiusamine". Peaauhind läks rumeenlase Cristi Puiu filmile "Aurora". Grand prix´sai Augustĺ Vila film "La mosquitera". Teisi preemiasaajaid

  1. Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells

    NARCIS (Netherlands)

    Chan, M.F.; van Amerongen, R.; Nijjar, T.; Cuppen, E.; Jones, P.A.; Laird, P.W.

    2001-01-01

    Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by

  2. Varied line-space gratings and applications

    International Nuclear Information System (INIS)

    McKinney, W.R.

    1991-01-01

    This paper presents a straightforward analytical and numerical method for the design of a specific type of varied line-space grating system. The mathematical development will assume plane or nearly-plane spherical gratings which are illuminated by convergent light, which covers many interesting cases for synchrotron radiation. The gratings discussed will have straight grooves whose spacing varies across the principal plane of the grating. Focal relationships and formulae for the optical grating-pole-to-exist-slit distance and grating radius previously presented by other authors will be derived with a symbolic algebra system. It is intended to provide the optical designer with the tools necessary to design such a system properly. Finally, some possible advantages and disadvantages for application to synchrotron to synchrotron radiation beamlines will be discussed

  3. The Thermal Collector With Varied Glass Covers

    International Nuclear Information System (INIS)

    Luminosu, I.; Pop, N.

    2010-01-01

    The thermal collector with varied glass covers represents an innovation realized in order to build a collector able to reach the desired temperature by collecting the solar radiation from the smallest surface, with the highest efficiency. In the case of the thermal collector with variable cover glasses, the number of the glass plates covering the absorber increases together with the length of the circulation pipe for the working fluid. The thermal collector with varied glass covers compared to the conventional collector better meet user requirements because: for the same temperature increase, has the collecting area smaller; for the same collection area, realizes the highest temperature increase and has the highest efficiency. This works is addressed to researchers in the solar energy and to engineers responsible with air-conditioning systems design or industrial and agricultural products drying.

  4. Spatially varying dispersion to model breakthrough curves.

    Science.gov (United States)

    Li, Guangquan

    2011-01-01

    Often the water flowing in a karst conduit is a combination of contaminated water entering at a sinkhole and cleaner water released from the limestone matrix. Transport processes in the conduit are controlled by advection, mixing (dilution and dispersion), and retention-release. In this article, a karst transport model considering advection, spatially varying dispersion, and dilution (from matrix seepage) is developed. Two approximate Green's functions are obtained using transformation of variables, respectively, for the initial-value problem and for the boundary-value problem. A numerical example illustrates that mixing associated with strong spatially varying conduit dispersion can cause strong skewness and long tailing in spring breakthrough curves. Comparison of the predicted breakthrough curve against that measured from a dye-tracing experiment between Ames Sink and Indian Spring, Northwest Florida, shows that the conduit dispersivity can be as large as 400 m. Such a large number is believed to imply strong solute interaction between the conduit and the matrix and/or multiple flow paths in a conduit network. It is concluded that Taylor dispersion is not dominant in transport in a karst conduit, and the complicated retention-release process between mobile- and immobile waters may be described by strong spatially varying conduit dispersion. Copyright © 2010 The Author(s). Journal compilation © 2010 National Ground Water Association.

  5. New varying speed of light theories

    CERN Document Server

    Magueijo, J

    2003-01-01

    We review recent work on the possibility of a varying speed of light (VSL). We start by discussing the physical meaning of a varying $c$, dispelling the myth that the constancy of $c$ is a matter of logical consistency. We then summarize the main VSL mechanisms proposed so far: hard breaking of Lorentz invariance; bimetric theories (where the speeds of gravity and light are not the same); locally Lorentz invariant VSL theories; theories exhibiting a color dependent speed of light; varying $c$ induced by extra dimensions (e.g. in the brane-world scenario); and field theories where VSL results from vacuum polarization or CPT violation. We show how VSL scenarios may solve the cosmological problems usually tackled by inflation, and also how they may produce a scale-invariant spectrum of Gaussian fluctuations, capable of explaining the WMAP data. We then review the connection between VSL and theories of quantum gravity, showing how ``doubly special'' relativity has emerged as a VSL effective model of quantum space...

  6. Anistropically varying conductivity in irreversible electroporation simulations.

    Science.gov (United States)

    Labarbera, Nicholas; Drapaca, Corina

    2017-11-01

    One recent area of cancer research is irreversible electroporation (IRE). Irreversible electroporation is a minimally invasive procedure where needle electrodes are inserted into the body to ablate tumor cells with electricity. The aim of this paper is to propose a mathematical model that incorporates a tissue's conductivity increasing more in the direction of the electrical field as this has been shown to occur in experiments. It was necessary to mathematically derive a valid form of the conductivity tensor such that it is dependent on the electrical field direction and can be easily implemented into numerical software. The derivation of a conductivity tensor that can take arbitrary functions for the conductivity in the directions tangent and normal to the electrical field is the main contribution of this paper. Numerical simulations were performed for isotropic-varying and anisotropic-varying conductivities to evaluate the importance of including the electrical field's direction in the formulation for conductivity. By starting from previously published experimental results, this paper derived a general formulation for an anistropic-varying tensor for implementation into irreversible electroporation modeling software. The anistropic-varying tensor formulation allows the conductivity to take into consideration both electrical field direction and magnitude, as opposed to previous published works that only took into account electrical field magnitude. The anisotropic formulation predicts roughly a five percent decrease in ablation size for the monopolar simulation and approximately a ten percent decrease in ablation size for the bipolar simulations. This is a positive result as previously reported results found the isotropic formulation to overpredict ablation size for both monopolar and bipolar simulations. Furthermore, it was also reported that the isotropic formulation overpredicts the ablation size more for the bipolar case than the monopolar case. Thus, our

  7. Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

    Directory of Open Access Journals (Sweden)

    Korchagina Natalia

    2011-08-01

    Full Text Available Abstract Background Dlx (Distal-less genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development.

  8. Progress on MEVVA source VARIS at GSI

    Science.gov (United States)

    Adonin, A.; Hollinger, R.

    2018-05-01

    For the last few years, the development of the VARIS (vacuum arc ion source) was concentrated on several aspects. One of them was the production of high current ion beams of heavy metals such as Au, Pb, and Bi. The requested ion charge state for these ion species is 4+. This is quite challenging to produce in vacuum arc driven sources for reasonable beam pulse length (>120 µs) due to the physical properties of these elements. However, the situation can be dramatically improved by using the composite materials or alloys with enhanced physical properties of the cathodes. Another aspect is an increase of the beam brilliance for intense U4+ beams by the optimization of the geometry of the extraction system. A new 7-hole triode extraction system allows an increase of the extraction voltage from 30 kV to 40 kV and also reduces the outer aperture of the extracted ion beam. Thus, a record beam brilliance for the U4+ beam in front of the RFQ (Radio-Frequency Quadrupole) has been achieved, exceeding the RFQ space charge limit for an ion current of 15 mA. Several new projectiles in the middle-heavy region have been successfully developed from VARIS to fulfill the requirements of the future FAIR (Facility for Antiproton and Ion Research) programs. An influence of an auxiliary gas on the production performance of certain ion charge states as well as on operation stability has been investigated. The optimization of the ion source parameters for a maximum production efficiency and highest particle current in front of the RFQ has been performed. The next important aspect of the development will be the increase of the operation repetition rate of VARIS for all elements especially for uranium to 2.7 Hz in order to provide the maximum availability of high current ion beams for future FAIR experiments.

  9. New varying speed of light theories

    International Nuclear Information System (INIS)

    Magueijo, Joao

    2003-01-01

    We review recent work on the possibility of a varying speed of light (VSL). We start by discussing the physical meaning of a varying-c, dispelling the myth that the constancy of c is a matter of logical consistency. We then summarize the main VSL mechanisms proposed so far: hard breaking of Lorentz invariance; bimetric theories (where the speeds of gravity and light are not the same); locally Lorentz invariant VSL theories; theories exhibiting a colour-dependent speed of light; varying-c induced by extra dimensions (e.g. in the brane-world scenario); and field theories where VSL results from vacuum polarization or CPT violation. We show how VSL scenarios may solve the cosmological problems usually tackled by inflation, and also how they may produce a scale-invariant spectrum of Gaussian fluctuations, capable of explaining the WMAP data. We then review the connection between VSL and theories of quantum gravity, showing how 'doubly special' relativity has emerged as a VSL effective model of quantum space-time, with observational implications for ultra-high energy cosmic rays (UHECRs) and gamma ray bursts. Some recent work on the physics of 'black' holes and other compact objects in VSL theories is also described, highlighting phenomena associated with spatial (as opposed to temporal) variations in c. Finally, we describe the observational status of the theory. The evidence is currently slim-redshift dependence in the atomic fine structure, anomalies with UHECRs, and (to a much lesser extent) the acceleration of the universe and the WMAP data. The constraints (e.g. those arising from nucleosynthesis or geological bounds) are tight but not insurmountable. We conclude with the observational predictions of the theory and the prospects for its refutation or vindication

  10. Conceptual Modeling of Time-Varying Information

    DEFF Research Database (Denmark)

    Gregersen, Heidi; Jensen, Christian S.

    2004-01-01

    A wide range of database applications manage information that varies over time. Many of the underlying database schemas of these were designed using the Entity-Relationship (ER) model. In the research community as well as in industry, it is common knowledge that the temporal aspects of the mini......-world are important, but difficult to capture using the ER model. Several enhancements to the ER model have been proposed in an attempt to support the modeling of temporal aspects of information. Common to the existing temporally extended ER models, few or no specific requirements to the models were given...

  11. A time-varying magnetic flux concentrator

    International Nuclear Information System (INIS)

    Kibret, B; Premaratne, M; Lewis, P M; Thomson, R; Fitzgerald, P B

    2016-01-01

    It is known that diverse technological applications require the use of focused magnetic fields. This has driven the quest for controlling the magnetic field. Recently, the principles in transformation optics and metamaterials have allowed the realization of practical static magnetic flux concentrators. Extending such progress, here, we propose a time-varying magnetic flux concentrator cylindrical shell that uses electric conductors and ferromagnetic materials to guide magnetic flux to its center. Its performance is discussed based on finite-element simulation results. Our proposed design has potential applications in magnetic sensors, medical devices, wireless power transfer, and near-field wireless communications. (paper)

  12. Linear Parameter Varying Control of Induction Motors

    DEFF Research Database (Denmark)

    Trangbæk, Klaus

    The subject of this thesis is the development of linear parameter varying (LPV) controllers and observers for control of induction motors. The induction motor is one of the most common machines in industrial applications. Being a highly nonlinear system, it poses challenging control problems...... for high performance applications. This thesis demonstrates how LPV control theory provides a systematic way to achieve good performance for these problems. The main contributions of this thesis are the application of the LPV control theory to induction motor control as well as various contributions...

  13. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  14. Varying prior information in Bayesian inversion

    International Nuclear Information System (INIS)

    Walker, Matthew; Curtis, Andrew

    2014-01-01

    Bayes' rule is used to combine likelihood and prior probability distributions. The former represents knowledge derived from new data, the latter represents pre-existing knowledge; the Bayesian combination is the so-called posterior distribution, representing the resultant new state of knowledge. While varying the likelihood due to differing data observations is common, there are also situations where the prior distribution must be changed or replaced repeatedly. For example, in mixture density neural network (MDN) inversion, using current methods the neural network employed for inversion needs to be retrained every time prior information changes. We develop a method of prior replacement to vary the prior without re-training the network. Thus the efficiency of MDN inversions can be increased, typically by orders of magnitude when applied to geophysical problems. We demonstrate this for the inversion of seismic attributes in a synthetic subsurface geological reservoir model. We also present results which suggest that prior replacement can be used to control the statistical properties (such as variance) of the final estimate of the posterior in more general (e.g., Monte Carlo based) inverse problem solutions. (paper)

  15. Brown Dwarf Variability: What's Varying and Why?

    Science.gov (United States)

    Marley, Mark Scott

    2014-01-01

    Surveys by ground based telescopes, HST, and Spitzer have revealed that brown dwarfs of most spectral classes exhibit variability. The spectral and temporal signatures of the variability are complex and apparently defy simplistic classification which complicates efforts to model the changes. Important questions include understanding if clearings are forming in an otherwise uniform cloud deck or if thermal perturbations, perhaps associated with breaking gravity waves, are responsible. If clouds are responsible how long does it take for the atmospheric thermal profile to relax from a hot cloudy to a cooler cloudless state? If thermal perturbations are responsible then what atmospheric layers are varying? How do the observed variability timescales compare to atmospheric radiative, chemical, and dynamical timescales? I will address such questions by presenting modeling results for time-varying partly cloudy atmospheres and explore the importance of various atmospheric processes over the relevant timescales for brown dwarfs of a range of effective temperatures. Regardless of the origin of the observed variability, the complexity seen in the atmospheres of the field dwarfs hints at the variability that we may encounter in the next few years in directly imaged young Jupiters. Thus understanding the nature of variability in the field dwarfs, including sensitivity to gravity and metallicity, is of particular importance for exoplanet characterization.

  16. Time-Varying Periodicity in Intraday Volatility

    DEFF Research Database (Denmark)

    Andersen, Torben Gustav; Thyrsgaard, Martin; Todorov, Viktor

    We develop a nonparametric test for deciding whether return volatility exhibits time-varying intraday periodicity using a long time-series of high-frequency data. Our null hypothesis, commonly adopted in work on volatility modeling, is that volatility follows a stationary process combined...... with a constant time-of-day periodic component. We first construct time-of-day volatility estimates and studentize the high-frequency returns with these periodic components. If the intraday volatility periodicity is invariant over time, then the distribution of the studentized returns should be identical across...... with estimating volatility moments through their sample counterparts. Critical values are computed via easy-to-implement simulation. In an empirical application to S&P 500 index returns, we find strong evidence for variation in the intraday volatility pattern driven in part by the current level of volatility...

  17. Flexible time-varying filter banks

    Science.gov (United States)

    Tuncer, Temel E.; Nguyen, Truong Q.

    1993-09-01

    Linear phase maximally flat FIR Butterworth filter approximations are discussed and a new filter design method is introduced. This variable cutoff filter design method uses the cosine modulated versions of a prototype filter. The design procedure is simple and different variants of this procedure can be used to obtain close to optimum linear phase filters. Using this method, flexible time-varying filter banks with good reconstruction error are introduced. These types of oversampled filter banks have small magnitude error which can be easily controlled by the appropriate choice of modulation frequency. This error can be further decreased by magnitude equalization without increasing the computational complexity considerably. Two dimensional design examples are also given.

  18. Behavior of varying-alpha cosmologies

    International Nuclear Information System (INIS)

    Barrow, John D.; Sandvik, Haavard Bunes; Magueijo, Joao

    2002-01-01

    We determine the behavior of a time-varying fine structure 'constant' α(t) during the early and late phases of universes dominated by the kinetic energy of changing α(t), radiation, dust, curvature, and lambda, respectively. We show that after leaving an initial vacuum-dominated phase during which α increases, α remains constant in universes such as our own during the radiation era, and then increases slowly, proportional to a logarithm of cosmic time, during the dust era. If the universe becomes dominated by a negative curvature or a positive cosmological constant then α tends rapidly to a constant value. The effect of an early period of de Sitter or power-law inflation is to drive α to a constant value. Various cosmological consequences of these results are discussed with reference to recent observational studies of the value of α from quasar absorption spectra and to the existence of life in expanding universes

  19. Emergence of epidemics in rapidly varying networks

    International Nuclear Information System (INIS)

    Kohar, Vivek; Sinha, Sudeshna

    2013-01-01

    We describe a simple model mimicking disease spreading on a network with dynamically varying connections, and investigate the dynamical consequences of switching links in the network. Our central observation is that the disease cycles get more synchronized, indicating the onset of epidemics, as the underlying network changes more rapidly. This behavior is found for periodically switched links, as well as links that switch randomly in time. We find that the influence of changing links is more pronounced in networks where the nodes have lower degree, and the disease cycle has a longer infective stage. Further, when the switching of links is periodic we observe finer dynamical features, such as beating patterns in the emergent oscillations and resonant enhancement of synchronization, arising from the interplay between the time-scales of the connectivity changes and that of the epidemic outbreaks

  20. Time varying, multivariate volume data reduction

    Energy Technology Data Exchange (ETDEWEB)

    Ahrens, James P [Los Alamos National Laboratory; Fout, Nathaniel [UC DAVIS; Ma, Kwan - Liu [UC DAVIS

    2010-01-01

    Large-scale supercomputing is revolutionizing the way science is conducted. A growing challenge, however, is understanding the massive quantities of data produced by large-scale simulations. The data, typically time-varying, multivariate, and volumetric, can occupy from hundreds of gigabytes to several terabytes of storage space. Transferring and processing volume data of such sizes is prohibitively expensive and resource intensive. Although it may not be possible to entirely alleviate these problems, data compression should be considered as part of a viable solution, especially when the primary means of data analysis is volume rendering. In this paper we present our study of multivariate compression, which exploits correlations among related variables, for volume rendering. Two configurations for multidimensional compression based on vector quantization are examined. We emphasize quality reconstruction and interactive rendering, which leads us to a solution using graphics hardware to perform on-the-fly decompression during rendering. In this paper we present a solution which addresses the need for data reduction in large supercomputing environments where data resulting from simulations occupies tremendous amounts of storage. Our solution employs a lossy encoding scheme to acrueve data reduction with several options in terms of rate-distortion behavior. We focus on encoding of multiple variables together, with optional compression in space and time. The compressed volumes can be rendered directly with commodity graphics cards at interactive frame rates and rendering quality similar to that of static volume renderers. Compression results using a multivariate time-varying data set indicate that encoding multiple variables results in acceptable performance in the case of spatial and temporal encoding as compared to independent compression of variables. The relative performance of spatial vs. temporal compression is data dependent, although temporal compression has the

  1. Do North Atlantic eels show parallel patterns of spatially varying selection?

    DEFF Research Database (Denmark)

    Ulrik, Malene G.; Pujolar, Jose Martin; Ferchaud, Anne-Laure

    2014-01-01

    was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in European eel by searching for elevated genetic differentiation using F-ST-based outlier tests and by testing...... for significant associations between allele frequencies and environmental variables. Results: We found signatures of possible selection at a total of 11 coding-gene SNPs. Candidate genes for local selection constituted mainly genes with a major role in metabolism as well as defense genes. Contrary to what has...... been found for American eel, only 2 SNPs in our study correlated with differences in temperature, which suggests that other explanatory variables may play a role. None of the genes found to be associated with explanatory variables in European eel showed any correlations with environmental factors...

  2. Modelling tourists arrival using time varying parameter

    Science.gov (United States)

    Suciptawati, P.; Sukarsa, K. G.; Kencana, Eka N.

    2017-06-01

    The importance of tourism and its related sectors to support economic development and poverty reduction in many countries increase researchers’ attentions to study and model tourists’ arrival. This work is aimed to demonstrate time varying parameter (TVP) technique to model the arrival of Korean’s tourists to Bali. The number of Korean tourists whom visiting Bali for period January 2010 to December 2015 were used to model the number of Korean’s tourists to Bali (KOR) as dependent variable. The predictors are the exchange rate of Won to IDR (WON), the inflation rate in Korea (INFKR), and the inflation rate in Indonesia (INFID). Observing tourists visit to Bali tend to fluctuate by their nationality, then the model was built by applying TVP and its parameters were approximated using Kalman Filter algorithm. The results showed all of predictor variables (WON, INFKR, INFID) significantly affect KOR. For in-sample and out-of-sample forecast with ARIMA’s forecasted values for the predictors, TVP model gave mean absolute percentage error (MAPE) as much as 11.24 percent and 12.86 percent, respectively.

  3. Microsatellites in varied arenas of research

    Directory of Open Access Journals (Sweden)

    K S Remya

    2010-01-01

    Full Text Available Microsatellites known as simple-sequence repeats (SSRs or short-tandem repeats (STRs, represent specific sequences of DNA consisting of tandemly repeated units of one to six nucleotides. The repetitive nature of microsatellites makes them particularly prone to grow or shrink in length and these changes can have both good and bad consequences for the organisms that possess them. They are responsible for various neurological diseases and hence the same cause is now utilized for the early detection of various diseases, such as, Schizophrenia and Bipolar Disorder, Congenital generalized Hypertrichosis, Asthma, and Bronchial Hyperresponsiveness. These agents are widely used for forensic identification and relatedness testing, and are predominant genetic markers in this area of application. The application of microsatellites is an extending web and covers the varied scenarios of science, such as, conservation biology, plant genetics, and population studies. At present, researches are progressing round the globe to extend the use of these genetic repeaters to unmask the hidden genetic secrets behind the creation of the world.

  4. Varying coefficients model with measurement error.

    Science.gov (United States)

    Li, Liang; Greene, Tom

    2008-06-01

    We propose a semiparametric partially varying coefficient model to study the relationship between serum creatinine concentration and the glomerular filtration rate (GFR) among kidney donors and patients with chronic kidney disease. A regression model is used to relate serum creatinine to GFR and demographic factors in which coefficient of GFR is expressed as a function of age to allow its effect to be age dependent. GFR measurements obtained from the clearance of a radioactively labeled isotope are assumed to be a surrogate for the true GFR, with the relationship between measured and true GFR expressed using an additive error model. We use locally corrected score equations to estimate parameters and coefficient functions, and propose an expected generalized cross-validation (EGCV) method to select the kernel bandwidth. The performance of the proposed methods, which avoid distributional assumptions on the true GFR and residuals, is investigated by simulation. Accounting for measurement error using the proposed model reduced apparent inconsistencies in the relationship between serum creatinine and GFR among different clinical data sets derived from kidney donor and chronic kidney disease source populations.

  5. Stratospheric Impact of Varying Sea Surface Temperatures

    Science.gov (United States)

    Newman, Paul A.; Nash, Eric R.; Nielsen, Jon E.; Waugh, Darryn; Pawson, Steven

    2004-01-01

    The Finite-Volume General Circulation Model (FVGCM) has been run in 50 year simulations with the: 1) 1949-1999 Hadley Centre sea surface temperatures (SST), and 2) a fixed annual cycle of SSTs. In this presentation we first show that the 1949-1999 FVGCM simulation produces a very credible stratosphere in comparison to an NCEP/NCAR reanalysis climatology. In particular, the northern hemisphere has numerous major and minor stratospheric warming, while the southern hemisphere has only a few over the 50-year simulation. During the northern hemisphere winter, temperatures are both warmer in the lower stratosphere and the polar vortex is weaker than is found in the mid-winter southern hemisphere. Mean temperature differences in the lower stratosphere are shown to be small (less than 2 K), and planetary wave forcing is found to be very consistent with the climatology. We then will show the differences between our varying SST simulation and the fixed SST simulation in both the dynamics and in two parameterized trace gases (ozone and methane). In general, differences are found to be small, with subtle changes in planetary wave forcing that lead to reduced temperatures in the SH and increased temperatures in the NH.

  6. TIME-VARYING DYNAMICAL STAR FORMATION RATE

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eve J.; Chang, Philip; Murray, Norman, E-mail: evelee@berkeley.edu [Canadian Institute for Theoretical Astrophysics, 60 St. George Street, University of Toronto, Toronto, ON M5S 3H8 (Canada)

    2015-02-10

    We present numerical evidence of dynamic star formation in which the accreted stellar mass grows superlinearly with time, roughly as t {sup 2}. We perform simulations of star formation in self-gravitating hydrodynamic and magnetohydrodynamic turbulence that is continuously driven. By turning the self-gravity of the gas in the simulations on or off, we demonstrate that self-gravity is the dominant physical effect setting the mass accretion rate at early times before feedback effects take over, contrary to theories of turbulence-regulated star formation. We find that gravitational collapse steepens the density profile around stars, generating the power-law tail on what is otherwise a lognormal density probability distribution function. Furthermore, we find turbulent velocity profiles to flatten inside collapsing regions, altering the size-line width relation. This local flattening reflects enhancements of turbulent velocity on small scales, as verified by changes to the velocity power spectra. Our results indicate that gas self-gravity dynamically alters both density and velocity structures in clouds, giving rise to a time-varying star formation rate. We find that a substantial fraction of the gas that forms stars arrives via low-density flows, as opposed to accreting through high-density filaments.

  7. Partially linear varying coefficient models stratified by a functional covariate

    KAUST Repository

    Maity, Arnab; Huang, Jianhua Z.

    2012-01-01

    We consider the problem of estimation in semiparametric varying coefficient models where the covariate modifying the varying coefficients is functional and is modeled nonparametrically. We develop a kernel-based estimator of the nonparametric

  8. Mutant genes in pea breeding

    International Nuclear Information System (INIS)

    Swiecicki, W.K.

    1990-01-01

    Full text: Mutations of genes Dpo (dehiscing pods) and A (anthocyanin synthesis) played a role in pea domestication. A number of other genes were important in cultivar development for 3 types of usage (dry seeds, green vegetable types, fodder), e.g. fn, fna, le, p, v, fas and af. New genes (induced and spontaneous), are important for present ideotypes and are registered by the Pisum Genetics Association (PGA). Comparison of a pea variety ideotype with the variation available in gene banks shows that breeders need 'new' features. In mutation induction experiments, genotype, mutagen and method of treatment (e.g. combined or fractionated doses) are varied for broadening the mutation spectrum and selecting more genes of agronomic value. New genes are genetically analysed. In Poland, some mutant varieties with the gene afila were registered, controlling lodging by a shorter stem and a higher number of internodes. Really non-lodging pea varieties could strongly increase seed yield. But the probability of detecting a major gene for lodging resistance is low. Therefore, mutant genes with smaller influence on plant architecture are sought, to combine their effect by crossing. Promising seem to be the genes rogue, reductus and arthritic as well as a number of mutant genes not yet genetically identified. The gene det for terminal inflorescence - similarly to Vicia faba - changes plant development. Utilisation of assimilates and ripening should be better. Improvement of harvest index should give higher seed yield. A number of genes controlling disease resistance are well known (eg. Fw, Fnw, En, mo and sbm). Important in mass screening of resistance are closely linked gene markers. Pea gene banks collect respective lines, but mutants induced in highly productive cultivars would be better. Inducing gene markers sometimes seems to be easier than transfer by crossing. Mutation induction in pea breeding is probably more important because a high number of monogenic features are

  9. Comparison of Linear Microinstability Calculations of Varying Input Realism

    International Nuclear Information System (INIS)

    Rewoldt, G.

    2003-01-01

    The effect of varying ''input realism'' or varying completeness of the input data for linear microinstability calculations, in particular on the critical value of the ion temperature gradient for the ion temperature gradient mode, is investigated using gyrokinetic and gyrofluid approaches. The calculations show that varying input realism can have a substantial quantitative effect on the results

  10. Comparison of linear microinstability calculations of varying input realism

    International Nuclear Information System (INIS)

    Rewoldt, G.; Kinsey, J.E.

    2004-01-01

    The effect of varying 'input realism' or varying completeness of the input data for linear microinstability calculations, in particular on the critical value of the ion temperature gradient for the ion temperature gradient mode, is investigated using gyrokinetic and gyrofluid approaches. The calculations show that varying input realism can have a substantial quantitative effect on the results

  11. Transcriptomic profiling of Arabidopsis gene expression in response to varying micronutrient zinc supply

    NARCIS (Netherlands)

    Azevedo, Herlânder; Azinheiro, Sarah Gaspar; Muñoz-Mérida, Antonio; Castro, Pedro Humberto; Huettel, Bruno; Aarts, Mark M.G.; Assunção, Ana G.L.

    2016-01-01

    Deficiency of the micronutrient zinc is a widespread condition in agricultural soils, causing a negative impact on crop quality and yield. Nevertheless, there is an insufficient knowledge on the regulatory and molecular mechanisms underlying the plant response to inadequate zinc nutrition [1].

  12. Holographic cinematography of time-varying reflecting and time-varying phase objects using a Nd:YAG laser

    Science.gov (United States)

    Decker, A. J.

    1982-01-01

    The use of a Nd:YAG laser to record holographic motion pictures of time-varying reflecting objects and time-varying phase objects is discussed. Sample frames from both types of holographic motion pictures are presented. The holographic system discussed is intended for three-dimensional flow visualization of the time-varying flows that occur in jet-engine components.

  13. Gene expression

    International Nuclear Information System (INIS)

    Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

    1983-01-01

    We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

  14. The Caenorhabditis chemoreceptor gene families

    Directory of Open Access Journals (Sweden)

    Robertson Hugh M

    2008-10-01

    Full Text Available Abstract Background Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Conclusion Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.

  15. The Caenorhabditis chemoreceptor gene families.

    Science.gov (United States)

    Thomas, James H; Robertson, Hugh M

    2008-10-06

    Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.

  16. Effects of weight loss and long-term weight maintenance with diets varying in protein and glycemic index on cardiovascular risk factors

    DEFF Research Database (Denmark)

    Gögebakan, Özlem; Kohl, Angela; Osterhoff, Martin A.

    2011-01-01

    We sought to separately examine the effects of either weight loss or diets varying in protein content and glycemic index without further changes in body weight on cardiovascular risk factors within the Diet, Obesity, and Genes study (DiOGenes).......We sought to separately examine the effects of either weight loss or diets varying in protein content and glycemic index without further changes in body weight on cardiovascular risk factors within the Diet, Obesity, and Genes study (DiOGenes)....

  17. Estimating varying coefficients for partial differential equation models.

    Science.gov (United States)

    Zhang, Xinyu; Cao, Jiguo; Carroll, Raymond J

    2017-09-01

    Partial differential equations (PDEs) are used to model complex dynamical systems in multiple dimensions, and their parameters often have important scientific interpretations. In some applications, PDE parameters are not constant but can change depending on the values of covariates, a feature that we call varying coefficients. We propose a parameter cascading method to estimate varying coefficients in PDE models from noisy data. Our estimates of the varying coefficients are shown to be consistent and asymptotically normally distributed. The performance of our method is evaluated by a simulation study and by an empirical study estimating three varying coefficients in a PDE model arising from LIDAR data. © 2017, The International Biometric Society.

  18. The small nucleoid protein Fis is involved in Vibrio cholerae quorum sensing.

    Science.gov (United States)

    Lenz, Derrick H; Bassler, Bonnie L

    2007-02-01

    Quorum sensing is a process of cell-cell communication that bacteria use to relay information to one another about the cell density and species composition of the bacterial community. Quorum sensing involves the production, secretion and population-wide detection of small signalling molecules called autoinducers. This process allows bacteria to synchronize group behaviours and act as multicellular units. The human pathogen, Vibrio cholerae, uses quorum sensing to co-ordinate such complex behaviours as pathogenicity and biofilm formation. The quorum-sensing circuit of V. cholerae consists of two autoinducer/sensor systems, CAI-1/CqsS and AI-2/LuxPQ, and the VarS/A-CsrA/BCD growth-phase regulatory system. Genetic analysis suggests that an additional regulatory arm involved in quorum sensing exists in V. cholerae. All of these systems channel information into the histidine phosphotransfer protein, LuxU, and/or the response regulator, LuxO. LuxO, when phosphorylated, activates the expression of four genes encoding the Qrr (quorum regulatory RNAs) small RNAs (sRNAs). The Qrr sRNAs destabilize the hapR transcript encoding the master regulator of quorum sensing, HapR. Here we identify the nucleoid protein Fis as playing a major role in the V. cholerae quorum-sensing circuit. Fis fulfils the predictions required to be the putative additional component that inputs information into the cascade: its expression is regulated in a growth phase-dependent manner; it requires LuxO but acts independently of LuxU, and it regulates all four qrr genes and, in turn, HapR by directly binding to the qrr gene promoters and modulating their expression.

  19. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

    Science.gov (United States)

    Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

    2018-01-01

    When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

  20. How Do Parenting Concepts Vary within and between the Families?

    Science.gov (United States)

    Roskam, Isabelle; Meunier, Jean Christophe

    2009-01-01

    How do parenting concepts vary within and between the families? The present study regards parenting as a complex family process by considering three concepts of parenting: styles, differential treatment and coparenting consistency. A main question was addressed: whether and how these parenting concepts vary within the families towards siblings or…

  1. Specimen loading list for the varying temperature experiment

    International Nuclear Information System (INIS)

    Qualls, A.L.; Sitterson, R.G.

    1998-01-01

    The varying temperature experiment HFIR-RB-13J has been assembled and inserted in the reactor. Approximately 5300 specimens were cleaned, inspected, matched, and loaded into four specimen holders. A listing of each specimen loaded into the steady temperature holder, its position in the capsule, and the identification of the corresponding specimen loaded into the varying temperature holder is presented in this report

  2. Response of rabbits to varying levels of cassava and Leucaena ...

    African Journals Online (AJOL)

    Response of rabbits to varying levels of cassava and Leucaena leucocephala leaf meal diets. ... Bulletin of Animal Health and Production in Africa ... An experiment was carried out to determine the performance, haematology, carcass characteristics and sensory evaluation of meat from rabbits (n = 30) fed varying levels of ...

  3. Analysis of time-varying psoriasis lesion image patterns

    DEFF Research Database (Denmark)

    Maletti, Gabriela Mariel; Ersbøll, Bjarne Kjær; Nielsen, Allan Aasbjerg

    2004-01-01

    The multivariate alteration detection transform is applied to pairs of within and between time varying registered psoriasis image patterns. Color band contribution to the variates explaining maximal change is analyzed.......The multivariate alteration detection transform is applied to pairs of within and between time varying registered psoriasis image patterns. Color band contribution to the variates explaining maximal change is analyzed....

  4. Multivariate time-varying volatility modeling using probabilistic fuzzy systems

    NARCIS (Netherlands)

    Basturk, N.; Almeida, R.J.; Golan, R.; Kaymak, U.

    2016-01-01

    Methods to accurately analyze financial risk have drawn considerable attention in financial institutions. One difficulty in financial risk analysis is the fact that banks and other financial institutions invest in several assets which show time-varying volatilities and hence time-varying financial

  5. Reduction of Salmonella Enteritidis in the spleens of hens by bacterins that vary in fimbrial protein SefD

    Science.gov (United States)

    Gene sefD is part of operon sefABCD, and it is required for production of the SEF14 fimbria by Salmonella Enteritidis. We compared strains that varied in SefD content for their ability to reduce recovery of Salmonella Enteritidis from the spleens of hens infected by parenteral challenge. The two bac...

  6. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  7. Time varying voltage combustion control and diagnostics sensor

    Science.gov (United States)

    Chorpening, Benjamin T [Morgantown, WV; Thornton, Jimmy D [Morgantown, WV; Huckaby, E David [Morgantown, WV; Fincham, William [Fairmont, WV

    2011-04-19

    A time-varying voltage is applied to an electrode, or a pair of electrodes, of a sensor installed in a fuel nozzle disposed adjacent the combustion zone of a continuous combustion system, such as of the gas turbine engine type. The time-varying voltage induces a time-varying current in the flame which is measured and used to determine flame capacitance using AC electrical circuit analysis. Flame capacitance is used to accurately determine the position of the flame from the sensor and the fuel/air ratio. The fuel and/or air flow rate (s) is/are then adjusted to provide reduced flame instability problems such as flashback, combustion dynamics and lean blowout, as well as reduced emissions. The time-varying voltage may be an alternating voltage and the time-varying current may be an alternating current.

  8. Robust Stabilization of Nonlinear Systems with Uncertain Varying Control Coefficient

    Directory of Open Access Journals (Sweden)

    Zaiyue Yang

    2014-01-01

    Full Text Available This paper investigates the stabilization problem for a class of nonlinear systems, whose control coefficient is uncertain and varies continuously in value and sign. The study emphasizes the development of a robust control that consists of a modified Nussbaum function to tackle the uncertain varying control coefficient. By such a method, the finite-time escape phenomenon has been prevented when the control coefficient is crossing zero and varying its sign. The proposed control guarantees the asymptotic stabilization of the system and boundedness of all closed-loop signals. The control performance is illustrated by a numerical simulation.

  9. Features of cryptic promoters and their varied reliance on bromodomain-containing factors.

    Directory of Open Access Journals (Sweden)

    Samantha G Pattenden

    Full Text Available The Set2-Rpd3S pathway is important for the control of transcription memory. Mutation of components of this pathway results in cryptic transcription initiation within the coding region of approximately 30% of yeast genes. Specifically, deletion of the Set2 histone methyltransferase or Rco1, a component of the Rpd3S histone deacetylase complex leads to hyperacetylation of certain open reading frames (ORFs. We used this mutant as a system to study the role of histone modifications and co-activator recruitment in preinitiation complex (PIC formation. Specifically, we looked at the dependence of promoters on the bromodomain-containing RSC complex and the Bdf1 protein. We found that the dependence of cryptic promoters for these proteins varied. Overall, our data indicate that cryptic promoters are independently regulated, and their activation is dependent on factors that govern gene activation at canonical promoters.

  10. Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.

    Science.gov (United States)

    Goettel, Wolfgang; Xia, Eric; Upchurch, Robert; Wang, Ming-Li; Chen, Pengyin; An, Yong-Qiang Charles

    2014-04-23

    Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.

  11. Uus Eesti film pandi eile Karlovy Varys projektorisse / Kristiina Davidjants

    Index Scriptorium Estoniae

    Davidjants, Kristiina, 1974-

    2008-01-01

    8. juulil esilinastus Karlovy Vary filmifestivalil Rene Vilbre noortefilm "Mina olin siin", mille aluseks on Sass Henno romaan "Mina olin siin. Esimene arest". Film võistleb võistlusprogrammis "East of the West"

  12. Enhancement of heat transfer using varying width twisted tape inserts

    African Journals Online (AJOL)

    International Journal of Engineering, Science and Technology ... experimental investigations of the augmentation of turbulent flow heat transfer in a horizontal tube by means of varying width twisted tape inserts with air as the working fluid.

  13. Influence of feeding varying crude protein and digestible energy ...

    African Journals Online (AJOL)

    Influence of feeding varying crude protein and digestible energy levels on the development of individual muscles, rate of lean and fat deposition in pigs reared from 9 to 60kg liveweight in a humid tropical environment.

  14. Ageing genes

    DEFF Research Database (Denmark)

    Rattan, Suresh

    2018-01-01

    The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

  15. PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

    Science.gov (United States)

    Csaszar, Elizabeth; Yu, Mei; Morris, Quaid; Zandstra, Peter W.

    2012-01-01

    The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells). Only PERT's predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity. PMID:23284283

  16. Varying occurrence of extended-spectrum beta-lactamase bacteria among three produce types

    KAUST Repository

    Toh, Benjamin E. W.

    2017-07-07

    A monitoring effort that spanned across 1.5 years was conducted to examine three types of produce-associated microbiota. The average amount of antibiotic-resistant bacteria recovered from lettuce, tomato, and cucumber was 1.02 × 1010, 2.05 × 107, and 4.78 × 109 cells per 50 g of each produce, respectively. A total of 480 bacterial isolates were obtained and identified from their 16S rRNA genes, revealing isolates that were ubiquitously recovered from all three types of produce. However, sporadic presence of Klebsiella pneumoniae and Acinetobacter baumannii was detected on lettuce and cucumbers but not tomatoes. End-point PCR revealed that the K. pneumoniae and A. baumannii isolates were positive for genes encoding extended spectrum beta-lactamase. Whole genome sequencing of two of the K. pneumoniae isolates further suggested the presence of the blaCTX-M-15 gene in a conjugative plasmid, as well as other antibiotic resistance genes and virulence-associated traits in either conjugative plasmids or the chromosomal genome. Quantitative microbial risk assessment indicated varying levels of ingestion risk associated with different types of produce. In particular, the risk arising from ESBL-positive K. pneumoniae in lettuce, but not in cucumbers or tomatoes, was higher than the acceptable annual risk of 10−4. Practical applications Three types of vegetables were sampled and evaluated over 1.5 years to determine differences in their associated bacterial isolates. Particular emphasis was placed on identifying pathogenic strains that were positive for extended spectrum beta-lactamase (ESBL). Quantitative estimates of the microbial risk associated with the ESBL-positive pathogens showed that different produce types may incur varying levels of ingestion risk. Most of the currently reported ESBL-positive bacterial isolates have been identified in nosocomial environments. However, the carriage of such drug-resistant bacteria in vegetables suggests a possible connection

  17. Design of 2D Time-Varying Vector Fields

    KAUST Repository

    Chen, Guoning; Kwatra, Vivek; Wei, Li-Yi; Hansen, Charles D.; Zhang, Eugene

    2012-01-01

    Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects. © 1995-2012 IEEE.

  18. Design of 2D time-varying vector fields.

    Science.gov (United States)

    Chen, Guoning; Kwatra, Vivek; Wei, Li-Yi; Hansen, Charles D; Zhang, Eugene

    2012-10-01

    Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects.

  19. Design of 2D Time-Varying Vector Fields

    KAUST Repository

    Chen, Guoning

    2012-10-01

    Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects. © 1995-2012 IEEE.

  20. Do Time-Varying Covariances, Volatility Comovement and Spillover Matter?

    OpenAIRE

    Lakshmi Balasubramanyan

    2005-01-01

    Financial markets and their respective assets are so intertwined; analyzing any single market in isolation ignores important information. We investigate whether time varying volatility comovement and spillover impact the true variance-covariance matrix under a time-varying correlation set up. Statistically significant volatility spillover and comovement between US, UK and Japan is found. To demonstrate the importance of modelling volatility comovement and spillover, we look at a simple portfo...

  1. Performance of a solar chimney by varying design parameters

    CSIR Research Space (South Africa)

    Kumirai, T

    2015-08-01

    Full Text Available the design of solar chimneys to ensure optimal performance. The purpose of this chapter is to discuss the performance of an example solar chimney by varying the design parameters and examining their effects on the interior ventilation performance... chimney by varying design parameters Tichaona Kumirai, Researcher, Built Environment CSIR Jan-Hendrik Grobler, DPSS CSIR Dr D.C.U. Conradie, Senior researcher, Built Environment CSIR 1 Introduction Trombe walls and solar chimneys are not widely...

  2. Perturbation methods and the Melnikov functions for slowly varying oscillators

    International Nuclear Information System (INIS)

    Lakrad, Faouzi; Charafi, Moulay Mustapha

    2005-01-01

    A new approach to obtaining the Melnikov function for homoclinic orbits in slowly varying oscillators is proposed. The present method applies the Lindstedt-Poincare method to determine an approximation of homoclinic solutions. It is shown that the resultant Melnikov condition is the same as that obtained in the usual way involving distance functions in three dimensions by Wiggins and Holmes [Homoclinic orbits in slowly varying oscillators. SIAM J Math Anal 1987;18(3):612

  3. Marketingový mix HC Enegie Karlovy Vary

    OpenAIRE

    Štrobl, Adam

    2016-01-01

    Title: Marketing mix of HC Energie Karlovy Vary Objectives: This thesis is based on a questionnaire responses obtained from HC Energie Karlovy Vary fans. Its objective is focused on evaluation of their opinions on the marketing mix, their subsequent interpretation, and finally even development of recommendations for improvement based on previous analysis. Methods: Two methods are used to analyse the marketing mix. The first method is qualitative participant observation. The second method is a...

  4. Testing for time-varying loadings in dynamic factor models

    DEFF Research Database (Denmark)

    Mikkelsen, Jakob Guldbæk

    Abstract: In this paper we develop a test for time-varying factor loadings in factor models. The test is simple to compute and is constructed from estimated factors and residuals using the principal components estimator. The hypothesis is tested by regressing the squared residuals on the squared...... there is evidence of time-varying loadings on the risk factors underlying portfolio returns for around 80% of the portfolios....

  5. Bounds and asymptotics for orthogonal polynomials for varying weights

    CERN Document Server

    Levin, Eli

    2018-01-01

    This book establishes bounds and asymptotics under almost minimal conditions on the varying weights, and applies them to universality limits and entropy integrals.  Orthogonal polynomials associated with varying weights play a key role in analyzing random matrices and other topics.  This book will be of use to a wide community of mathematicians, physicists, and statisticians dealing with techniques of potential theory, orthogonal polynomials, approximation theory, as well as random matrices. .

  6. Pemodelan Markov Switching Dengan Time-varying Transition Probability

    OpenAIRE

    Savitri, Anggita Puri; Warsito, Budi; Rahmawati, Rita

    2016-01-01

    Exchange rate or currency is an economic variable which reflects country's state of economy. It fluctuates over time because of its ability to switch the condition or regime caused by economic and political factors. The changes in the exchange rate are depreciation and appreciation. Therefore, it could be modeled using Markov Switching with Time-Varying Transition Probability which observe the conditional changes and use information variable. From this model, time-varying transition probabili...

  7. Quantum capacity under adversarial quantum noise: arbitrarily varying quantum channels

    OpenAIRE

    Ahlswede, Rudolf; Bjelakovic, Igor; Boche, Holger; Noetzel, Janis

    2010-01-01

    We investigate entanglement transmission over an unknown channel in the presence of a third party (called the adversary), which is enabled to choose the channel from a given set of memoryless but non-stationary channels without informing the legitimate sender and receiver about the particular choice that he made. This channel model is called arbitrarily varying quantum channel (AVQC). We derive a quantum version of Ahlswede's dichotomy for classical arbitrarily varying channels. This includes...

  8. [Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

    Science.gov (United States)

    Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

    2012-07-01

    In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

  9. Gene doping.

    Science.gov (United States)

    Haisma, H J; de Hon, O

    2006-04-01

    Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

  10. Empirical study of supervised gene screening

    Directory of Open Access Journals (Sweden)

    Ma Shuangge

    2006-12-01

    Full Text Available Abstract Background Microarray studies provide a way of linking variations of phenotypes with their genetic causations. Constructing predictive models using high dimensional microarray measurements usually consists of three steps: (1 unsupervised gene screening; (2 supervised gene screening; and (3 statistical model building. Supervised gene screening based on marginal gene ranking is commonly used to reduce the number of genes in the model building. Various simple statistics, such as t-statistic or signal to noise ratio, have been used to rank genes in the supervised screening. Despite of its extensive usage, statistical study of supervised gene screening remains scarce. Our study is partly motivated by the differences in gene discovery results caused by using different supervised gene screening methods. Results We investigate concordance and reproducibility of supervised gene screening based on eight commonly used marginal statistics. Concordance is assessed by the relative fractions of overlaps between top ranked genes screened using different marginal statistics. We propose a Bootstrap Reproducibility Index, which measures reproducibility of individual genes under the supervised screening. Empirical studies are based on four public microarray data. We consider the cases where the top 20%, 40% and 60% genes are screened. Conclusion From a gene discovery point of view, the effect of supervised gene screening based on different marginal statistics cannot be ignored. Empirical studies show that (1 genes passed different supervised screenings may be considerably different; (2 concordance may vary, depending on the underlying data structure and percentage of selected genes; (3 evaluated with the Bootstrap Reproducibility Index, genes passed supervised screenings are only moderately reproducible; and (4 concordance cannot be improved by supervised screening based on reproducibility.

  11. Mediation analysis with time varying exposures and mediators.

    Science.gov (United States)

    VanderWeele, Tyler J; Tchetgen Tchetgen, Eric J

    2017-06-01

    In this paper we consider causal mediation analysis when exposures and mediators vary over time. We give non-parametric identification results, discuss parametric implementation, and also provide a weighting approach to direct and indirect effects based on combining the results of two marginal structural models. We also discuss how our results give rise to a causal interpretation of the effect estimates produced from longitudinal structural equation models. When there are time-varying confounders affected by prior exposure and mediator, natural direct and indirect effects are not identified. However, we define a randomized interventional analogue of natural direct and indirect effects that are identified in this setting. The formula that identifies these effects we refer to as the "mediational g-formula." When there is no mediation, the mediational g-formula reduces to Robins' regular g-formula for longitudinal data. When there are no time-varying confounders affected by prior exposure and mediator values, then the mediational g-formula reduces to a longitudinal version of Pearl's mediation formula. However, the mediational g-formula itself can accommodate both mediation and time-varying confounders and constitutes a general approach to mediation analysis with time-varying exposures and mediators.

  12. Varying ultrasound power level to distinguish surgical instruments and tissue.

    Science.gov (United States)

    Ren, Hongliang; Anuraj, Banani; Dupont, Pierre E

    2018-03-01

    We investigate a new framework of surgical instrument detection based on power-varying ultrasound images with simple and efficient pixel-wise intensity processing. Without using complicated feature extraction methods, we identified the instrument with an estimated optimal power level and by comparing pixel values of varying transducer power level images. The proposed framework exploits the physics of ultrasound imaging system by varying the transducer power level to effectively distinguish metallic surgical instruments from tissue. This power-varying image-guidance is motivated from our observations that ultrasound imaging at different power levels exhibit different contrast enhancement capabilities between tissue and instruments in ultrasound-guided robotic beating-heart surgery. Using lower transducer power levels (ranging from 40 to 75% of the rated lowest ultrasound power levels of the two tested ultrasound scanners) can effectively suppress the strong imaging artifacts from metallic instruments and thus, can be utilized together with the images from normal transducer power levels to enhance the separability between instrument and tissue, improving intraoperative instrument tracking accuracy from the acquired noisy ultrasound volumetric images. We performed experiments in phantoms and ex vivo hearts in water tank environments. The proposed multi-level power-varying ultrasound imaging approach can identify robotic instruments of high acoustic impedance from low-signal-to-noise-ratio ultrasound images by power adjustments.

  13. Newtonian cosmology with a time-varying constant of gravitation

    International Nuclear Information System (INIS)

    McVittie, G.C.

    1978-01-01

    Newtonian cosmology is based on the Eulerian equations of fluid mechanics combined with Poisson's equation modified by the introduction of a time-varying G. Spherically symmetric model universes are worked out with instantaneously uniform densities. They are indeterminate unless instantaneous uniformity of the pressure is imposed. When G varies as an inverse power of the time, the models can in some cases be shown to depend on the solution of a second-order differential equation which also occurs in the Friedmann models of general relativity. In Section 3, a method for 'passing through' a singularity of this equation is proposed which entails making four arbitrary mathematical assumptions. When G varies as (time) -1 , models with initially cycloidal motion are possible, each cycle becoming longer as time progresses. Finally, gravitation becomes so weak that the model expands to infinity. Kinetic and potential energies for the whole model are derived from the basic equations; their sum is not constant. (author)

  14. Brane world cosmologies with varying speed of light

    International Nuclear Information System (INIS)

    Youm, Donam

    2001-02-01

    We study cosmologies in the Randall-Sundrum models, incorporating the possibility of time-varying speed of light and Newton's constant. The cosmologies with varying speed of light (VSL) were proposed by Moffat and by Albrecht and Magueijo as an alternative to inflation for solving the cosmological problems. We consider the case in which the speed of light varies with time after the radion or the scale of the extra dimension has been stabilized. We elaborate on the conditions under which the flatness problem and the cosmological constant problem can be resolved. Particularly, the VSL cosmologies may provide a possible mechanism for bringing the quantum corrections to the fine-tuned brane tensions after the SUSY breaking under control. (author)

  15. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...... of flexibility in calculating genetic linkage and displaying linkage group. Among other features, this software enables user to identify linkage groups with output visualized graphically. The program calculates interference and coefficient of coincidence with elevated accuracy in sample datasets. AVAILABILITY...

  16. Partially linear varying coefficient models stratified by a functional covariate

    KAUST Repository

    Maity, Arnab

    2012-10-01

    We consider the problem of estimation in semiparametric varying coefficient models where the covariate modifying the varying coefficients is functional and is modeled nonparametrically. We develop a kernel-based estimator of the nonparametric component and a profiling estimator of the parametric component of the model and derive their asymptotic properties. Specifically, we show the consistency of the nonparametric functional estimates and derive the asymptotic expansion of the estimates of the parametric component. We illustrate the performance of our methodology using a simulation study and a real data application.

  17. Varied appearance of lymphoma in patients with AIDS

    International Nuclear Information System (INIS)

    Sider, L.; Weiss, A.

    1988-01-01

    Lymphoma is frequently present in patients with acquired immunodeficiency (AIDS). But unlike in the general population, the appearance of lymphoma in patients with AIDS is extremely varied. The computed tomographic scans, chest radiographs, and subsequent hospital courses of 15 patients with AIDS-related lymphoma are presented. The patients presented with isolated pleural effusion (six patients), pleural and pericardial effusion (one patient), pulmonary infiltrates (five patients), and mediastinal adenopathy (three patients). This varied manner of presentation of lymphoma in AIDS patients should be recognized if diagnosis is to be made in the earlier stages of presentation

  18. Entropy Rate of Time-Varying Wireless Networks

    DEFF Research Database (Denmark)

    Cika, Arta; Badiu, Mihai Alin; Coon, Justin P.

    2018-01-01

    In this paper, we present a detailed framework to analyze the evolution of the random topology of a time-varying wireless network via the information theoretic notion of entropy rate. We consider a propagation channel varying over time with random node positions in a closed space and Rayleigh...... fading affecting the connections between nodes. The existence of an edge between two nodes at given locations is modeled by a Markov chain, enabling memory effects in network dynamics. We then derive a lower and an upper bound on the entropy rate of the spatiotemporal network. The entropy rate measures...

  19. Investigating Time-Varying Drivers of Grid Project Emissions Impacts

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, Emily L.; Thayer, Brandon L.; Pal, Seemita; Studarus, Karen E.

    2017-11-15

    The emissions consequences of smart grid technologies depend heavily on their context and vary not only by geographical location, but by time of year. The same technology operated to meet the same objective may increase the emissions associated with energy generation for part of the year and decrease emissions during other times. The Grid Project Impact Quantification (GridPIQ) tool provides the ability to estimate these seasonal variations and garner insight into the time-varying drivers of grid project emissions impacts. This work leverages GridPIQ to examine the emissions implications across years and seasons of adding energy storage technology to reduce daily peak demand in California and New York.

  20. Codon usage and amino acid usage influence genes expression level.

    Science.gov (United States)

    Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

    2018-02-01

    Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

  1. Overcoming Spurious Regression Using time-Varying Fourier ...

    African Journals Online (AJOL)

    Non-stationary time series data have been traditionally analyzed in the frequency domain by assuming constant amplitudes regardless of the timelag. A new approach called time-varying amplitude method (TVAM) is presented here. Oscillations are analyzed for changes in the magnitude of Fourier Coefficients which are ...

  2. Electromagnetic radiation in a time-varying background medium

    NARCIS (Netherlands)

    Budko, N.V.

    2009-01-01

    Analytical solutions are presented for the electromagnetic radiation by an arbitrary pulsed source into a homogeneous time-varying background medium. In the constant-impedance case an explicit radiation formula is obtained for the synchronous permittivity and permeability described by any positive

  3. Computation of gradually varied flow in compound open channel ...

    Indian Academy of Sciences (India)

    The flow of water in an open channel can be treated as steady, gradually varied flow for ... channel between two nodes is treated as a single reach to calculate the loss ... dition at control points and (iii) critical depth is also required to verify the ...

  4. Adenoma detection rate varies greatly during colonoscopy training

    NARCIS (Netherlands)

    van Doorn, Sascha C.; Klanderman, Robert B.; Hazewinkel, Yark; Fockens, Paul; Dekker, Evelien

    2015-01-01

    The adenoma detection rate (ADR) is considered the most important quality indicator for colonoscopy and varies widely among colonoscopists. It is unknown whether the ADR of gastroenterology consultants can already be predicted during their colonoscopy training. To evaluate the ADR of fellows in

  5. Peer influence on school learning among students of varying socio ...

    African Journals Online (AJOL)

    This study examined peer Influence on School Learning among students of varying socio-economic backgrounds. One hundred and twenty students (60 males and 60 females) with a mean age 15.1 years were randomly selected from four co-educational Secondary Schools in Ikenne Local Government area of Ogun State.

  6. Projected space-time and varying speed of light

    International Nuclear Information System (INIS)

    Iovane, G.; Bellucci, S.; Benedetto, E.

    2008-01-01

    In this paper starting from El Naschie's Cantorian space-time and our model of projected Universe, we consider its properties in connection with varying speed of light. A possible way-out of the related problem is provided by the Fantappie group approach

  7. Frontal Neurons Modulate Memory Retrieval across Widely Varying Temporal Scales

    Science.gov (United States)

    Zhang, Wen-Hua; Williams, Ziv M.

    2015-01-01

    Once a memory has formed, it is thought to undergo a gradual transition within the brain from short- to long-term storage. This putative process, however, also poses a unique problem to the memory system in that the same learned items must also be retrieved across broadly varying time scales. Here, we find that neurons in the ventrolateral…

  8. Time Varying Market Integration and Expected Rteurns in Emerging Markets

    NARCIS (Netherlands)

    de Jong, F.C.J.M.; de Roon, F.A.

    2001-01-01

    We use a simple model in which the expected returns in emerging markets depend on their systematic risk as measured by their beta relative to the world portfolio as well as on the level of integration in that market.The level of integration is a time-varying variable that depends on the market value

  9. Branching of positive discharge streamers in air at varying pressures

    NARCIS (Netherlands)

    Briels, T.M.P.; Veldhuizen, van E.M.; Ebert, U.M.

    2005-01-01

    The formation of positive streamers in a 17-mm gap in air is studied at pressures varying in the range from 1010 to 100 mbar. An intensified charge coupled device camera is used to image the discharge. At high pressures, the discharge shows many branches, while at low pressure, fewer branches arise.

  10. Conductivity studies of lithium zinc silicate glasses with varying ...

    Indian Academy of Sciences (India)

    WINTEC

    Values of activation energy derived from σd.c., ωh and τ are almost equal within the ... materials can be changed by varying the proportion of the .... The solid line is a guide to the eye. ... does not show a maximum as d.c. conductivity drops to a.

  11. Varying the exchange interaction between NiO nanoparticles

    DEFF Research Database (Denmark)

    Bahl, Christian Robert Haffenden; Mørup, Steen

    2006-01-01

    We demonstrate that exchange interactions between antiferromagnetic nanoparticles of 57Fe-doped NiO can be varied by simple macroscopic treatments. Mössbauer spectroscopy studies of the superparamagnetic relaxation behaviour show that grinding or suspension in water of nanoparticles of NiO can...

  12. Performance and cost implication of finisher turkeys fed varying ...

    African Journals Online (AJOL)

    A 28-day experiment was conducted to determine the effect of feeding varying levels of rice milling waste as a substitute on maize on the performance, nutrient utilization and the economics implication on finisher turkeys. Five turkey finisher diets were formulated by substituting maize with rice milling waste at 0%, 25%, 50%, ...

  13. Sheep response to sugar cane tops supplemented with varying ...

    African Journals Online (AJOL)

    Twenty WAD sheep averaging 10.14kg were randomly divided into four groups of 5 replicates, and each group was fed sugarcane tops (SCT) supplemented with varying levels (0%, 25%, 50 and 75%) of Leucaena leucocephala foliage (LLF) in a completely randomized design. Results showed that sugarcane tops (SCT) ...

  14. Scattering of a TEM wave from a time varying surface

    Science.gov (United States)

    Elcrat, Alan R.; Harder, T. Mark; Stonebraker, John T.

    1990-03-01

    A solution is given for reflection of a plane wave with TEM polarization from a planar surface with time varying properties. These properties are given in terms of the currents on the surface. The solution is obtained by numerically solving a system of differential-delay equations in the time domain.

  15. Adolescent Sexual Behaviors at Varying Levels of Substance Use Frequency

    Science.gov (United States)

    Floyd, Leah J.; Latimer, William

    2010-01-01

    Combining substance use and sex compounds the risk of contracting sexually transmitted diseases, including HIV. However, the association between substance use and sexual behaviors may vary by substance and sexual behavior. The current study sought to examine the relationship between alcohol and marijuana use frequency and specific sexual…

  16. Karlovy Varys linastub kaks Eesti filmi / Andris Feldmanis

    Index Scriptorium Estoniae

    Feldmanis, Andris, 1982-

    2007-01-01

    Ilmar Raagi mängufilm "Klass" osaleb 42. Karlovy Vary rahvusvahelise filmifestivali võistlusprogrammis "East of the West" ja Asko Kase lühimängufilm "Zen läbi prügi" on valitud festivali kõrvalprogrammi "Forum of Independents"

  17. Time-varying correlation and common structures in volatility

    NARCIS (Netherlands)

    Liu, Yang

    2016-01-01

    This thesis studies time series properties of the covariance structure of multivariate asset returns. First, the time-varying feature of correlation is investigated at the intraday level with a new correlation model incorporating the intraday correlation dynamics. Second, the thesis develops a

  18. microwave oven-induced decalcification at varying temperatures

    African Journals Online (AJOL)

    Uwaifoh

    2012-09-30

    Sep 30, 2012 ... This study was designed to evaluate the effect of decalcifying fluid types on bone tissue architecture and its staining properties following decalcification at varying temperatures. A decalcification methodology using Golding and. Stewards (GS) fluid, and Jenkings fluid (JK), and a modern household ...

  19. Contact Dynamics of EHL Contacts under Time Varying Conditions

    NARCIS (Netherlands)

    Venner, Cornelis H.; Popovici, G.; Wijnant, Ysbrand H.; Dalmaz, G.; Lubrecht, A.A.; Priest, M

    2004-01-01

    By means of numerical simulations of two situations with time varying operating conditions it is shown that the dynamic behaviour of Elasto-Hydrodynamically Lubricated contacts in terms of vibrations can be characterized as: Changes in the mutual approach lead to film thickness changes in the inlet

  20. Electricity Futures Prices : Time Varying Sensitivity to Fundamentals

    NARCIS (Netherlands)

    S-E. Fleten (Stein-Erik); R. Huisman (Ronald); M. Kilic (Mehtap); H.P.G. Pennings (Enrico); S. Westgaard (Sjur)

    2014-01-01

    textabstractThis paper provides insight in the time-varying relation between electricity futures prices and fundamentals in the form of prices of contracts for fossil fuels. As supply curves are not constant and different producers have different marginal costs of production, we argue that the

  1. Visualizing time-varying harmonics using filter banks

    NARCIS (Netherlands)

    Duque, C.A.; Da Silveira, P.M.; Ribeiro, P.F.

    2011-01-01

    Although it is well known that Fourier analysis is in reality only accurately applicable to steady state waveforms, it is a widely used tool to study and monitor time-varying signals, such as are commonplace in electrical power systems. The disadvantages of Fourier analysis, such as frequency

  2. Time-Varying Value of Energy Efficiency in Michigan

    Energy Technology Data Exchange (ETDEWEB)

    Mims, Natalie; Eckman, Tom; Schwartz, Lisa C.

    2018-04-02

    Quantifying the time-varying value of energy efficiency is necessary to properly account for all of its benefits and costs and to identify and implement efficiency resources that contribute to a low-cost, reliable electric system. Historically, most quantification of the benefits of efficiency has focused largely on the economic value of annual energy reduction. Due to the lack of statistically representative metered end-use load shape data in Michigan (i.e., the hourly or seasonal timing of electricity savings), the ability to confidently characterize the time-varying value of energy efficiency savings in the state, especially for weather-sensitive measures such as central air conditioning, is limited. Still, electric utilities in Michigan can take advantage of opportunities to incorporate the time-varying value of efficiency into their planning. For example, end-use load research and hourly valuation of efficiency savings can be used for a variety of electricity planning functions, including load forecasting, demand-side management and evaluation, capacity planning, long-term resource planning, renewable energy integration, assessing potential grid modernization investments, establishing rates and pricing, and customer service (KEMA 2012). In addition, accurately calculating the time-varying value of efficiency may help energy efficiency program administrators prioritize existing offerings, set incentive or rebate levels that reflect the full value of efficiency, and design new programs.

  3. The early evolution of stars and planets with varying mass

    International Nuclear Information System (INIS)

    Bhattacharjee, S.K.

    1980-09-01

    In this thesis some aspects of stellar and planetary evolution with varying mass are examined. It is divided into two sections. The first section deals with the evolution of stars in the pre-main-sequence phase with mass accretion while in the second section we discuss the spin angular momentum of the planets with mass loss. (author)

  4. Additional Surgery after Breast-Conserving Surgery Varies Widely

    Science.gov (United States)

    A study published in the Feb. 1, 2012, issue of JAMA found that the number of women who have one or more additional surgeries to remove suspected residual tumor tissue (re-excisions) following breast-conserving surgery (BCS) for breast cancer varies widely across surgeons and hospitals.

  5. Steady shear viscosity of stirred yoghurts with varying ropiness

    NARCIS (Netherlands)

    van Marle, M.E.; van Marle, M.E.; van den Ende, Henricus T.M.; de Kruif, C.G.; de Kruif, C.G.; Mellema, J.

    1999-01-01

    Stirred yogurt was viewed as a concentrated dispersion of aggregates consisting of protein particles. The steady-shear behavior of three types of stirred yogurt with varying ropiness was investigated experimentally. To describe the shear-dependent viscosity, a microrheological model was used which

  6. Effect of varying concentrations of orally ingested glucose on platelet ...

    African Journals Online (AJOL)

    The physiologic basis of bleeding is a function of normal platelets and coagulation factors. This study is aimed at ascertaining the effect of varying concentrations of orally ingested glucose on platelet count and hemoglobin concentration during menstruation. Forty menstruating students between the ages of 18 and 25 from ...

  7. Vesicle biomechanics in a time-varying magnetic field.

    Science.gov (United States)

    Ye, Hui; Curcuru, Austen

    2015-01-01

    Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a time-varying magnetic field. Following previous publications and to simplify the calculation, this model treated the inner and suspending media as lossy dielectrics, the membrane thickness set at zero, and the electric resistance of the membrane assumed to be negligible. This work provided the first analytical solutions for the surface charges, electric field, radial pressure, overall translational forces, and rotational torques introduced on a vesicle by the time-varying magnetic field. Frequency responses of these measures were analyzed, particularly the frequency used clinically by transcranial magnetic stimulation (TMS). The induced surface charges interacted with the electric field to produce a biomechanical impact upon the vesicle. The distribution of the induced surface charges depended on the orientation of the coil and field frequency. The densities of these charges were trivial at low frequency ranges, but significant at high frequency ranges. The direction of the radial force on the vesicle was dependent on the conductivity ratio between the vesicle and the medium. At relatively low frequencies (biomechanics under a time-varying magnetic field. Biological effects of clinical TMS are not likely to occur via alteration of the biomechanics of brain

  8. Time-varying properties of renal autoregulatory mechanisms

    DEFF Research Database (Denmark)

    Zou, Rui; Cupples, Will A; Yip, K P

    2002-01-01

    In order to assess the possible time-varying properties of renal autoregulation, time-frequency and time-scaling methods were applied to renal blood flow under broad-band forced arterial blood pressure fluctuations and single-nephron renal blood flow with spontaneous oscillations obtained from...... normotensive (Sprague-Dawley, Wistar, and Long-Evans) rats, and spontaneously hypertensive rats. Time-frequency analyses of normotensive and hypertensive blood flow data obtained from either the whole kidney or the single-nephron show that indeed both the myogenic and tubuloglomerular feedback (TGF) mechanisms...... have time-varying characteristics. Furthermore, we utilized the Renyi entropy to measure the complexity of blood-flow dynamics in the time-frequency plane in an effort to discern differences between normotensive and hypertensive recordings. We found a clear difference in Renyi entropy between...

  9. Performance of Traffic Noise Barriers with Varying Cross-Section

    Directory of Open Access Journals (Sweden)

    Sanja Grubeša

    2011-05-01

    Full Text Available The efficiency of noise barriers largely depends on their geometry. In this paper, the performance of noise barriers was simulated using the numerical Boundary Element Method (BEM. Traffic noise was particularly considered with its standardized noise spectrum adapted to human hearing. The cross-section of the barriers was varied with the goal of finding the optimum shape in comparison to classical rectangular barriers. The barrier performance was calculated at different receiver points for a fixed barrier height and source position. The magnitude of the insertion loss parameter was used to evaluate the performance change, both in one-third octave bands and as the broadband mean insertion loss value. The proposed barriers of varying cross-section were also compared with a typical T-shape barrier of the same height.

  10. Electron dynamics in solid state via time varying wavevectors

    Science.gov (United States)

    Khaneja, Navin

    2018-06-01

    In this paper, we study electron wavepacket dynamics in electric and magnetic fields. We rigorously derive the semiclassical equations of electron dynamics in electric and magnetic fields. We do it both for free electron and electron in a periodic potential. We do this by introducing time varying wavevectors k(t). In the presence of magnetic field, our wavepacket reproduces the classical cyclotron orbits once the origin of the Schröedinger equation is correctly chosen to be center of cyclotron orbit. In the presence of both electric and magnetic fields, our equations for wavepacket dynamics differ from classical Lorentz force equations. We show that in a periodic potential, on application of electric field, the electron wave function adiabatically follows the wavefunction of a time varying Bloch wavevector k(t), with its energies suitably shifted with time. We derive the effective mass equation and discuss conduction in conductors and insulators.

  11. Control of Linear Parameter Varying Systems with Applications

    CERN Document Server

    Mohammadpour, Javad

    2012-01-01

    Control of Linear Parameter Varying Systems with Applications compiles state-of-the-art contributions on novel analytical and computational methods to address system modeling and identification, complexity reduction, performance analysis and control design for time-varying and nonlinear systems in the LPV framework. The book has an interdisciplinary character by emphasizing techniques that can be commonly applied in various engineering fields. It also includes a rich collection of illustrative applications in diverse domains to substantiate the effectiveness of the design methodologies and provide pointers to open research directions. The book is divided into three parts. The first part collects chapters of a more tutorial character on the background of LPV systems modeling and control. The second part gathers chapters devoted to the theoretical advancement of LPV analysis and synthesis methods to cope with the design constraints such as uncertainties and time delay. The third part of the volume showcases con...

  12. Time varying determinants of bond flows to emerging markets

    Directory of Open Access Journals (Sweden)

    Yasemin Erduman

    2016-06-01

    Full Text Available This paper investigates the time varying nature of the determinants of bond flows with a focus on the global financial crisis period. We estimate a time varying regression model using Bayesian estimation methods, where the posterior distribution is approximated by Gibbs sampling algorithm. Our findings suggest that the interest rate differential is the most significant pull factor of portfolio bond flows, along with the inflation rate, while the growth rate does not play a significant role. Among the push factors, global liquidity is the most important driver of bond flows. It matters the most, when unconventional monetary easing policies were first announced; and its importance as a determinant of portfolio bond flows decreases over time, starting with the Eurozone crisis, and diminishes with the tapering talk. Global risk appetite and the risk perception towards the emerging countries also have relatively small and stable significant effects on bond flows.

  13. Λ( t ) cosmology induced by a slowly varying Elko field

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, S.H.; Pinho, A.S.S.; Silva, J.M. Hoff da [Universidade Estadual Paulista (Unesp), Faculdade de Engenharia, Guaratinguetá, Departamento de Física e Química Av. Dr. Ariberto Pereira da Cunha 333, 12516-410—Guaratinguetá, SP (Brazil); Jesus, J.F., E-mail: shpereira@feg.unesp.br, E-mail: alexandre.pinho510@gmail.com, E-mail: hoff@feg.unesp.br, E-mail: jfjesus@itapeva.unesp.br [Universidade Estadual Paulista (Unesp), Campus Experimental de Itapeva, R. Geraldo Alckmin, 519 Itapeva, SP (Brazil)

    2017-01-01

    In this work the exact Friedmann-Robertson-Walker equations for an Elko spinor field coupled to gravity in an Einstein-Cartan framework are presented. The torsion functions coupling the Elko field spin-connection to gravity can be exactly solved and the FRW equations for the system assume a relatively simple form. In the limit of a slowly varying Elko spinor field there is a relevant contribution to the field equations acting exactly as a time varying cosmological model Λ( t )=Λ{sub *}+3β H {sup 2}, where Λ{sub *} and β are constants. Observational data using distance luminosity from magnitudes of supernovae constraint the parameters Ω {sub m} and β, which leads to a lower limit to the Elko mass. Such model mimics, then, the effects of a dark energy fluid, here sourced by the Elko spinor field. The density perturbations in the linear regime were also studied in the pseudo-Newtonian formalism.

  14. Modelling Time-Varying Volatility in Financial Returns

    DEFF Research Database (Denmark)

    Amado, Cristina; Laakkonen, Helinä

    2014-01-01

    The “unusually uncertain” phase in the global financial markets has inspired many researchers to study the effects of ambiguity (or “Knightian uncertainty”) on the decisions made by investors and their implications for the capital markets. We contribute to this literature by using a modified...... version of the time-varying GARCH model of Amado and Teräsvirta (2013) to analyze whether the increasing uncertainty has caused excess volatility in the US and European government bond markets. In our model, volatility is multiplicatively decomposed into two time-varying conditional components: the first...... being captured by a stable GARCH(1,1) process and the second driven by the level of uncertainty in the financial market....

  15. Non-minimally coupled varying constants quantum cosmologies

    International Nuclear Information System (INIS)

    Balcerzak, Adam

    2015-01-01

    We consider gravity theory with varying speed of light and varying gravitational constant. Both constants are represented by non-minimally coupled scalar fields. We examine the cosmological evolution in the near curvature singularity regime. We find that at the curvature singularity the speed of light goes to infinity while the gravitational constant vanishes. This corresponds to the Newton's Mechanics limit represented by one of the vertex of the Bronshtein-Zelmanov-Okun cube [1,2]. The cosmological evolution includes both the pre-big-bang and post-big-bang phases separated by the curvature singularity. We also investigate the quantum counterpart of the considered theory and find the probability of transition of the universe from the collapsing pre-big-bang phase to the expanding post-big-bang phase

  16. Epidemic spread in coupled populations with seasonally varying migration rates

    Science.gov (United States)

    Muzyczyn, Adam; Shaw, Leah B.

    2009-03-01

    The H5N1 strain of avian influenza has spread worldwide, and this spread may be due to seasonal migration of birds and mixing of birds from different regions in the wintering grounds. We studied a multipatch model for avian influenza with seasonally varying migration rates. The bird population was divided into two spatially distinct patches, or subpopulations. Within each patch, the disease followed the SIR (susceptible-infected-recovered) model for epidemic spread. Migration rates were varied periodically, with a net flux toward the breeding grounds during the spring and towards the wintering grounds during the fall. The case of two symmetric patches reduced to single-patch SIR dynamics. However, asymmetry in the birth and contact rates in the breeding grounds and wintering grounds led to bifurcations to longer period orbits and chaotic dynamics. We studied the bifurcation structure of the model and the phase relationships between outbreaks in the two patches.

  17. Scaling properties in time-varying networks with memory

    Science.gov (United States)

    Kim, Hyewon; Ha, Meesoon; Jeong, Hawoong

    2015-12-01

    The formation of network structure is mainly influenced by an individual node's activity and its memory, where activity can usually be interpreted as the individual inherent property and memory can be represented by the interaction strength between nodes. In our study, we define the activity through the appearance pattern in the time-aggregated network representation, and quantify the memory through the contact pattern of empirical temporal networks. To address the role of activity and memory in epidemics on time-varying networks, we propose temporal-pattern coarsening of activity-driven growing networks with memory. In particular, we focus on the relation between time-scale coarsening and spreading dynamics in the context of dynamic scaling and finite-size scaling. Finally, we discuss the universality issue of spreading dynamics on time-varying networks for various memory-causality tests.

  18. Local Feature Learning for Face Recognition under Varying Poses

    DEFF Research Database (Denmark)

    Duan, Xiaodong; Tan, Zheng-Hua

    2015-01-01

    In this paper, we present a local feature learning method for face recognition to deal with varying poses. As opposed to the commonly used approaches of recovering frontal face images from profile views, the proposed method extracts the subject related part from a local feature by removing the pose...... related part in it on the basis of a pose feature. The method has a closed-form solution, hence being time efficient. For performance evaluation, cross pose face recognition experiments are conducted on two public face recognition databases FERET and FEI. The proposed method shows a significant...... recognition improvement under varying poses over general local feature approaches and outperforms or is comparable with related state-of-the-art pose invariant face recognition approaches. Copyright ©2015 by IEEE....

  19. Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics.

    Directory of Open Access Journals (Sweden)

    Jane R Allison

    Full Text Available Evolutionary arms races between pathogens and their hosts may be manifested as selection for rapid evolutionary change of key genes, and are sometimes detectable through sequence-level analyses. In the case of protein-coding genes, such analyses frequently predict that specific codons are under positive selection. However, detecting positive selection can be non-trivial, and false positive predictions are a common concern in such analyses. It is therefore helpful to place such predictions within a structural and functional context. Here, we focus on the p19 protein from tombusviruses. P19 is a homodimer that sequesters siRNAs, thereby preventing the host RNAi machinery from shutting down viral infection. Sequence analysis of the p19 gene is complicated by the fact that it is constrained at the sequence level by overprinting of a viral movement protein gene. Using homology modeling, in silico mutation and molecular dynamics simulations, we assess how non-synonymous changes to two residues involved in forming the dimer interface-one invariant, and one predicted to be under positive selection-impact molecular function. Interestingly, we find that both observed variation and potential variation (where a non-synonymous change to p19 would be synonymous for the overprinted movement protein does not significantly impact protein structure or RNA binding. Consequently, while several methods identify residues at the dimer interface as being under positive selection, MD results suggest they are functionally indistinguishable from a site that is free to vary. Our analyses serve as a caveat to using sequence-level analyses in isolation to detect and assess positive selection, and emphasize the importance of also accounting for how non-synonymous changes impact structure and function.

  20. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  1. effect of gasket of varying thickness on spark ignition engines

    African Journals Online (AJOL)

    DJFLEX

    In the study of Toyota, In-line, 4 cylinders, spark ignition engine using gaskets of varying thicknesses. (1.75mm, 3.5mm, 5.25mm, 7mm and 8.75mm) between the cylinder head and the engine block, the performance characteristics of the engine was investigated via the effect of engine speed on brake power, brake thermal ...

  2. Housing Cycles in Switzerland - A Time-Varying Approach

    OpenAIRE

    Drechsel, Dirk

    2015-01-01

    In light of the strong increase of house prices in Switzerland, we analyze the effects of mortgage rate shocks, changes in the interplay between housing demand and supply and GDP growth on house prices for the time period 1981- 2014. We employ Bayesian time-varying coefficients vector autoregressions to allow different monetary and immigration regimes over time. A number of structural changes, such as regulatory changes in the aftermath of the 1990s real estate crisis, the introduction of fre...

  3. Method and apparatus of prefetching streams of varying prefetch depth

    Science.gov (United States)

    Gara, Alan [Mount Kisco, NY; Ohmacht, Martin [Yorktown Heights, NY; Salapura, Valentina [Chappaqua, NY; Sugavanam, Krishnan [Mahopac, NY; Hoenicke, Dirk [Seebruck-Seeon, DE

    2012-01-24

    Method and apparatus of prefetching streams of varying prefetch depth dynamically changes the depth of prefetching so that the number of multiple streams as well as the hit rate of a single stream are optimized. The method and apparatus in one aspect monitor a plurality of load requests from a processing unit for data in a prefetch buffer, determine an access pattern associated with the plurality of load requests and adjust a prefetch depth according to the access pattern.

  4. Tracking time-varying parameters with local regression

    DEFF Research Database (Denmark)

    Joensen, Alfred Karsten; Nielsen, Henrik Aalborg; Nielsen, Torben Skov

    2000-01-01

    This paper shows that the recursive least-squares (RLS) algorithm with forgetting factor is a special case of a varying-coe\\$cient model, and a model which can easily be estimated via simple local regression. This observation allows us to formulate a new method which retains the RLS algorithm, bu......, but extends the algorithm by including polynomial approximations. Simulation results are provided, which indicates that this new method is superior to the classical RLS method, if the parameter variations are smooth....

  5. Attitudes as Object-Evaluation Associations of Varying Strength

    OpenAIRE

    Fazio, Russell H.

    2007-01-01

    Historical developments regarding the attitude concept are reviewed, and set the stage for consideration of a theoretical perspective that views attitude, not as a hypothetical construct, but as evaluative knowledge. A model of attitudes as object-evaluation associations of varying strength is summarized, along with research supporting the model’s contention that at least some attitudes are represented in memory and activated automatically upon the individual’s encountering the attitude objec...

  6. Denitrification activity in mangrove sediments varies with associated vegetation

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, S.O.; Dutta, P.; Gonsalves, M.J.B.D.; Bonin, P.C.; LokaBharathi, P.A.

    . Eng.: 95; 2016; 671-681 Denitrification activity in mangrove sediments varies with associated vegetation Sheryl Oliveira Fernandes a, #, Pinky Dutta b, Maria-Judith Gonsalves a, Patricia C. Bonin c, P. A. LokaBharathi a, *  a Biological... in tropical and subtropical regions of the world (Giri et al., 2011). They provide a range of ecosystem services like soil formation, wood production, fish spawning grounds, carbon (C) storage and nutrient cycling (Murdiyarso et al., 2015). However, over...

  7. Does the availability of snack foods in supermarkets vary internationally?

    OpenAIRE

    Thornton, Lukar E; Cameron, Adrian J; McNaughton, Sarah A; Waterlander, Wilma E; Sodergren, Marita; Svastisalee, Chalida; Blanchard, Laurence; Liese, Angela D; Battersby, Sarah; Carter, Mary-Ann; Sheeshka, Judy; Kirkpatrick, Sharon I; Sherman, Sandy; Cowburn, Gill; Foster, Charlie

    2013-01-01

    Background Cross-country differences in dietary behaviours and obesity rates have been previously reported. Consumption of energy-dense snack foods and soft drinks are implicated as contributing to weight gain, however little is known about how the availability of these items within supermarkets varies internationally. This study assessed variations in the display of snack foods and soft drinks within a sample of supermarkets across eight countries. Methods Within-store audits were used to ev...

  8. Simple Model with Time-Varying Fine-Structure ``Constant''

    Science.gov (United States)

    Berman, M. S.

    2009-10-01

    Extending the original version written in colaboration with L.A. Trevisan, we study the generalisation of Dirac's LNH, so that time-variation of the fine-structure constant, due to varying electrical and magnetic permittivities is included along with other variations (cosmological and gravitational ``constants''), etc. We consider the present Universe, and also an inflationary scenario. Rotation of the Universe is a given possibility in this model.

  9. Influence of varying diets on radiosensitivity of quinea pigs

    International Nuclear Information System (INIS)

    Darenskaya, N.G.; Kuznetsova, S.S.; Lebengarts, Ya.Z.

    1975-01-01

    Seven groups of 25-day-old Guinea pig males given different diets during the entire observation period. Six groups received full-ration granulated mixed food varying in the contents of protein and cellulose, while the seventh group ate natural food. Experiments with irradiation failed to reveal any essential differences in radiosensitivity of animals grown on natural and mixed food, which enabled us to propose full-ration granulated mixed food for feeding laboratory guinea pigs

  10. Weakly Coupled Oscillators in a Slowly Varying World

    OpenAIRE

    Park, Youngmin; Ermentrout, Bard

    2016-01-01

    We extend the theory of weakly coupled oscillators to incorporate slowly varying inputs and parameters. We employ a combination of regular perturbation and an adiabatic approximation to derive equations for the phase-difference between a pair of oscillators. We apply this to the simple Hopf oscillator and then to a biophysical model. The latter represents the behavior of a neuron that is subject to slow modulation of a muscarinic current such as would occur during transient attention through ...

  11. Influence of varying diets on radiosensitivity of quinea pigs

    Energy Technology Data Exchange (ETDEWEB)

    Darenskaya, N G; Kuznetsova, S S; Lebengarts, Ya Z

    1975-07-01

    Seven groups of 25-day-old Guinea pig males given different diets during the entire observation period. Six groups received full-ration granulated mixed food varying in the contents of protein and cellulose, while the seventh group ate natural food. Experiments with irradiation failed to reveal any essential differences in radiosensitivity of animals grown on natural and mixed food, which enabled us to propose full-ration granulated mixed food for feeding laboratory guinea pigs.

  12. Phototrophic microvegetation of thermal springs in Karlovy Vary, Czech Republic

    Czech Academy of Sciences Publication Activity Database

    Kaštovský, J.; span class="emphasis">Komárek, Jiříspan>

    2001-01-01

    Roč. 123, - (2001), s. 107-120 ISSN 1438-9134. [International conference: Algae and extreme environments. Třeboň, 11.09.2000-16.09.2000] R&D Projects: GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6005908 Keywords : Cyanobacteria * algae * biodiversity * thermal springs * Karlovy Vary Spa * ecology * seasonality * anthropogenic factors * conservation Subject RIV: EF - Botanics Impact factor: 0.488, year: 2000

  13. A reciprocal Wald theorem for varying gravitational function

    International Nuclear Information System (INIS)

    Fay, Stephane

    2004-01-01

    We study when a cosmological constant is a natural issue if it is mimicked by the potential of a massive Hyperextended Scalar Tensor theory with a perfect fluid for Bianchi type I and V models. We then deduce a reciprocal Wald theorem giving the conditions such that the potential tends to a non vanishing constant when the gravitational function varies. We also get the conditions allowing the potential to vanish or diverge. (orig.)

  14. Model Complexities of Shallow Networks Representing Highly Varying Functions

    Czech Academy of Sciences Publication Activity Database

    Kůrková, Věra; Sanguineti, M.

    2016-01-01

    Roč. 171, 1 January (2016), s. 598-604 ISSN 0925-2312 R&D Projects: GA MŠk(CZ) LD13002 Grant - others:grant for Visiting Professors(IT) GNAMPA-INdAM Institutional support: RVO:67985807 Keywords : shallow networks * model complexity * highly varying functions * Chernoff bound * perceptrons * Gaussian kernel units Subject RIV: IN - Informatics, Computer Science Impact factor: 3.317, year: 2016

  15. Modeling information diffusion in time-varying community networks

    Science.gov (United States)

    Cui, Xuelian; Zhao, Narisa

    2017-12-01

    Social networks are rarely static, and they typically have time-varying network topologies. A great number of studies have modeled temporal networks and explored social contagion processes within these models; however, few of these studies have considered community structure variations. In this paper, we present a study of how the time-varying property of a modular structure influences the information dissemination. First, we propose a continuous-time Markov model of information diffusion where two parameters, mobility rate and community attractiveness, are introduced to address the time-varying nature of the community structure. The basic reproduction number is derived, and the accuracy of this model is evaluated by comparing the simulation and theoretical results. Furthermore, numerical results illustrate that generally both the mobility rate and community attractiveness significantly promote the information diffusion process, especially in the initial outbreak stage. Moreover, the strength of this promotion effect is much stronger when the modularity is higher. Counterintuitively, it is found that when all communities have the same attractiveness, social mobility no longer accelerates the diffusion process. In addition, we show that the local spreading in the advantage group has been greatly enhanced due to the agglomeration effect caused by the social mobility and community attractiveness difference, which thus increases the global spreading.

  16. Edge Modeling by Two Blur Parameters in Varying Contrasts.

    Science.gov (United States)

    Seo, Suyoung

    2018-06-01

    This paper presents a method of modeling edge profiles with two blur parameters, and estimating and predicting those edge parameters with varying brightness combinations and camera-to-object distances (COD). First, the validity of the edge model is proven mathematically. Then, it is proven experimentally with edges from a set of images captured for specifically designed target sheets and with edges from natural images. Estimation of the two blur parameters for each observed edge profile is performed with a brute-force method to find parameters that produce global minimum errors. Then, using the estimated blur parameters, actual blur parameters of edges with arbitrary brightness combinations are predicted using a surface interpolation method (i.e., kriging). The predicted surfaces show that the two blur parameters of the proposed edge model depend on both dark-side edge brightness and light-side edge brightness following a certain global trend. This is similar across varying CODs. The proposed edge model is compared with a one-blur parameter edge model using experiments of the root mean squared error for fitting the edge models to each observed edge profile. The comparison results suggest that the proposed edge model has superiority over the one-blur parameter edge model in most cases where edges have varying brightness combinations.

  17. Time-varying linear control for tiltrotor aircraft

    Directory of Open Access Journals (Sweden)

    Jing ZHANG

    2018-04-01

    Full Text Available Tiltrotor aircraft have three flight modes: helicopter mode, airplane mode, and transition mode. A tiltrotor has characteristics of highly nonlinear, time-varying flight dynamics and inertial/control couplings in its transition mode. It can transit from the helicopter mode to the airplane mode by tilting its nacelles, and an effective controller is crucial to accomplish tilting transition missions. Longitudinal dynamic characteristics of the tiltrotor are described by a nonlinear Lagrange-form model, which takes into account inertial/control couplings and aerodynamic interferences. Reference commands for airspeed velocity and attitude in the transition mode are calculated dynamically by visiting a command library which is founded in advance by analyzing the flight envelope of the tiltrotor. A Time-Varying Linear (TVL model is obtained using a Taylor-expansion based online linearization technique from the nonlinear model. Subsequently, based on an optimal control concept, an online optimization based control method with input constraints considered is proposed. To validate the proposed control method, three typical tilting transition missions are simulated using the nonlinear model of XV-15 tiltrotor aircraft. Simulation results show that the controller can be used to control the tiltrotor throughout its operating envelop which includes a transition flight, and can also deal with vertical gust disturbances. Keywords: Constrained optimal control, Inertia/control couplings, Tiltrotor aircraft, Time-varying control, Transition mode

  18. Radiation damage in stainless steel under varying temperature neutron irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Naoaki [Kyushu Univ., Kasuga, Fukuoka (Japan). Research Inst. for Applied Mechanics

    1998-03-01

    Microstructural evolution of model alloys of 316SS was examined by neutron irradiation at JMTR under cyclic temperature varying condition. In the case of Fe-16Cr-17Ni, formation of interstitial loops and voids are strongly suppressed by varying the temperature from 473K to 673K. By adding Ti as miner element (0.25wt%), however, abnormal accumulation of vacancies (void swelling of 11%dpa at 0.1dpa) was observed. Theoretical analysis standing on the rate theory of defect clustering and simulation irradiation experiments with heavy ions indicates that the vacancy-rich condition which appears temporally during and after changing the temperature from low to high brings these results. It was also shown that only 1 dpa pre-irradiation at low temperature changes swelling behavior at high temperature above several 10 dpa. The understanding of non-steady-state defect processes under temperature varying irradiation is very important to estimate the radiation damage under fusion environment where short-term and long-term temperature variation is expected. (author)

  19. Shape and Spatially-Varying Reflectance Estimation from Virtual Exemplars.

    Science.gov (United States)

    Hui, Zhuo; Sankaranarayanan, Aswin C

    2017-10-01

    This paper addresses the problem of estimating the shape of objects that exhibit spatially-varying reflectance. We assume that multiple images of the object are obtained under a fixed view-point and varying illumination, i.e., the setting of photometric stereo. At the core of our techniques is the assumption that the BRDF at each pixel lies in the non-negative span of a known BRDF dictionary. This assumption enables a per-pixel surface normal and BRDF estimation framework that is computationally tractable and requires no initialization in spite of the underlying problem being non-convex. Our estimation framework first solves for the surface normal at each pixel using a variant of example-based photometric stereo. We design an efficient multi-scale search strategy for estimating the surface normal and subsequently, refine this estimate using a gradient descent procedure. Given the surface normal estimate, we solve for the spatially-varying BRDF by constraining the BRDF at each pixel to be in the span of the BRDF dictionary; here, we use additional priors to further regularize the solution. A hallmark of our approach is that it does not require iterative optimization techniques nor the need for careful initialization, both of which are endemic to most state-of-the-art techniques. We showcase the performance of our technique on a wide range of simulated and real scenes where we outperform competing methods.

  20. Varying hemin concentrations affect Porphyromonas gingivalis strains differently.

    Science.gov (United States)

    Ohya, Manabu; Cueno, Marni E; Tamura, Muneaki; Ochiai, Kuniyasu

    2016-05-01

    Porphyromonas gingivalis requires heme to grow, however, heme availability and concentration in the periodontal pockets vary. Fluctuations in heme concentration may affect each P. gingivalis strain differently, however, this was never fully demonstrated. Here, we elucidated the effects of varying hemin concentrations in representative P. gingivalis strains. Throughout this study, representative P. gingivalis strains [FDC381 (type I), MPWIb-01 (type Ib), TDC60 (type II), ATCC49417 (type III), W83 (type IV), and HNA99 (type V)] were used and grown for 24 h in growth media under varying hemin concentrations (5 × , 1 × , 0.5 × , 0.1 × ). Samples were lysed and protein standardized. Arg-gingipain (Rgp), H2O2, and superoxide dismutase (SOD) levels were subsequently measured. We focused our study on 24 h-grown strains which excluded MPWIb-01 and HNA99. Rgp activity among the 4 remaining strains varied with Rgp peaking at: 1 × for FDC381, 5 × for TDC60, 0.5 × for ATCC49417, 5 × and 0.5 × for W83. With regards to H2O2 and SOD amounts: FDC381 had similar H2O2 amounts in all hemin concentrations while SOD levels varied; TDC60 had the lowest H2O2 amount at 1 × while SOD levels became higher in relation to hemin concentration; ATCC49417 also had similar H2O2 amounts in all hemin concentrations while SOD levels were higher at 1 × and 0.5 × ; and W83 had statistically similar H2O2 and SOD amounts regardless of hemin concentration. Our results show that variations in hemin concentration affect each P. gingivalis strain differently. Published by Elsevier Ltd.

  1. Observation of intermittency in gene expression on cDNA microarrays

    CERN Document Server

    Peterson, L E

    2002-01-01

    We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on moderately expressed genes, generally not tackled by conventional techniques.

  2. Gene doping: gene delivery for olympic victory

    OpenAIRE

    Gould, David

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  3. Time-varying value of electric energy efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Mims, Natalie A.; Eckman, Tom; Goldman, Charles

    2017-06-30

    Electric energy efficiency resources save energy and may reduce peak demand. Historically, quantification of energy efficiency benefits has largely focused on the economic value of energy savings during the first year and lifetime of the installed measures. Due in part to the lack of publicly available research on end-use load shapes (i.e., the hourly or seasonal timing of electricity savings) and energy savings shapes, consideration of the impact of energy efficiency on peak demand reduction (i.e., capacity savings) has been more limited. End-use load research and the hourly valuation of efficiency savings are used for a variety of electricity planning functions, including load forecasting, demand-side management and evaluation, capacity and demand response planning, long-term resource planning, renewable energy integration, assessing potential grid modernization investments, establishing rates and pricing, and customer service. This study reviews existing literature on the time-varying value of energy efficiency savings, provides examples in four geographically diverse locations of how consideration of the time-varying value of efficiency savings impacts the calculation of power system benefits, and identifies future research needs to enhance the consideration of the time-varying value of energy efficiency in cost-effectiveness screening analysis. Findings from this study include: -The time-varying value of individual energy efficiency measures varies across the locations studied because of the physical and operational characteristics of the individual utility system (e.g., summer or winter peaking, load factor, reserve margin) as well as the time periods during which savings from measures occur. -Across the four locations studied, some of the largest capacity benefits from energy efficiency are derived from the deferral of transmission and distribution system infrastructure upgrades. However, the deferred cost of such upgrades also exhibited the greatest range

  4. Global Stability of Polytopic Linear Time-Varying Dynamic Systems under Time-Varying Point Delays and Impulsive Controls

    Directory of Open Access Journals (Sweden)

    M. de la Sen

    2010-01-01

    Full Text Available This paper investigates the stability properties of a class of dynamic linear systems possessing several linear time-invariant parameterizations (or configurations which conform a linear time-varying polytopic dynamic system with a finite number of time-varying time-differentiable point delays. The parameterizations may be timevarying and with bounded discontinuities and they can be subject to mixed regular plus impulsive controls within a sequence of time instants of zero measure. The polytopic parameterization for the dynamics associated with each delay is specific, so that (q+1 polytopic parameterizations are considered for a system with q delays being also subject to delay-free dynamics. The considered general dynamic system includes, as particular cases, a wide class of switched linear systems whose individual parameterizations are timeinvariant which are governed by a switching rule. However, the dynamic system under consideration is viewed as much more general since it is time-varying with timevarying delays and the bounded discontinuous changes of active parameterizations are generated by impulsive controls in the dynamics and, at the same time, there is not a prescribed set of candidate potential parameterizations.

  5. Genes and Hearing Loss

    Science.gov (United States)

    ... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

  6. Lichen Persistence and Recovery in Response to Varied Volcanic Disturbances

    Science.gov (United States)

    Nelson, P.; Wheeler, T. B.

    2015-12-01

    Volcanic eruptions produce many ecological disturbances that structure vegetation. While lichens are sensitive to disturbances, little is known about their responses to volcanic disturbances, except for colonization of lava. We examined lichen community responses through time to different disturbances produced by the May 1, 2008 eruption of Volcan Chaiten in south-central Chile. Pre-eruption vegetation near the volcano was old-growth Valdivian temperate rainforest dominated by closed-canopy Nothofagus sp... In 2012, we installed thirteen 1-acre plots across volcanic disturbance zones on which a time-constrained search was done for all macrolichen species, each of which was assigned an approximate log10 categorical abundance. We also installed a 0.2 m2 quadrat on two representative trees per plot for repeat photography of lichen cover. We remeasured at least one plot per disturbance zone in 2014 and re-photographed tree quadrats in 2013 and 2014. We then analyzed species composition and abundance differences among disturbance zones. In 2012, the blast (pyroclastic density flow), scorch (standing scorched forest at the edge of the blast) and deep tephra (>10 cm) zones had the lowest lichen species richness (5-13 species), followed by reference (unimpacted) and shallow (lichen species since 2012 while the light tephra and reference were essentially unchanged. Gravel rain, gravel rain + pumice and flooded forest plots all had about the same number of species in 2014 as 2012. Lichen colonization and growth in tree quadrats varied widely, from very little colonization in the blast to prolific colonization in the gravel rain + pumice zone. Lichen's varied responses to different volcanic disturbances were attributable to varying degrees of mortality and subsequent availability of substrate, quantity of light and removal of competitors. While sensitive to disturbance, lichens are apparently resilient to and can quickly recolonize after a variety of large, violent volcanic

  7. Forming of Zr-4 alloy guide tube with varied diameters

    International Nuclear Information System (INIS)

    Wei Songyan; Tian Zhenye

    1989-10-01

    A new built-up mould method to manufacture Zr-4 alloy guide tubes with varied diameters at the middle of tube is introduced. The guide tube is used in nuclear power plants for guiding the control rods. This method has many advantages such as simple in forming, low cost of manufacturing, no need of special devices and favour of batch processing. The test results show that the accuracy of size, mechanical properties, resistance to corrosion, grain size and hydrogenate orientation of the end-products can meet the technical needs for nuclear reactor operation

  8. Varied clinico-radiological presentations of transmigrated canines

    Directory of Open Access Journals (Sweden)

    Ishita Gupta

    2015-01-01

    Full Text Available Canine is one of the most commonly impacted teeth in the dental arch. An unerupted permanent canine crossing the midline is called transmigration and is an unusual event. We report nine cases of impacted canine transmigration. Maxillary canine transmigration, bilateral transmigration, and transmigration associated with odontoma are rare presentations. This article discusses the varied clinico-radiologic presentations, etiology, and treatment options of transmigration. It also emphasizes the importance of panoramic radiographs for evaluation of over-retained deciduous canines or missing permanent canines.

  9. Plasma acceleration in a wave with varying frequency

    International Nuclear Information System (INIS)

    Petrzilka, V.A.

    1978-01-01

    The averaged velocity of a test particle and the averaged velocity of a plasma in an electromagnetic wave packet with varying frequency (e.g., a radiation pulse from pulsar) is derived. The total momentum left by the wave packet in regions of plasma inhomogeneity is found. In case the plasma concentration is changing due to ionization the plasma may be accelerated parallelly or antiparallelly to the direction of the wave packet propagation which is relevant for a laser induced breakdown in gas. (author)

  10. Structured Linear Parameter Varying Control of Wind Turbines

    DEFF Research Database (Denmark)

    Adegas, Fabiano Daher; Sloth, Christoffer; Stoustrup, Jakob

    2012-01-01

    High performance and reliability are required for wind turbines to be competitive within the energy market. To capture their nonlinear behavior, wind turbines are often modeled using parameter-varying models. In this chapter, a framework for modelling and controller design of wind turbines is pre...... in the controller synthesis are solved by an iterative LMI-based algorithm. The resulting controllers can also be easily implemented in practice due to low data storage and simple math operations. The performance of the LPV controllers is assessed by nonlinear simulations results....

  11. Toluene metabolism during exposure to varying concentrations combined with exercise

    DEFF Research Database (Denmark)

    Bælum, Jesper; Døssing, M; Hansen, S H

    1987-01-01

    . In Study A, four males were exposed to clean air and to constant and varying concentrations of toluene in combination with rest and with 100 W exercise in 140 min. Exercise increased end exposure excretion rate of HA and O-cr by 47 and 114%, respectively. After exposure, all excess HA was excreted within 4...... weight and smoking habits, thus influencing the metabolite concentration standardised in relation to creatinine. It is concluded that both metabolites are estimates of toluene exposure. O-cr is more specific than HA, but the individual variation in excretion of both metabolites is large, and when...

  12. Reduced dielectric response in spatially varying electric fields

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt

    2015-01-01

    relations between the flux and the gradient of the polarization. Comparison between the theory and molecular dynamics simulations confirms this effect. The effect is significant for small length scale electric field variations and the inclusion of the flux is thus important in nanoscale modeling......In this paper, the dynamical equation for polarization is derived. From this the dielectric response to a spatially varying electric field is analyzed showing a reduced response due to flux of polarization in the material. This flux is modeled as a diffusive process through linear constitutive...

  13. Time Varying Market Integration and Expected Rteurns in Emerging Markets

    OpenAIRE

    Jong, F.C.J.M. de; Roon, F.A. de

    2001-01-01

    We use a simple model in which the expected returns in emerging markets depend on their systematic risk as measured by their beta relative to the world portfolio as well as on the level of integration in that market.The level of integration is a time-varying variable that depends on the market value of the assets that can be held by domestic investors only versus the market value of the assets that can be traded freely.Our empirical analysis for 30 emerging markets shows that there are strong...

  14. Robust topology optimization accounting for spatially varying manufacturing errors

    DEFF Research Database (Denmark)

    Schevenels, M.; Lazarov, Boyan Stefanov; Sigmund, Ole

    2011-01-01

    This paper presents a robust approach for the design of macro-, micro-, or nano-structures by means of topology optimization, accounting for spatially varying manufacturing errors. The focus is on structures produced by milling or etching; in this case over- or under-etching may cause parts...... optimization problem is formulated in a probabilistic way: the objective function is defined as a weighted sum of the mean value and the standard deviation of the structural performance. The optimization problem is solved by means of a Monte Carlo method: in each iteration of the optimization scheme, a Monte...

  15. Measurement of periodically varying ECE spectra using a Michelson interferometer

    International Nuclear Information System (INIS)

    Laurent, L.; Rodriguez, L.; Talvard, M.

    1987-01-01

    In some tokamak experiments the ECE spectrum is periodically varying. If the modulation frequency is small enough (less than 10 Hz) the plasma can be considered as quasi-stationary during the typical scan time of most of the Michelson interferometers. It is possible to measure simply ECE spectra at different times of the oscillation. We present here a technique which allows to measure smaller fluctuations at larger frequencies. However the analysis requires a large number of periods of oscillation at constant frequency and a scanning mirror moving at constant velocity

  16. Modelling Acoustic Wave Propagation in Axisymmetric Varying-Radius Waveguides

    DEFF Research Database (Denmark)

    Bæk, David; Willatzen, Morten

    2008-01-01

    A computationally fast and accurate model (a set of coupled ordinary differential equations) for fluid sound-wave propagation in infinite axisymmetric waveguides of varying radius is proposed. The model accounts for fluid heat conduction and fluid irrotational viscosity. The model problem is solved...... by expanding solutions in terms of cross-sectional eigenfunctions following Stevenson’s method. A transfer matrix can be easily constructed from simple model responses of a given waveguide and later used in computing the response to any complex wave input. Energy losses due to heat conduction and viscous...

  17. One-dimensional radionuclide transport under time-varying conditions

    International Nuclear Information System (INIS)

    Gelbard, F.; Olague, N.E.; Longsine, D.E.

    1990-01-01

    This paper discusses new analytical and numerical solutions presented for one-dimensional radionuclide transport under time-varying fluid-flow conditions including radioactive decay. The analytical solution assumes that all radionuclides have identical retardation factors, and is limited to instantaneous releases. The numerical solution does not have these limitations, but is tested against the limiting case given for the analytical solution. Reasonable agreement between the two solutions was found. Examples are given for the transport of a three-member radionuclide chain transported over distances and flow rates comparable to those reported for Yucca Mountain, the proposed disposal site for high-level nuclear waste

  18. Timed arrays wideband and time varying antenna arrays

    CERN Document Server

    Haupt, Randy L

    2015-01-01

    Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

  19. Epidemic spreading in time-varying community networks.

    Science.gov (United States)

    Ren, Guangming; Wang, Xingyuan

    2014-06-01

    The spreading processes of many infectious diseases have comparable time scale as the network evolution. Here, we present a simple networks model with time-varying community structure, and investigate susceptible-infected-susceptible epidemic spreading processes in this model. By both theoretic analysis and numerical simulations, we show that the efficiency of epidemic spreading in this model depends intensively on the mobility rate q of the individuals among communities. We also find that there exists a mobility rate threshold qc. The epidemic will survive when q > qc and die when q epidemic spreading in complex networks with community structure.

  20. The extinction probability in systems randomly varying in time

    Directory of Open Access Journals (Sweden)

    Imre Pázsit

    2017-09-01

    Full Text Available The extinction probability of a branching process (a neutron chain in a multiplying medium is calculated for a system randomly varying in time. The evolution of the first two moments of such a process was calculated previously by the authors in a system randomly shifting between two states of different multiplication properties. The same model is used here for the investigation of the extinction probability. It is seen that the determination of the extinction probability is significantly more complicated than that of the moments, and it can only be achieved by pure numerical methods. The numerical results indicate that for systems fluctuating between two subcritical or two supercritical states, the extinction probability behaves as expected, but for systems fluctuating between a supercritical and a subcritical state, there is a crucial and unexpected deviation from the predicted behaviour. The results bear some significance not only for neutron chains in a multiplying medium, but also for the evolution of biological populations in a time-varying environment.

  1. Vibration condition monitoring of planetary gearbox under varying external load

    Energy Technology Data Exchange (ETDEWEB)

    Bartelmus, W.; Zimroz, R. [Wroclaw University of Technology, Wroclaw (Poland)

    2009-01-15

    The paper shows that for condition monitoring of planetary gearboxes it is important to identify the external varying load condition. In the paper, systematic consideration has been taken of the influence of many factors on the vibration signals generated by a system in which a planetary gearbox is included. These considerations give the basis for vibration signal interpretation, development of the means of condition monitoring, and for the scenario of the degradation of the planetary gearbox. Real measured vibration signals obtained in the industrial environment are processed. The signals are recorded during normal operation of the diagnosed objects, namely planetary gearboxes, which are a part of the driving system used in a bucket wheel excavator, used in lignite mines. It has been found that the most important factor of the proper planetary gearbox condition is connected with perturbation of arm rotation, where an arm rotation gives rise to a specific vibration signal whose properties are depicted by a short-time Fourier transform (STFT) and Wigner-Ville distribution presented as a time-frequency map. The paper gives evidence that there are two dominant low-frequency causes that influence vibration signal modulation, i.e. the varying load, which comes from the nature of the bucket wheel digging process, and the arm/carrier rotation. These two causes determine the condition of the planetary gearboxes considered.

  2. Stochastic analysis of epidemics on adaptive time varying networks

    Science.gov (United States)

    Kotnis, Bhushan; Kuri, Joy

    2013-06-01

    Many studies investigating the effect of human social connectivity structures (networks) and human behavioral adaptations on the spread of infectious diseases have assumed either a static connectivity structure or a network which adapts itself in response to the epidemic (adaptive networks). However, human social connections are inherently dynamic or time varying. Furthermore, the spread of many infectious diseases occur on a time scale comparable to the time scale of the evolving network structure. Here we aim to quantify the effect of human behavioral adaptations on the spread of asymptomatic infectious diseases on time varying networks. We perform a full stochastic analysis using a continuous time Markov chain approach for calculating the outbreak probability, mean epidemic duration, epidemic reemergence probability, etc. Additionally, we use mean-field theory for calculating epidemic thresholds. Theoretical predictions are verified using extensive simulations. Our studies have uncovered the existence of an “adaptive threshold,” i.e., when the ratio of susceptibility (or infectivity) rate to recovery rate is below the threshold value, adaptive behavior can prevent the epidemic. However, if it is above the threshold, no amount of behavioral adaptations can prevent the epidemic. Our analyses suggest that the interaction patterns of the infected population play a major role in sustaining the epidemic. Our results have implications on epidemic containment policies, as awareness campaigns and human behavioral responses can be effective only if the interaction levels of the infected populace are kept in check.

  3. Constitutive Equation with Varying Parameters for Superplastic Flow Behavior

    Science.gov (United States)

    Guan, Zhiping; Ren, Mingwen; Jia, Hongjie; Zhao, Po; Ma, Pinkui

    2014-03-01

    In this study, constitutive equations for superplastic materials with an extra large elongation were investigated through mechanical analysis. From the view of phenomenology, firstly, some traditional empirical constitutive relations were standardized by restricting some strain paths and parameter conditions, and the coefficients in these relations were strictly given new mechanical definitions. Subsequently, a new, general constitutive equation with varying parameters was theoretically deduced based on the general mechanical equation of state. The superplastic tension test data of Zn-5%Al alloy at 340 °C under strain rates, velocities, and loads were employed for building a new constitutive equation and examining its validity. Analysis results indicated that the constitutive equation with varying parameters could characterize superplastic flow behavior in practical superplastic forming with high prediction accuracy and without any restriction of strain path or deformation condition, showing good industrial or scientific interest. On the contrary, those empirical equations have low prediction capabilities due to constant parameters and poor applicability because of the limit of special strain path or parameter conditions based on strict phenomenology.

  4. Marijuana smoking: effects of varying puff volume and breathhold duration.

    Science.gov (United States)

    Azorlosa, J L; Greenwald, M K; Stitzer, M L

    1995-02-01

    Two studies were conducted to quantify biological and behavioral effects resulting from exposure to controlled doses of marijuana smoke. In one study, puff volume (30, 60 and 90 ml) and in a second study, breathhold duration (0, 10 and 20 sec) were systematically varied while holding constant other smoking topography parameters (number of puffs = 10, interpuff interval = 60 sec and inhalation volume = 25% of vital capacity). Each study also varied levels of delta 9-tetrahydro-cannabinol marijuana cigarette content (1.75% and 3.55%). Regular marijuana users served as subjects (n = 7 in each experiment). Subjects smoked 10 puffs in each of six sessions; a seventh, nonsmoking session (all measures recorded at the same times as in active smoking sessions) served as a control. Variations in puff volume produced significant dose-related changes in postsmoking plasma delta 9-tetrahydro-cannabinol levels, carbon monoxide boost and subjective effects (e.g., "high"). In contrast, breathholding for 10 or 20 sec versus 0 sec increased plasma delta 9-tetrahydro-cannabinol levels but not CO boost or subjective effects. Task performance measures were not reliably influenced by marijuana smoke exposure within the dosing ranges examined. These findings confirm the utility of the controlled smoking technology, support the notion that cumulative puff volume systematically influences biological exposure and subjective effects, but cast doubt on the common belief that prolonged breathholding of marijuana smoke enhances classical subjective effects associated with its reinforcing value in humans.

  5. Student throughput variables and properties: Varying cohort sizes

    Directory of Open Access Journals (Sweden)

    Lucas C.A. Stoop

    2017-11-01

    Full Text Available A recent research paper described how student throughput variables and properties combine to explain the behaviour of stationary or simplified throughput systems. Such behaviour can be understood in terms of the locus of a point in the triangular admissible region of the H-S plane, where H represents headcounts and S successful credits, each depending on the system properties at that point. The efficiency of the student throughput process is given by the ratio S/H. Simplified throughput systems are characterised by stationary graduation and dropout patterns of students as well as by annual intakes of student cohorts of equal size. The effect of varying the size of the annual intakes of student cohorts is reported on here. The observations made lead to the establishment of a more generalised student throughput theory which includes the simplified theory as a special case. The generalised theory still retains the notion of a triangular admissible region in the H-S plane but with the size and shape of the triangle depending on the size of the student cohorts. The ratio S/H again emerges as the process efficiency measure for throughput systems in general with unchanged roles assigned to important system properties. This theory provides for a more fundamental understanding of student throughput systems encountered in real life. Significance: A generalised stationary student throughput theory through varying cohort sizes allows for a far better understanding of real student throughput systems.

  6. Tolerable Time-Varying Overflow on Grass-Covered Slopes

    Directory of Open Access Journals (Sweden)

    Steven A. Hughes

    2015-03-01

    Full Text Available Engineers require estimates of tolerable overtopping limits for grass-covered levees, dikes, and embankments that might experience steady overflow. Realistic tolerance estimates can be used for both resilient design and risk assessment. A simple framework is developed for estimating tolerable overtopping on grass-covered slopes caused by slowly-varying (in time overtopping discharge (e.g., events like storm surges or river flood waves. The framework adapts the well-known Hewlett curves of tolerable limiting velocity as a function of overflow duration. It has been hypothesized that the form of the Hewlett curves suggests that the grass erosion process is governed by the flow work on the slope above a critical threshold velocity (referred to as excess work, and the tolerable erosional limit is reached when the cumulative excess work exceeds a given value determined from the time-dependent Hewlett curves. The cumulative excess work is expressed in terms of overflow discharge above a critical discharge that slowly varies in time, similar to a discharge hydrograph. The methodology is easily applied using forecast storm surge hydrographs at specific locations where wave action is minimal. For preliminary planning purposes, when storm surge hydrographs are unavailable, hypothetical equations for the water level and overflow discharge hydrographs are proposed in terms of the values at maximum overflow and the total duration of overflow. An example application is given to illustrate use of the methodology.

  7. Slowly varying dilaton cosmologies and their field theory duals

    International Nuclear Information System (INIS)

    Awad, Adel; Das, Sumit R.; Ghosh, Archisman; Oh, Jae-Hyuk; Trivedi, Sandip P.

    2009-01-01

    We consider a deformation of the AdS 5 xS 5 solution of IIB supergravity obtained by taking the boundary value of the dilaton to be time dependent. The time dependence is taken to be slowly varying on the anti-de Sitter (AdS) scale thereby introducing a small parameter ε. The boundary dilaton has a profile which asymptotes to a constant in the far past and future and attains a minimum value at intermediate times. We construct the supergravity (sugra) solution to first nontrivial order in ε, and find that it is smooth, horizon-free, and asymptotically AdS 5 xS 5 in the far future. When the intermediate values of the dilaton becomes small enough the curvature becomes of order the string scale and the sugra approximation breaks down. The resulting dynamics is analyzed in the dual SU(N) gauge theory on S 3 with a time dependent coupling constant which varies slowly. When Nε 5 xS 5 again. When Nε>>1, we formulate a classical adiabatic perturbation theory based on coherent states which arises in the large N limit. For large values of the 't Hooft coupling this reproduces the supergravity results. For small 't Hooft coupling the coherent state calculations become involved and we cannot reach a definite conclusion. We argue that the final state should have a dual description which is mostly smooth AdS 5 space with the possible presence of a small black hole.

  8. Plant Mating Systems Often Vary Widely Among Populations

    Directory of Open Access Journals (Sweden)

    Michael R. Whitehead

    2018-04-01

    Full Text Available Most flowering plants are hermaphroditic, yet the proportion of seeds fertilized by self and outcross pollen varies widely among species, ranging from predominant self-fertilization to exclusive outcrossing. A population's rate of outcrossing has important evolutionary outcomes as it influences genetic structure, effective population size, and offspring fitness. Because most mating system studies have quantified outcrossing rates for just one or two populations, past reviews of mating system diversity have not been able to characterize the extent of variation among populations. Here we present a new database of more than 30 years of mating system studies that report outcrossing rates for three or more populations per species. This survey, which includes 741 populations from 105 species, illustrates substantial and prevalent among-population variation in the mating system. Intermediate outcrossing rates (mixed mating are common; 63% of species had at least one mixed mating population. The variance among populations and within species was not significantly correlated with pollination mode or phylogeny. Our review underscores the need for studies exploring variation in the relative influence of ecological and genetic factors on the mating system, and how this varies among populations. We conclude that estimates of outcrossing rates from single populations are often highly unreliable indicators of the mating system of an entire species.

  9. Study of selected phenotype switching strategies in time varying environment

    Energy Technology Data Exchange (ETDEWEB)

    Horvath, Denis, E-mail: horvath.denis@gmail.com [Centre of Interdisciplinary Biosciences, Institute of Physics, Faculty of Science, P.J. Šafárik University in Košice, Jesenná 5, 040 01 Košice (Slovakia); Brutovsky, Branislav, E-mail: branislav.brutovsky@upjs.sk [Department of Biophysics, Institute of Physics, P.J. Šafárik University in Košice, Jesenná 5, 040 01 Košice (Slovakia)

    2016-03-22

    Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback–Leibler functional distances and the Hamming distance. - Highlights: • Relation between phenotype switching and environment is studied. • The Markov chain Monte Carlo based model is developed. • Stochastic and deterministic strategies of phenotype switching are utilized. • Statistical measures of the dynamic heterogeneity reveal universal properties. • The results extend to higher lattice dimensions.

  10. Study of selected phenotype switching strategies in time varying environment

    International Nuclear Information System (INIS)

    Horvath, Denis; Brutovsky, Branislav

    2016-01-01

    Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback–Leibler functional distances and the Hamming distance. - Highlights: • Relation between phenotype switching and environment is studied. • The Markov chain Monte Carlo based model is developed. • Stochastic and deterministic strategies of phenotype switching are utilized. • Statistical measures of the dynamic heterogeneity reveal universal properties. • The results extend to higher lattice dimensions.

  11. Quantum Capacity under Adversarial Quantum Noise: Arbitrarily Varying Quantum Channels

    Science.gov (United States)

    Ahlswede, Rudolf; Bjelaković, Igor; Boche, Holger; Nötzel, Janis

    2013-01-01

    We investigate entanglement transmission over an unknown channel in the presence of a third party (called the adversary), which is enabled to choose the channel from a given set of memoryless but non-stationary channels without informing the legitimate sender and receiver about the particular choice that he made. This channel model is called an arbitrarily varying quantum channel (AVQC). We derive a quantum version of Ahlswede's dichotomy for classical arbitrarily varying channels. This includes a regularized formula for the common randomness-assisted capacity for entanglement transmission of an AVQC. Quite surprisingly and in contrast to the classical analog of the problem involving the maximal and average error probability, we find that the capacity for entanglement transmission of an AVQC always equals its strong subspace transmission capacity. These results are accompanied by different notions of symmetrizability (zero-capacity conditions) as well as by conditions for an AVQC to have a capacity described by a single-letter formula. In the final part of the paper the capacity of the erasure-AVQC is computed and some light shed on the connection between AVQCs and zero-error capacities. Additionally, we show by entirely elementary and operational arguments motivated by the theory of AVQCs that the quantum, classical, and entanglement-assisted zero-error capacities of quantum channels are generically zero and are discontinuous at every positivity point.

  12. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

    Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

  13. Neutron fluctuations in a medium randomly varying in time

    Energy Technology Data Exchange (ETDEWEB)

    Lenard, Pal [KFKI Atomic Energy Research Institute, Budapest (Hungary); Imre, Pazsit [Chalmers Univ. of Technology, Dept. of Nuclear Engineering, SE, Goteborg (Sweden)

    2005-07-01

    The master equation approach, which has traditionally been used for the calculation of neutron fluctuations in zero power systems with constant parameters, is extended to a case when the parameters of the system change randomly in time. We consider a forward type master equation for the probability distribution of the number of particles in a multiplying system whose properties jump randomly between two discrete states, both with and without an external source. The first two factorial moments are calculated, including the covariance. This model can be considered the unification of stochastic methods that were used either in a constant multiplying medium via the master equation technique, or in a fluctuating medium via the Langevin technique. In contrast to these methods, the one presented here can calculate the inherent noise in time-varying systems. The results obtained show a much richer characteristics of the zero power noise than that in constant systems. Even the concept of criticality has to be given a probabilistic interpretation. The asymptotic behaviour of the variance will be also qualitatively different from that in constant systems. The covariance of the neutron number in a subcritical system with a source, and the corresponding power spectrum, shows both the inherent and parametrically induced noise components. The results are relevant in medium power subcritical systems where the zero power noise is still significant, but they also have a bearing on all types of branching processes, such as evolution of biological systems, spreading of epidemics etc., which are set in a time-varying environment. (authors)

  14. Neutron fluctuations in a medium randomly varying in time

    International Nuclear Information System (INIS)

    Lenard, Pal; Imre, Pazsit

    2005-01-01

    The master equation approach, which has traditionally been used for the calculation of neutron fluctuations in zero power systems with constant parameters, is extended to a case when the parameters of the system change randomly in time. We consider a forward type master equation for the probability distribution of the number of particles in a multiplying system whose properties jump randomly between two discrete states, both with and without an external source. The first two factorial moments are calculated, including the covariance. This model can be considered the unification of stochastic methods that were used either in a constant multiplying medium via the master equation technique, or in a fluctuating medium via the Langevin technique. In contrast to these methods, the one presented here can calculate the inherent noise in time-varying systems. The results obtained show a much richer characteristics of the zero power noise than that in constant systems. Even the concept of criticality has to be given a probabilistic interpretation. The asymptotic behaviour of the variance will be also qualitatively different from that in constant systems. The covariance of the neutron number in a subcritical system with a source, and the corresponding power spectrum, shows both the inherent and parametrically induced noise components. The results are relevant in medium power subcritical systems where the zero power noise is still significant, but they also have a bearing on all types of branching processes, such as evolution of biological systems, spreading of epidemics etc., which are set in a time-varying environment. (authors)

  15. Wave scattering by an axisymmetric ice floe of varying thickness

    Science.gov (United States)

    Bennetts, Luke G.; Biggs, Nicholas R. T.; Porter, David

    2009-04-01

    The problem of water wave scattering by a circular ice floe, floating in fluid of finite depth, is formulated and solved numerically. Unlike previous investigations of such situations, here we allow the thickness of the floe (and the fluid depth) to vary axisymmetrically and also incorporate a realistic non-zero draught. A numerical approximation to the solution of this problem is obtained to an arbitrary degree of accuracy by combining a Rayleigh-Ritz approximation of the vertical motion with an appropriate variational principle. This numerical solution procedure builds upon the work of Bennets et al. (2007, J. Fluid Mech., 579, 413-443). As part of the numerical formulation, we utilize a Fourier cosine expansion of the azimuthal motion, resulting in a system of ordinary differential equations to solve in the radial coordinate for each azimuthal mode. The displayed results concentrate on the response of the floe rather than the scattered wave field and show that the effects of introducing the new features of varying floe thickness and a realistic draught are significant.

  16. Soil erosion under multiple time-varying rainfall events

    Science.gov (United States)

    Heng, B. C. Peter; Barry, D. Andrew; Jomaa, Seifeddine; Sander, Graham C.

    2010-05-01

    Soil erosion is a function of many factors and process interactions. An erosion event produces changes in surface soil properties such as texture and hydraulic conductivity. These changes in turn alter the erosion response to subsequent events. Laboratory-scale soil erosion studies have typically focused on single independent rainfall events with constant rainfall intensities. This study investigates the effect of multiple time-varying rainfall events on soil erosion using the EPFL erosion flume. The rainfall simulator comprises ten Veejet nozzles mounted on oscillating bars 3 m above a 6 m × 2 m flume. Spray from the nozzles is applied onto the soil surface in sweeps; rainfall intensity is thus controlled by varying the sweeping frequency. Freshly-prepared soil with a uniform slope was subjected to five rainfall events at daily intervals. In each 3-h event, rainfall intensity was ramped up linearly to a maximum of 60 mm/h and then stepped down to zero. Runoff samples were collected and analysed for particle size distribution (PSD) as well as total sediment concentration. We investigate whether there is a hysteretic relationship between sediment concentration and discharge within each event and how this relationship changes from event to event. Trends in the PSD of the eroded sediment are discussed and correlated with changes in sediment concentration. Close-up imagery of the soil surface following each event highlight changes in surface soil structure with time. This study enhances our understanding of erosion processes in the field, with corresponding implications for soil erosion modelling.

  17. Flexible Demand Management under Time-Varying Prices

    Science.gov (United States)

    Liang, Yong

    In this dissertation, the problem of flexible demand management under time-varying prices is studied. This generic problem has many applications, which usually have multiple periods in which decisions on satisfying demand need to be made, and prices in these periods are time-varying. Examples of such applications include multi-period procurement problem, operating room scheduling, and user-end demand scheduling in the Smart Grid, where the last application is used as the main motivating story throughout the dissertation. The current grid is experiencing an upgrade with lots of new designs. What is of particular interest is the idea of passing time-varying prices that reflect electricity market conditions to end users as incentives for load shifting. One key component, consequently, is the demand management system at the user-end. The objective of the system is to find the optimal trade-off between cost saving and discomfort increment resulted from load shifting. In this dissertation, we approach this problem from the following aspects: (1) construct a generic model, solve for Pareto optimal solutions, and analyze the robust solution that optimizes the worst-case payoffs, (2) extend to a distribution-free model for multiple types of demand (appliances), for which an approximate dynamic programming (ADP) approach is developed, and (3) design other efficient algorithms for practical purposes of the flexible demand management system. We first construct a novel multi-objective flexible demand management model, in which there are a finite number of periods with time-varying prices, and demand arrives in each period. In each period, the decision maker chooses to either satisfy or defer outstanding demand to minimize costs and discomfort over a certain number of periods. We consider both the deterministic model, models with stochastic demand or prices, and when only partial information about the stochastic demand or prices is known. We first analyze the stochastic

  18. Gene expression and gene therapy imaging

    International Nuclear Information System (INIS)

    Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

    2007-01-01

    The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

  19. Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions.

    Science.gov (United States)

    Song, Li; Prince, Silvas; Valliyodan, Babu; Joshi, Trupti; Maldonado dos Santos, Joao V; Wang, Jiaojiao; Lin, Li; Wan, Jinrong; Wang, Yongqin; Xu, Dong; Nguyen, Henry T

    2016-01-15

    Soybean is a major crop that provides an important source of protein and oil to humans and animals, but its production can be dramatically decreased by the occurrence of drought stress. Soybeans can survive drought stress if there is a robust and deep root system at the early vegetative growth stage. However, little is known about the genome-wide molecular mechanisms contributing to soybean root system architecture. This study was performed to gain knowledge on transcriptome changes and related molecular mechanisms contributing to soybean root development under water limited conditions. The soybean Williams 82 genotype was subjected to very mild stress (VMS), mild stress (MS) and severe stress (SS) conditions, as well as recovery from the severe stress after re-watering (SR). In total, 6,609 genes in the roots showed differential expression patterns in response to different water-deficit stress levels. Genes involved in hormone (Auxin/Ethylene), carbohydrate, and cell wall-related metabolism (XTH/lipid/flavonoids/lignin) pathways were differentially regulated in the soybean root system. Several transcription factors (TFs) regulating root growth and responses under varying water-deficit conditions were identified and the expression patterns of six TFs were found to be common across the stress levels. Further analysis on the whole plant level led to the finding of tissue-specific or water-deficit levels specific regulation of transcription factors. Analysis of the over-represented motif of different gene groups revealed several new cis-elements associated with different levels of water deficit. The expression patterns of 18 genes were confirmed byquantitative reverse transcription polymerase chain reaction method and demonstrated the accuracy and effectiveness of RNA-Seq. The primary root specific transcriptome in soybean can enable a better understanding of the root response to water deficit conditions. The genes detected in root tissues that were associated with

  20. Imaging reporter gene for monitoring gene therapy

    International Nuclear Information System (INIS)

    Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

    2002-01-01

    Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

  1. Multivariate Option Pricing with Time Varying Volatility and Correlations

    DEFF Research Database (Denmark)

    Rombouts, Jeroen V.K.; Stentoft, Lars Peter

    In recent years multivariate models for asset returns have received much attention, in particular this is the case for models with time varying volatility. In this paper we consider models of this class and examine their potential when it comes to option pricing. Specifically, we derive the risk...... neutral dynamics for a general class of multivariate heteroskedastic models, and we provide a feasible way to price options in this framework. Our framework can be used irrespective of the assumed underlying distribution and dynamics, and it nests several important special cases. We provide an application...... to options on the minimum of two indices. Our results show that not only is correlation important for these options but so is allowing this correlation to be dynamic. Moreover, we show that for the general model exposure to correlation risk carries an important premium, and when this is neglected option...

  2. Spall Strength Measurements of Concrete for Varying Aggregate Sizes

    International Nuclear Information System (INIS)

    Chhabildas, Lalit C.; Kipp, Marlin E.; Reinhart, William D.; Wilson, Leonard T.

    1999-01-01

    Controlled impact experiments have been performed to determine the spall strength of four different concrete compositions. The four concrete compositions are identified as, 'SAC-5, CSPC', (''3/4'') large, and (''3/8'') small, Aggregate. They differ primarily in aggregate size but with average densities varying by less than five percent. Wave profiles from sixteen experiments, with shock amplitudes of 0.07 to 0.55 GPa, concentrate primarily within the elastic regime. Free-surface particle velocity measurements indicate consistent pullback signals in the release profiles, denoting average span strength of approximately 40 MPa. It is the purpose of this paper to present spall measurements under uniaxial strain loading. Notwithstanding considerable wave structure that is a unique characteristic to the heterogeneous nature of the scaled concrete, the spall amplitudes appear reproducible and consistent over the pressure range reported in this study

  3. Time-varying Capital Requirements and Disclosure Rules

    DEFF Research Database (Denmark)

    Kragh, Jonas; Rangvid, Jesper

    , implying that resilience in the banking system is also increased. The increase in capital ratios is partly due to a modest reduction in lending. Using a policy changes, we show that banks react stronger to changes in capital requirements when these are public. Our results further suggest that the impact......Unique and confidential Danish data allow us to identify how changes in disclosure requirements and bank-specific time-varying capital requirements affect banks' lending and capital accumu-lation decisions. We find that banks increase their capital ratios after capital requirements are increased...... of capital requirements differ for small and large banks. Large banks raise their capital ratios more, reduce lending less, and accumulate more new capital compared to small banks....

  4. Systems and methods of varying charged particle beam spot size

    Science.gov (United States)

    Chen, Yu-Jiuan

    2014-09-02

    Methods and devices enable shaping of a charged particle beam. A modified dielectric wall accelerator includes a high gradient lens section and a main section. The high gradient lens section can be dynamically adjusted to establish the desired electric fields to minimize undesirable transverse defocusing fields at the entrance to the dielectric wall accelerator. Once a baseline setting with desirable output beam characteristic is established, the output beam can be dynamically modified to vary the output beam characteristics. The output beam can be modified by slightly adjusting the electric fields established across different sections of the modified dielectric wall accelerator. Additional control over the shape of the output beam can be excreted by introducing intentional timing de-synchronization offsets and producing an injected beam that is not fully matched to the entrance of the modified dielectric accelerator.

  5. Epidemic spreading in time-varying community networks

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Guangming, E-mail: wangxy@dlut.edu.cn, E-mail: ren-guang-ming@163.com [School of Electronic and Information, Guangdong Polytechnic Normal University, Guangzhou 510665 (China); Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024 (China); Wang, Xingyuan, E-mail: wangxy@dlut.edu.cn, E-mail: ren-guang-ming@163.com [Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024 (China)

    2014-06-15

    The spreading processes of many infectious diseases have comparable time scale as the network evolution. Here, we present a simple networks model with time-varying community structure, and investigate susceptible-infected-susceptible epidemic spreading processes in this model. By both theoretic analysis and numerical simulations, we show that the efficiency of epidemic spreading in this model depends intensively on the mobility rate q of the individuals among communities. We also find that there exists a mobility rate threshold q{sub c}. The epidemic will survive when q > q{sub c} and die when q < q{sub c}. These results can help understanding the impacts of human travel on the epidemic spreading in complex networks with community structure.

  6. Time-varying risk aversion. An application to energy hedging

    Energy Technology Data Exchange (ETDEWEB)

    Cotter, John [Centre for Financial Markets, School of Business, University College Dublin, Blackrock, Co. Dublin (Ireland); Hanly, Jim [School of Accounting and Finance, Dublin Institute of Technology, Dublin 2 (Ireland)

    2010-03-15

    Risk aversion is a key element of utility maximizing hedge strategies; however, it has typically been assigned an arbitrary value in the literature. This paper instead applies a GARCH-in-Mean (GARCH-M) model to estimate a time-varying measure of risk aversion that is based on the observed risk preferences of energy hedging market participants. The resulting estimates are applied to derive explicit risk aversion based optimal hedge strategies for both short and long hedgers. Out-of-sample results are also presented based on a unique approach that allows us to forecast risk aversion, thereby estimating hedge strategies that address the potential future needs of energy hedgers. We find that the risk aversion based hedges differ significantly from simpler OLS hedges. When implemented in-sample, risk aversion hedges for short hedgers outperform the OLS hedge ratio in a utility based comparison. (author)

  7. Endogenous time-varying risk aversion and asset returns.

    Science.gov (United States)

    Berardi, Michele

    2016-01-01

    Stylized facts about statistical properties for short horizon returns in financial markets have been identified in the literature, but a satisfactory understanding for their manifestation is yet to be achieved. In this work, we show that a simple asset pricing model with representative agent is able to generate time series of returns that replicate such stylized facts if the risk aversion coefficient is allowed to change endogenously over time in response to unexpected excess returns under evolutionary forces. The same model, under constant risk aversion, would instead generate returns that are essentially Gaussian. We conclude that an endogenous time-varying risk aversion represents a very parsimonious way to make the model match real data on key statistical properties, and therefore deserves careful consideration from economists and practitioners alike.

  8. Time-varying risk aversion. An application to energy hedging

    International Nuclear Information System (INIS)

    Cotter, John; Hanly, Jim

    2010-01-01

    Risk aversion is a key element of utility maximizing hedge strategies; however, it has typically been assigned an arbitrary value in the literature. This paper instead applies a GARCH-in-Mean (GARCH-M) model to estimate a time-varying measure of risk aversion that is based on the observed risk preferences of energy hedging market participants. The resulting estimates are applied to derive explicit risk aversion based optimal hedge strategies for both short and long hedgers. Out-of-sample results are also presented based on a unique approach that allows us to forecast risk aversion, thereby estimating hedge strategies that address the potential future needs of energy hedgers. We find that the risk aversion based hedges differ significantly from simpler OLS hedges. When implemented in-sample, risk aversion hedges for short hedgers outperform the OLS hedge ratio in a utility based comparison. (author)

  9. Network Coded Cooperation Over Time-Varying Channels

    DEFF Research Database (Denmark)

    Khamfroush, Hana; Roetter, Daniel Enrique Lucani; Barros, João

    2014-01-01

    transmissions, e.g., in terms of the rate of packet transmission or the energy consumption. A comprehensive analysis of the MDP solution is carried out under different network conditions to extract optimal rules of packet transmission. Inspired by the extracted rules, we propose two near-optimal heuristics......In this paper, we investigate the optimal design of cooperative network-coded strategies for a three-node wireless network with time-varying, half-duplex erasure channels. To this end, we formulate the problem of minimizing the total cost of transmitting M packets from source to two receivers...... as a Markov Decision Process (MDP). The actions of the MDP model include the source and the type of transmission to be used in a given time slot given perfect knowledge of the system state. The cost of packet transmission is defined such that it can incorporate the difference between broadcast and unicast...

  10. Conditional CAPM: Time-varying Betas in the Brazilian Market

    Directory of Open Access Journals (Sweden)

    Frances Fischberg Blank

    2014-10-01

    Full Text Available The conditional CAPM is characterized by time-varying market beta. Based on state-space models approach, beta behavior can be modeled as a stochastic process dependent on conditioning variables related to business cycle and estimated using Kalman filter. This paper studies alternative models for portfolios sorted by size and book-to-market ratio in the Brazilian stock market and compares their adjustment to data. Asset pricing tests based on time-series and cross-sectional approaches are also implemented. A random walk process combined with conditioning variables is the preferred model, reducing pricing errors compared to unconditional CAPM, but the errors are still significant. Cross-sectional test show that book-to-market ratio becomes less relevant, but past returns still capture cross-section variation

  11. Pulsar spin down and cosmologies with varying gravity

    International Nuclear Information System (INIS)

    Mansfield, V.N.

    1976-01-01

    Reference is made to the measured spin down of the pulsar JP1953 and it is stated that this conflicts with conclusions concerning cosmologies having weakening gravity. An explanation is also given for the lack of long period pulsars in terms of group theory cosmologies with strengthening gravity. The implications of Dirac's large number hypothesis are considered, including possibilities for the implied continuous creation of matter, both 'additive creation' in which nucleons are created uniformly throughout space and 'multiplicative creation' in which matter is created where it already exists in proportion to the amount existing. Malin's suggestion (Phys. Rev. D9:3228 (1974)) that the mass of all particles varies inversely as the four-dimensional radius of curvature of the universe is also considered. (U.K.)

  12. Controlling Electricity Consumption by Forecasting its Response to Varying Prices

    DEFF Research Database (Denmark)

    Corradi, Olivier; Ochsenfeld, Henning Peter; Madsen, Henrik

    2013-01-01

    electricity consumption using a one-way price signal. Estimation of the price-response is based on data measurable at grid level, removing the need to install sensors and communication devices between each individual consumer and the price-generating entity. An application for price-responsive heating systems......In a real-time electricity pricing context where consumers are sensitive to varying prices, having the ability to anticipate their response to a price change is valuable. This paper proposes models for the dynamics of such price-response, and shows how these dynamics can be used to control...... is studied based on real data, before conducting a control by price experiment using a mixture of real and synthetic data. With the control objective of following a constant consumption reference, peak heating consumption is reduced by nearly 5%, and 11% of the mean daily heating consumption is shifted....

  13. Acute phase response to surgery of varying intensity in horses

    DEFF Research Database (Denmark)

    Jacobsen, Stine; Nielsen, Jon Vedding; Kjelgaard-Hansen, Mads

    2009-01-01

    OBJECTIVE: To evaluate the postoperative inflammatory response of horses to elective surgery of varying intensity. STUDY DESIGN: Prospective longitudinal study. ANIMALS: Horses referred to 2 hospitals for either arthroscopic removal of a unilateral osteochondritic lesion in the tibiotarsal joint...... (minimal surgical trauma, n=11), correction of recurrent laryngeal neuropathy by laryngoplasty and ventriculectomy (intermediate surgical trauma, n=10) or removal of an ovarian tumor by laparotomy (major surgical trauma, n=5). METHODS: Horses had a thorough clinical examination every day. White blood cell....... RESULTS: Postoperative concentrations of SAA and fibrinogen were significantly higher in horses that had laparotomy and ovariectomy than in horses that had laryngoplasty and ventriculectomy, or arthroscopy. Iron concentrations decreased to lower levels after intermediate and major surgical trauma than...

  14. Renormalization group theory for percolation in time-varying networks.

    Science.gov (United States)

    Karschau, Jens; Zimmerling, Marco; Friedrich, Benjamin M

    2018-05-22

    Motivated by multi-hop communication in unreliable wireless networks, we present a percolation theory for time-varying networks. We develop a renormalization group theory for a prototypical network on a regular grid, where individual links switch stochastically between active and inactive states. The question whether a given source node can communicate with a destination node along paths of active links is equivalent to a percolation problem. Our theory maps the temporal existence of multi-hop paths on an effective two-state Markov process. We show analytically how this Markov process converges towards a memoryless Bernoulli process as the hop distance between source and destination node increases. Our work extends classical percolation theory to the dynamic case and elucidates temporal correlations of message losses. Quantification of temporal correlations has implications for the design of wireless communication and control protocols, e.g. in cyber-physical systems such as self-organized swarms of drones or smart traffic networks.

  15. Hybrid Percolation Transition in Cluster Merging Processes: Continuously Varying Exponents

    Science.gov (United States)

    Cho, Y. S.; Lee, J. S.; Herrmann, H. J.; Kahng, B.

    2016-01-01

    Consider growing a network, in which every new connection is made between two disconnected nodes. At least one node is chosen randomly from a subset consisting of g fraction of the entire population in the smallest clusters. Here we show that this simple strategy for improving connection exhibits a more unusual phase transition, namely a hybrid percolation transition exhibiting the properties of both first-order and second-order phase transitions. The cluster size distribution of finite clusters at a transition point exhibits power-law behavior with a continuously varying exponent τ in the range 2 power-law behavior of the avalanche size distribution arising in models with link-deleting processes in interdependent networks.

  16. On generalized scaling laws with continuously varying exponents

    International Nuclear Information System (INIS)

    Sittler, Lionel; Hinrichsen, Haye

    2002-01-01

    Many physical systems share the property of scale invariance. Most of them show ordinary power-law scaling, where quantities can be expressed as a leading power law times a scaling function which depends on scaling-invariant ratios of the parameters. However, some systems do not obey power-law scaling, instead there is numerical evidence for a logarithmic scaling form, in which the scaling function depends on ratios of the logarithms of the parameters. Based on previous ideas by Tang we propose that this type of logarithmic scaling can be explained by a concept of local scaling invariance with continuously varying exponents. The functional dependence of the exponents is constrained by a homomorphism which can be expressed as a set of partial differential equations. Solving these equations we obtain logarithmic scaling as a special case. The other solutions lead to scaling forms where logarithmic and power-law scaling are mixed

  17. Superheated emulsions in neutron spectrometry by varying ambient pressure

    International Nuclear Information System (INIS)

    Das, Mala; Sawamura, Teruko

    2005-01-01

    The principle of present work lies on the dependence of the threshold neutron energy on the dimensionless quantity ''degree of metastability (ss)'' of superheated liquids. The response of the superheated emulsions consists of the drops of superheated liquid (C 2 Cl 2 F 4 , b.p. 3.77 deg. C) has been measured at different 'ss' by varying ambient pressure at different temperatures, in the presence of neutrons generated in Pb by a (γ,n) reaction from 45 MeV electron LINAC of Hokkaido University. To unfold the neutron energy spectrum, a relationship has been developed between the 'ss' of superheated liquids and the threshold neutron energy. The spectrum at the detector position has been calculated by the MCNP code and a comparison has been made with the experimental spectrum. The utilisation of 'ss' is more flexible as this relation can be applied to both positive and negative ambient pressures as well as at different ambient temperatures

  18. Cold fission description with constant and varying mass asymmetries

    International Nuclear Information System (INIS)

    Duarte, S.B.; Rodriguez, O.; Tavares, O.A.P.; Goncalves, M.; Garcia, F.; Guzman, F.

    1998-01-01

    Different description for varying the mass asymmetry in the fragmentation process are used to calculate the cold fission barrier penetrability. The relevance of the appropriate choice for both the description of the pre-scission phase and inertia coefficient to unify alpha decay, cluster radioactivity, and spontaneous cold fission processes in the same theoretical framework is explicitly shown. We calculate the half-life of all possible partition modes of nuclei of A > 200 following the most recent Mass Table by Audi and Wapstra. It is shown that if one uses the description in which the mass asymmetry is maintained constant during the fragmentation process, the experimental half-life-values and mass yield of 234 U cold fission are satisfactorily reproduced. (author)

  19. Motor skills under varied gravitoinertial force in parabolic flight

    Science.gov (United States)

    Ross, Helen E.

    Parabolic flight produces brief alternating periods of high and low gravitoinertial force. Subjects were tested on various paper-and-pencil aiming and tapping tasks during both normal and varied gravity in flight. It was found that changes in g level caused directional errors in the z body axis (the gravity axis), the arm aiming too high under 0g and too low under 2g. The standard deviation also increased for both vertical and lateral movements in the mid-frontal plane. Both variable and directional errors were greater under 0g than 2g. In an unpaced reciprocal tapping task subjects tended to increase their error rate rather than their movement time, but showed a non-significant trend towards slower speeds under 0g for all movement orientations. Larger variable errors or slower speeds were probably due to the difficulty of re-organising a motor skill in an unfamiliar force environment, combined with anchorage difficulties under 0g.

  20. Explicit analytical solution of a pendulum with periodically varying length

    International Nuclear Information System (INIS)

    Yang Tianzhi; Fang Bo; Li Song; Huang Wenhu

    2010-01-01

    A pendulum with periodically varying length is an interesting physical system. It has been studied by some researchers using traditional perturbation methods (for example, the averaging method). But due to the limitation of the conventional perturbation methods, the solutions are not valid for long-term prediction of the pendulum. In this paper, we use the homotopy analysis method to explore the approximate solution to this system. The method can easily self-adjust and control the convergence region. By applying the method to the governing equation of the pendulum, we obtain the approximation solution in a closed form. It is shown by the numerical method that the homotopy analysis method supplies a more accurate analytical solution for predicting the long-term behaviour of the pendulum. We believe that this system may be a good example for undergraduate and graduate students for better understanding of nonlinear oscillations.

  1. Time-varying vector fields and their flows

    CERN Document Server

    Jafarpour, Saber

    2014-01-01

    This short book provides a comprehensive and unified treatment of time-varying vector fields under a variety of regularity hypotheses, namely finitely differentiable, Lipschitz, smooth, holomorphic, and real analytic. The presentation of this material in the real analytic setting is new, as is the manner in which the various hypotheses are unified using functional analysis. Indeed, a major contribution of the book is the coherent development of locally convex topologies for the space of real analytic sections of a vector bundle, and the development of this in a manner that relates easily to classically known topologies in, for example, the finitely differentiable and smooth cases. The tools used in this development will be of use to researchers in the area of geometric functional analysis.

  2. A Diagnostic System for Speed-Varying Motor Rotary Faults

    Directory of Open Access Journals (Sweden)

    Chwan-Lu Tseng

    2014-01-01

    Full Text Available This study proposed an intelligent rotary fault diagnostic system for motors. A sensorless rotational speed detection method and an improved dynamic structural neural network are used. Moreover, to increase the convergence speed of training, a terminal attractor method and a hybrid discriminant analysis are also adopted. The proposed method can be employed to detect the rotary frequencies of motors with varying speeds and can enhance the discrimination of motor faults. To conduct the experiments, this study used wireless sensor nodes to transmit vibration data and employed MATLAB to write codes for functional modules, including the signal processing, sensorless rotational speed estimation, neural network, and stochastic process control chart. Additionally, Visual Basic software was used to create an integrated human-machine interface. The experimental results regarding the test of equipment faults indicated that the proposed novel diagnostic system can effectively estimate rotational speeds and provide superior ability of motor fault discrimination with fast training convergence.

  3. Parametric estimation of time varying baselines in airborne interferometric SAR

    DEFF Research Database (Denmark)

    Mohr, Johan Jacob; Madsen, Søren Nørvang

    1996-01-01

    A method for estimation of time varying spatial baselines in airborne interferometric synthetic aperture radar (SAR) is described. The range and azimuth distortions between two images acquired with a non-linear baseline are derived. A parametric model of the baseline is then, in a least square...... sense, estimated from image shifts obtained by cross correlation of numerous small patches throughout the image. The method has been applied to airborne EMISAR imagery from the 1995 campaign over the Storstrommen Glacier in North East Greenland conducted by the Danish Center for Remote Sensing. This has...... reduced the baseline uncertainties from several meters to the centimeter level in a 36 km scene. Though developed for airborne SAR the method can easily be adopted to satellite data...

  4. Consumer responses to time varying prices for electricity

    International Nuclear Information System (INIS)

    Thorsnes, Paul; Williams, John; Lawson, Rob

    2012-01-01

    We report new experimental evidence of the household response to weekday differentials in peak and off-peak electricity prices. The data come from Auckland, New Zealand, where peak residential electricity consumption occurs in winter for heating. Peak/off-peak price differentials ranged over four randomly selected groups from 1.0 to 3.5. On average, there was no response except in winter. In winter, participant households reduced electricity consumption by at least 10%, took advantage of lower off-peak prices but did not respond to the peak price differentials. Response varied with house and household size, time spent away from home, and whether water was heated with electricity. - Highlights: ► Seasonal effects in winter. ► High conservation effect from information. ► Higher peak prices no effect on peak use. ► Low off-peak prices encourage less conservation off-peak.

  5. Child-Langmuir flow with periodically varying anode voltage

    International Nuclear Information System (INIS)

    Rokhlenko, A.

    2015-01-01

    Using the Lagrangian technique, we study settled Child-Langmuir flows in a one dimensional planar diodes whose anode voltages periodically vary around given positive values. Our goal is to find analytically if the average currents in these systems can exceed the famous Child-Langmuir limit found for the stationary current a long time ago. The main result of our study is that in a periodic quasi-stationary regime the average current can be larger than the Child-Langmuir maximum even by 50% compared with its adiabatic average value. The cathode current in this case has the form of rectangular pulses which are formed by a very special triangular voltage modulation. This regime, i.e., periodicity, shape of pulses, and their amplitude, needs to be carefully chosen for the best performance

  6. Epidemic spreading in time-varying community networks

    International Nuclear Information System (INIS)

    Ren, Guangming; Wang, Xingyuan

    2014-01-01

    The spreading processes of many infectious diseases have comparable time scale as the network evolution. Here, we present a simple networks model with time-varying community structure, and investigate susceptible-infected-susceptible epidemic spreading processes in this model. By both theoretic analysis and numerical simulations, we show that the efficiency of epidemic spreading in this model depends intensively on the mobility rate q of the individuals among communities. We also find that there exists a mobility rate threshold q c . The epidemic will survive when q > q c and die when q  c . These results can help understanding the impacts of human travel on the epidemic spreading in complex networks with community structure

  7. Varied definitions of risk related to sensation seeking trait

    International Nuclear Information System (INIS)

    Daastoel, P.Oe.U.; Drottz-Sjoeberg, B.M.

    1999-01-01

    This pilot study is based on the assumption and the knowledge that previous results show that the normal use of the word risk varies across subjects. The risk definitions the subjects use have also been shown to be related to various educational interests. A related field of research has developed measures for Sensation Seeking personality trait, with four facets. Three independent groups of first year psychology students reported their normal definition of the word risk using one of three measurement formats. The results showed, e.g. that the typical open-ended response to the personal definition of risk was danger. Subjects who defined risk as the combination of probability and consequences tended to score higher on the total Sensation Seeking Scale, as compared to those defining risk as the probability of an event

  8. Varied definitions of risk related to sensation seeking trait

    Energy Technology Data Exchange (ETDEWEB)

    Daastoel, P.Oe.U.; Drottz-Sjoeberg, B.M. [Norwegian Univ. of Science and Technology, Trondheim (Norway). Dept. of Psychology

    1999-12-01

    This pilot study is based on the assumption and the knowledge that previous results show that the normal use of the word risk varies across subjects. The risk definitions the subjects use have also been shown to be related to various educational interests. A related field of research has developed measures for Sensation Seeking personality trait, with four facets. Three independent groups of first year psychology students reported their normal definition of the word risk using one of three measurement formats. The results showed, e.g. that the typical open-ended response to the personal definition of risk was danger. Subjects who defined risk as the combination of probability and consequences tended to score higher on the total Sensation Seeking Scale, as compared to those defining risk as the probability of an event.

  9. Path coefficient analysis of zinc dynamics in varying soil environment

    International Nuclear Information System (INIS)

    Rattan, R.K.; Phung, C.V.; Singhal, S.K.; Deb, D.L.; Singh, A.K.

    1994-01-01

    Influence of soil properties on labile zinc, as measured by diethylene-triamine pentaacetic acid (DTPA) and zinc-65, and self-diffusion coefficients of zinc was assessed on 22 surface soil samples varying widely in their characteristics following linear regression and path coefficient analysis techniques. DTPA extractable zinc could be predicted from organic carbon status and pH of the soil with a highly significant coefficient of determination (R 2 =0.84 ** ). Ninety seven per cent variation in isotopically exchangeable zinc was explained by pH, clay content and cation exchange capacity (CEC) of soil. The self-diffusion coefficients (DaZn and DpZn) and buffer power of zinc exhibited exponential relationship with soil properties, pH being the most dominant one. Soil properties like organic matter, clay content etc. exhibited indirect effects on zinc diffusion rates via pH only. (author). 13 refs., 6 tabs

  10. Spall behavior of cast iron with varying microstructures

    International Nuclear Information System (INIS)

    Plume, Gifford; Rousseau, Carl-Ernst

    2014-01-01

    The spall strength of cast iron with varying microstructures has been investigated using plate impact at moderate speed. Stress history measurements were made with manganin stress gauges embedded between the back face of the specimen and a low impedance polycarbonate backing. Five separate cast irons were tested. Four of these consisted of gray cast iron with graphite in flake form, with three classified as Type VII A2 and the fourth containing a bimodal distribution of Types VII A4 and VII D8. The fifth casting consisted of ductile cast iron with graphite in nodular form, classified as Type I, size class 5. The spall strength for the Type VII A2 gray cast irons varied between 40 and 370 MPa, and that of the additional gray cast iron, between 410 and 490 MPa. The spall strength of the ductile cast iron fell within the range of 0.94–1.2 GPa. It is shown that the spall strength is linked to the damage level at the spall plane, where an increased level of tensile stress is required to generate higher levels of damage. Post mortem analysis was performed on the recovered samples, revealing the graphite phase to be the primary factor governing the spall fracture of cast irons, where crack nucleation is directly correlated to the debonding of graphite from the metal matrix. The average length of graphite found within a casting is linked to the material's strength, where strength increases as a function of decreasing length. The morphology and mean free path of graphite precipitates further govern the subsequent coalescence of initiated cracks to form a complete fracture plane. In cases where graphite spacing is large, increased energy level is required to complete the fracture process. A secondary factor governing the spall fracture of cast irons has also been linked to the microstructure of the metal matrix, with pearlite yielding higher spall strengths than free ferrite.

  11. Spall behavior of cast iron with varying microstructures

    Energy Technology Data Exchange (ETDEWEB)

    Plume, Gifford; Rousseau, Carl-Ernst, E-mail: rousseau@uri.edu [Mechanical Engineering, University of Rhode Island, 92 Upper College Rd., Kingston, Rhode Island 02881 (United States)

    2014-07-21

    The spall strength of cast iron with varying microstructures has been investigated using plate impact at moderate speed. Stress history measurements were made with manganin stress gauges embedded between the back face of the specimen and a low impedance polycarbonate backing. Five separate cast irons were tested. Four of these consisted of gray cast iron with graphite in flake form, with three classified as Type VII A2 and the fourth containing a bimodal distribution of Types VII A4 and VII D8. The fifth casting consisted of ductile cast iron with graphite in nodular form, classified as Type I, size class 5. The spall strength for the Type VII A2 gray cast irons varied between 40 and 370 MPa, and that of the additional gray cast iron, between 410 and 490 MPa. The spall strength of the ductile cast iron fell within the range of 0.94–1.2 GPa. It is shown that the spall strength is linked to the damage level at the spall plane, where an increased level of tensile stress is required to generate higher levels of damage. Post mortem analysis was performed on the recovered samples, revealing the graphite phase to be the primary factor governing the spall fracture of cast irons, where crack nucleation is directly correlated to the debonding of graphite from the metal matrix. The average length of graphite found within a casting is linked to the material's strength, where strength increases as a function of decreasing length. The morphology and mean free path of graphite precipitates further govern the subsequent coalescence of initiated cracks to form a complete fracture plane. In cases where graphite spacing is large, increased energy level is required to complete the fracture process. A secondary factor governing the spall fracture of cast irons has also been linked to the microstructure of the metal matrix, with pearlite yielding higher spall strengths than free ferrite.

  12. Brazilian Soybean Yields and Yield Gaps Vary with Farm Size

    Science.gov (United States)

    Jeffries, G. R.; Cohn, A.; Griffin, T. S.; Bragança, A.

    2017-12-01

    Understanding the farm size-specific characteristics of crop yields and yield gaps may help to improve yields by enabling better targeting of technical assistance and agricultural development programs. Linking remote sensing-based yield estimates with property boundaries provides a novel view of the relationship between farm size and yield structure (yield magnitude, gaps, and stability over time). A growing literature documents variations in yield gaps, but largely ignores the role of farm size as a factor shaping yield structure. Research on the inverse farm size-productivity relationship (IR) theory - that small farms are more productive than large ones all else equal - has documented that yield magnitude may vary by farm size, but has not considered other yield structure characteristics. We examined farm size - yield structure relationships for soybeans in Brazil for years 2001-2015. Using out-of-sample soybean yield predictions from a statistical model, we documented 1) gaps between the 95th percentile of attained yields and mean yields within counties and individual fields, and 2) yield stability defined as the standard deviation of time-detrended yields at given locations. We found a direct relationship between soy yields and farm size at the national level, while the strength and the sign of the relationship varied by region. Soybean yield gaps were found to be inversely related to farm size metrics, even when yields were only compared to farms of similar size. The relationship between farm size and yield stability was nonlinear, with mid-sized farms having the most stable yields. The work suggests that farm size is an important factor in understanding yield structure and that opportunities for improving soy yields in Brazil are greatest among smaller farms.

  13. Supraglacial bacterial community structures vary across the Greenland ice sheet

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Zarsky, Jakub D.

    2016-01-01

    The composition and spatial variability of microbial communities that reside within the extensive (>200 000 km(2)) biologically active area encompassing the Greenland ice sheet (GrIS) is hypothesized to be variable. We examined bacterial communities from cryoconite debris and surface ice across...... the GrIS, using sequence analysis and quantitative PCR of 16S rRNA genes from co-extracted DNA and RNA. Communities were found to differ across the ice sheet, with 82.8% of the total calculated variation attributed to spatial distribution on a scale of tens of kilometers separation. Amplicons related...... to Sphingobacteriaceae, Pseudanabaenaceae and WPS-2 accounted for the greatest portion of calculated dissimilarities. The bacterial communities of ice and cryoconite were moderately similar (global R = 0.360, P = 0.002) and the sampled surface type (ice versus cryoconite) did not contribute heavily towards community...

  14. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

    Directory of Open Access Journals (Sweden)

    Walchli John

    2009-04-01

    Full Text Available Abstract Background With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. Results In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α, viral polymerase (HCV NS5B, and bacterial structural protein (FtsZ were expressed in both E. coli and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. Conclusion The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.

  15. The Roles and Evolutionary Patterns of Intronless Genes in Deuterostomes

    Directory of Open Access Journals (Sweden)

    Ming Zou

    2011-01-01

    Full Text Available Genes without introns are a characteristic feature of prokaryotes, but there are still a number of intronless genes in eukaryotes. To study these eukaryotic genes that have prokaryotic architecture could help to understand the evolutionary patterns of related genes and genomes. Our analyses revealed a number of intronless genes that reside in 6 deuterostomes (sea urchin, sea squirt, zebrafish, chicken, platypus, and human. We also determined the conservation for each intronless gene in archaea, bacteria, fungi, plants, metazoans, and other eukaryotes. Proportions of intronless genes that are inherited from the common ancestor of archaea, bacteria, and eukaryotes in these species were consistent with their phylogenetic positions, with more proportions of ancient intronless genes residing in more primitive species. In these species, intronless genes belong to different cellular roles and gene ontology (GO categories, and some of these functions are very basic. Part of intronless genes is derived from other intronless genes or multiexon genes in each species. In conclusion, we showed that a varying number and proportion of intronless genes reside in these 6 deuterostomes, and some of them function importantly. These genes are good candidates for subsequent functional and evolutionary analyses specifically.

  16. Overview of BioCreative II gene mention recognition

    NARCIS (Netherlands)

    Smith, L.; Tanabe, L.K.; Johnson, R.; Kuo, C.-J.; Chung, I-F.; Hsu, C.-N.; Lin, Y.-S.; Klinger, R.; Friedrich, C.M.; Ganchev, K.; Torii, M.; Liu, H.; Haddow, B.; Struble, C.A.; Povinelli, R.J.; Vlachos, A.; Baumgartner (jr.), W.A.; Hunter, L.; Carpenter, B.; Tsai, R.T.-H.; Dai, H.-J.; Liu, F.; Chen, Y.; Sun, C.; Katrenko, S.; Adriaans, P.; Blaschke, C.; Torres, R.; Neves, M.; Nakov, P.; Divoli, A.; Maña-López, M.; Mata, J.; Wilbur, W.J.

    2008-01-01

    Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1

  17. Evolution of perturbation in charge-varying dusty plasmas

    International Nuclear Information System (INIS)

    Popel, S.I.; Golub, A.P.; Losseva, T.V.; Bingham, R.; Benkadda, S.

    2001-01-01

    The nonstationary problem of the evolution of perturbation and its transformation into nonlinear wave structure in dusty plasmas is considered. For this purpose two one-dimensional models based on a set of fluid equations, Poisson's equation, and a charging equation for dust are developed. The first (simplified) model corresponds to the case [Popel et al., Phys. Plasmas 3, 4313 (1996)] when exact steady-state shock wave solutions can exist. This simplified model includes variable-charged dust grains, Boltzmann electrons, and inertial ions. The second (ionization source) model takes into account the variation of the ion density and the ion momentum dissipation due to dust particle charging as well as the source of plasma particles due to ionization process. The computational method for solving the set of equations which describe the evolution in time of a nonlinear structure in a charge-varying dusty plasma is developed. The case of the evolution of an intensive initial nonmoving region with a constant enhanced ion density is investigated on the basis of these two models. The consideration within the ionization source model is performed for the data of the laboratory experiment [Luo et al., Phys. Plasmas 6, 3455 (1999)]. It is shown that the ionization source model allows one to obtain shock structures as a result of evolution of an initial perturbation and to explain the experimental value of the width of the shock wave front. Comparison of the numerical data obtained on the basis of the ionization source model and the simplified model shows that the main characteristic features of the shock structure are the same for both models. Nevertheless, the ionization source model is much more sensitive to the form of the initial perturbation than the simplified model. The solution of the problem of the evolution of perturbation and its transformation into shock wave in charge-varying dusty plasmas opens up possibilities for description of the real phenomena like supernova

  18. Gene expression results in lipopolysaccharide-stimulated monocytes depend significantly on the choice of reference genes

    Directory of Open Access Journals (Sweden)

    Øvstebø Reidun

    2010-05-01

    Full Text Available Abstract Background Gene expression in lipopolysaccharide (LPS-stimulated monocytes is mainly studied by quantitative real-time reverse transcription PCR (RT-qPCR using GAPDH (glyceraldehyde 3-phosphate dehydrogenase or ACTB (beta-actin as reference gene for normalization. Expression of traditional reference genes has been shown to vary substantially under certain conditions leading to invalid results. To investigate whether traditional reference genes are stably expressed in LPS-stimulated monocytes or if RT-qPCR results are dependent on the choice of reference genes, we have assessed and evaluated gene expression stability of twelve candidate reference genes in this model system. Results Twelve candidate reference genes were quantified by RT-qPCR in LPS-stimulated, human monocytes and evaluated using the programs geNorm, Normfinder and BestKeeper. geNorm ranked PPIB (cyclophilin B, B2M (beta-2-microglobulin and PPIA (cyclophilin A as the best combination for gene expression normalization in LPS-stimulated monocytes. Normfinder suggested TBP (TATA-box binding protein and B2M as the best combination. Compared to these combinations, normalization using GAPDH alone resulted in significantly higher changes of TNF-α (tumor necrosis factor-alpha and IL10 (interleukin 10 expression. Moreover, a significant difference in TNF-α expression between monocytes stimulated with equimolar concentrations of LPS from N. meningitides and E. coli, respectively, was identified when using the suggested combinations of reference genes for normalization, but stayed unrecognized when employing a single reference gene, ACTB or GAPDH. Conclusions Gene expression levels in LPS-stimulated monocytes based on RT-qPCR results differ significantly when normalized to a single gene or a combination of stably expressed reference genes. Proper evaluation of reference gene stabiliy is therefore mandatory before reporting RT-qPCR results in LPS-stimulated monocytes.

  19. Good genes, complementary genes and human mate preferences.

    Science.gov (United States)

    Roberts, S Craig; Little, Anthony C

    2008-09-01

    The past decade has witnessed a rapidly growing interest in the biological basis of human mate choice. Here we review recent studies that demonstrate preferences for traits which might reveal genetic quality to prospective mates, with potential but still largely unknown influence on offspring fitness. These include studies assessing visual, olfactory and auditory preferences for potential good-gene indicator traits, such as dominance or bilateral symmetry. Individual differences in these robust preferences mainly arise through within and between individual variation in condition and reproductive status. Another set of studies have revealed preferences for traits indicating complementary genes, focussing on discrimination of dissimilarity at genes in the major histocompatibility complex (MHC). As in animal studies, we are only just beginning to understand how preferences for specific traits vary and inter-relate, how consideration of good and compatible genes can lead to substantial variability in individual mate choice decisions and how preferences expressed in one sensory modality may reflect those in another. Humans may be an ideal model species in which to explore these interesting complexities.

  20. Observational constraints on holographic dark energy with varying gravitational constant

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jianbo; Xu, Lixin [Institute of Theoretical Physics, School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian, 116024 (China); Saridakis, Emmanuel N. [College of Mathematics and Physics, Chongqing University of Posts and Telecommunications, Chongqing, 400065 (China); Setare, M.R., E-mail: lvjianbo819@163.com, E-mail: msaridak@phys.uoa.gr, E-mail: rezakord@ipm.ir, E-mail: lxxu@dlut.edu.cn [Department of Science of Bijar, University of Kurdistan, Bijar (Iran, Islamic Republic of)

    2010-03-01

    We use observational data from Type Ia Supernovae (SN), Baryon Acoustic Oscillations (BAO), Cosmic Microwave Background (CMB) and observational Hubble data (OHD), and the Markov Chain Monte Carlo (MCMC) method, to constrain the cosmological scenario of holographic dark energy with varying gravitational constant. We consider both flat and non-flat background geometry, and we present the corresponding constraints and contour-plots of the model parameters. We conclude that the scenario is compatible with observations. In 1σ we find Ω{sub Λ0} = 0.72{sup +0.03}{sub −0.03}, Ω{sub k0} = −0.0013{sup +0.0130}{sub −0.0040}, c = 0.80{sup +0.19}{sub −0.14} and Δ{sub G}≡G'/G = −0.0025{sup +0.0080}{sub −0.0050}, while for the present value of the dark energy equation-of-state parameter we obtain w{sub 0} = −1.04{sup +0.15}{sub −0.20}.

  1. Temporal-varying failures of nodes in networks

    Science.gov (United States)

    Knight, Georgie; Cristadoro, Giampaolo; Altmann, Eduardo G.

    2015-08-01

    We consider networks in which random walkers are removed because of the failure of specific nodes. We interpret the rate of loss as a measure of the importance of nodes, a notion we denote as failure centrality. We show that the degree of the node is not sufficient to determine this measure and that, in a first approximation, the shortest loops through the node have to be taken into account. We propose approximations of the failure centrality which are valid for temporal-varying failures, and we dwell on the possibility of externally changing the relative importance of nodes in a given network by exploiting the interference between the loops of a node and the cycles of the temporal pattern of failures. In the limit of long failure cycles we show analytically that the escape in a node is larger than the one estimated from a stochastic failure with the same failure probability. We test our general formalism in two real-world networks (air-transportation and e-mail users) and show how communities lead to deviations from predictions for failures in hubs.

  2. A thermal model for photovoltaic panels under varying atmospheric conditions

    International Nuclear Information System (INIS)

    Armstrong, S.; Hurley, W.G.

    2010-01-01

    The response of the photovoltaic (PV) panel temperature is dynamic with respect to the changes in the incoming solar radiation. During periods of rapidly changing conditions, a steady state model of the operating temperature cannot be justified because the response time of the PV panel temperature becomes significant due to its large thermal mass. Therefore, it is of interest to determine the thermal response time of the PV panel. Previous attempts to determine the thermal response time have used indoor measurements, controlling the wind flow over the surface of the panel with fans or conducting the experiments in darkness to avoid radiative heat loss effects. In real operating conditions, the effective PV panel temperature is subjected to randomly varying ambient temperature and fluctuating wind speeds and directions; parameters that are not replicated in controlled, indoor experiments. A new thermal model is proposed that incorporates atmospheric conditions; effects of PV panel material composition and mounting structure. Experimental results are presented which verify the thermal behaviour of a photovoltaic panel for low to strong winds.

  3. Vitamin A degradation in triglycerides varying by their saturation levels.

    Science.gov (United States)

    Moccand, Cyril; Martin, Fréderic; Martiel, Isabelle; Gancel, Charlotte; Michel, Martin; Fries, Lennart; Sagalowicz, Laurent

    2016-10-01

    Vitamin A deficiency has a widespread occurrence globally and is considered as one of the world's most serious health risk factors. Potential solutions to address this deficiency include dietary diversification or supplementation, but food fortification is generally accepted as the most cost-effective solution. The main issue with food fortification of this vitamin is related to its high instability in food matrices. Dilution of vitamin A in triglycerides is a natural and appropriate way to stabilize this compound. We show here that vitamin A palmitate stability increases with increasing concentration of triglycerides. Moreover, we found that vitamin A palmitate displays improved stability in more saturated oils. Using various temperatures, and Arrhenius plots of experiments performed at storage temperatures between 30°C and 60°C for oils varying by their saturation and crystallinity, we demonstrate that crystallization is not responsible for this phenomenon. Additionally, we show by centrifugation that vitamin A is preferably solubilized in the liquid phase compared to the crystalline phase, explaining that triglyceride crystallization does not stabilize vitamin A palmitate. It is proposed that unsaturated fats generate more oxidation products such as radicals and peroxides, leading to a quicker degradation of vitamin A. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Foot and Ankle Kinematics During Descent From Varying Step Heights.

    Science.gov (United States)

    Gerstle, Emily E; O'Connor, Kristian; Keenan, Kevin G; Cobb, Stephen C

    2017-12-01

    In the general population, one-third of incidences during step negotiation occur during the transition to level walking. Furthermore, falls during curb negotiation are a common cause of injury in older adults. Distal foot kinematics may be an important factor in determining injury risk associated with transition step negotiation. The purpose of this study was to identify foot and ankle kinematics of uninjured individuals during descent from varying step heights. A 7-segment foot model was used to quantify kinematics as participants walked on a level walkway, stepped down a single step (heights: 5 cm, 15 cm, 25 cm), and continued walking. As step height increased, landing strategy transitioned from the rearfoot to the forefoot, and the rearfoot, lateral and medial midfoot, and medial forefoot became more plantar flexed. During weight acceptance, sagittal plane range of motion of the rearfoot, lateral midfoot, and medial and lateral forefoot increased as step height increased. The changes in landing strategy and distal foot function suggest a less stable ankle position at initial contact and increased demand on the distal foot at initial contact and through the weight acceptance phase of transition step negotiation as step height increases.

  5. Home visits: why do rates vary so much?

    LENUS (Irish Health Repository)

    Stewart, P

    2012-03-01

    Data including information on patient age, gender, who initiated the visit and call classification was collected during office hours from 12 G.P. rural teaching practices with a combined GMS patient population of 24,720, over a 2 month period. There were a total of 603 home visits, giving an annual visiting rate of 143\\/1000. Visiting rates varied between practices from 45 to 305\\/1000 per year. When high visiting practices (>210\\/1000\\/year) were compared to low visiting rate practices (>90\\/1000\\/year), patients tended to be older (79.7 v. 74.5 years) and calls were 12 times more likely to be doctor initiated (16.6% v. 1.4%) or classified as routine( 50.7% v. 44.9%). The variation between practices was related in part to patient age but appears largely due to differences in doctor home visiting behaviour. There are no recent figures on home visiting in Ireland.

  6. Mutagenicity potential of commercial broth cubes at varying concentrations

    International Nuclear Information System (INIS)

    De Torres, Nelson Velasquez; Talain, Augusto Nicolas.

    1997-01-01

    Today, there has been a growing concern on the mutagenicity potential of environmental chemical systems. These environmental chemicals such as pesticides, food additives, synthetic drugs, water and atmospheric pollutants are possible causes of mutagenic activity. Meat products and some meat flavorings, were also reported to exhibit mutagenic activity. And since these products are normal part of the daily human diet, there is a need for extensive studies regarding the possible mutagenic activity associated with these products. This study aimed to evaluate the mutagenicity potential of commercial broth cubes at varying concentration. The researchers sought to answer the following questions: 1. Do beef, pork and chicken broth cubes exhibit mutagenic activity? 2. Are there significant differences in the mutagenic activity among the three samples? 3. Are these significant differences in the mutagenic activity exhibited by each of the samples compared to that of Mitomycin-C (positive control)? 4. Which of the sample of each specific concentration exhibit the greatest mutagenic activity? Three specific concentrations of beef, pork and chicken broth cubes were prepared and their mutagenicity potential was evaluated by using the Micronucleus test. The formation of micro nucleated polychromatic and micro nucleated normo chromatic erythrocytes in bone marrow cells of mice treated with these samples were detected using a Carl-Zeiss photo microscope. The statistical tool used to test the validity of the null hypothesis was analysis of variance using randomized complete block design and independent T- test. (author)

  7. Mutagenicity potential of commercial broth cubes at varying concentrations

    Energy Technology Data Exchange (ETDEWEB)

    De Torres, Nelson Velasquez; Talain, Augusto Nicolas

    1998-12-31

    Today, there has been a growing concern on the mutagenicity potential of environmental chemical systems. These environmental chemicals such as pesticides, food additives, synthetic drugs, water and atmospheric pollutants are possible causes of mutagenic activity. Meat products and some meat flavorings, were also reported to exhibit mutagenic activity. And since these products are normal part of the daily human diet, there is a need for extensive studies regarding the possible mutagenic activity associated with these products. This study aimed to evaluate the mutagenicity potential of commercial broth cubes at varying concentration. The researchers sought to answer the following questions: 1. Do beef, pork and chicken broth cubes exhibit mutagenic activity? 2. Are there significant differences in the mutagenic activity among the three samples? 3. Are these significant differences in the mutagenic activity exhibited by each of the samples compared to that of Mitomycin-C (positive control)? 4. Which of the sample of each specific concentration exhibit the greatest mutagenic activity? Three specific concentrations of beef, pork and chicken broth cubes were prepared and their mutagenicity potential was evaluated by using the Micronucleus test. The formation of micro nucleated polychromatic and micro nucleated normo chromatic erythrocytes in bone marrow cells of mice treated with these samples were detected using a Carl-Zeiss photo microscope. The statistical tool used to test the validity of the null hypothesis was analysis of variance using randomized complete block design and independent T- test. (author). 28 refs., 9 figs., 26 tabs.

  8. Bioventing of gasoline-contaminated soil under varied laboratory conditions

    International Nuclear Information System (INIS)

    Hallman, M.; Shewfelt, K.; Lee, H.; Zytner, R.G.

    2002-01-01

    Bioventing is becoming a popular in situ soil remediation technology for the treatment of hydrocarbon-contaminated soil. Bioventing relies on enhancing the growth of indigenous microorganisms, which can mineralize the contaminant in the presence of sufficient nutrients. Although bioventing is currently being used as a remediation technology, there are some important questions that remain to be answered in order to optimize the process. These questions include the optimum soil moisture content, type and amount of nutrients necessary, and the best means of producing these conditions in the field. To address these questions, two distinct phases of experiments were conducted. The first experimental phase was designed to determine the optimum moisture content, C:N ratio and form of nitrogen supply for this soil. Using approximately 200g of contaminated soil in each of a series of sealed respirometers, microbial degradation of gasoline under bioventing conditions was quantified for C:N ratios of 5, 10 and 20:1, using varying mixtures of NH 4 + - and NO 3 - -N. The results of the studies indicated that the optimum soil moisture content was 15 wt%, with a C:N ratio of 10:1, using a 100% ammonium application. Using the results of the first phase, a second phase of laboratory research was initiated. Five mesoscale reactors have been developed to simulate the bioventing process that takes place in the field. These reactors are filled with approximately 4kg of gasoline-contaminated soil. The initial results are favourable. (author)

  9. Spatially varying determinants of farmland conversion across Qiantang watershed, China.

    Science.gov (United States)

    Su, Shiliang; Xiao, Rui

    2013-10-01

    This paper employed geographically weighted regression (GWR) to characterize the determinants of farmland conversion at administrative scale between 1994 and 2003 across Qiantang watershed, China. Six determinants were identified: total area of forest, distance to highway, distance to second road, distance to river, population, and gross domestic product. Relationships between these identified determinants and farmland conversion showed great spatial non-stationarity, since their character, nature, and strength varied significantly across space. Typically, for cities whose development was heavily relied on road infrastructure development, the impacts of "distance to second road" and "distance to river" was negative. However, in mountainous areas, the restriction of terrain factors led to positive impacts from these two variables. For areas undergoing rapid socio-economic development, farmland conversion was accelerated by population growth and economic development. However, for more urbanized regions, a slow-down rate of farmland conversion would be expected. Our study highlighted that the problem of spatial non-stationarity should be addressed when qualifying the determinants of farmland conversion. Linking our results within the context of farmland protection, we argue that implementing local-specific land management practices, instead of the current one-size-fits-all framework, is the key for the success of farmland protection in China.

  10. Size matters: Perceived depth magnitude varies with stimulus height.

    Science.gov (United States)

    Tsirlin, Inna; Wilcox, Laurie M; Allison, Robert S

    2016-06-01

    Both the upper and lower disparity limits for stereopsis vary with the size of the targets. Recently, Tsirlin, Wilcox, and Allison (2012) suggested that perceived depth magnitude from stereopsis might also depend on the vertical extent of a stimulus. To test this hypothesis we compared apparent depth in small discs to depth in long bars with equivalent width and disparity. We used three estimation techniques: a virtual ruler, a touch-sensor (for haptic estimates) and a disparity probe. We found that depth estimates were significantly larger for the bar stimuli than for the disc stimuli for all methods of estimation and different configurations. In a second experiment, we measured perceived depth as a function of the height of the bar and the radius of the disc. Perceived depth increased with increasing bar height and disc radius suggesting that disparity is integrated along the vertical edges. We discuss size-disparity correlation and inter-neural excitatory connections as potential mechanisms that could account for these results. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Varied line-space gratings: past, present and future

    International Nuclear Information System (INIS)

    Hettrick, M.C.

    1985-08-01

    A classically ruled diffraction grating consists of grooves which are equidistant, straight and parallel. Conversely, the so-called ''holographic'' grating (formed by the interfering waves of coherent visible light), although severely constrained by the recording wavelength and recording geometry, has grooves which are typically neither equidistant, straight nor parallel. In contrast, a varied line-space (VLS) grating, in common nomenclature, is a design in which the groove positions are relatively unconstrained yet possess sufficient symmetry to permit mechanical ruling. Such seemingly exotic gratings are no longer only a theoretical curiosity, but have been ruled and used in a wide variety of applications. These include: (1) aberration-corrected normal incidence concave gratings for Seya-Namioka monochromators and optical de-multiplexers, (2) flat-field grazing incidence concave gratings for plasma diagnostics, (3) aberration-corrected grazing incidence plane gratings for space-borne spectrometers, (4) focusing grazing incidence plane grating for synchrotron radiation monochromators, and (5) wavefront generators for visible interferometry of optical surfaces (particularly aspheres). Future prospects of VLS gratings as dispersing elements, wavefront correctors and beamsplitters appear promising. The author discusses the history of VLS gratings, their present applications, and their potential in the future. 61 refs., 24 figs

  12. Pollinator effectiveness varies with experimental shifts in flowering time.

    Science.gov (United States)

    Rafferty, Nicole E; Ives, Anthony R

    2012-04-01

    The earlier flowering times exhibited by many plant species are a conspicuous sign of climate change. Altered phenologies have caused concern that species could suffer population declines if they flower at times when effective pollinators are unavailable. For two perennial wildflowers, Tradescantia ohiensis and Asclepias incarnata, we used an experimental approach to explore how changing phenology affects the taxonomic composition of the pollinator assemblage and the effectiveness of individual pollinator taxa. After finding in the previous year that fruit set varied with flowering time, we manipulated flowering onset in greenhouses, placed plants in the field over the span of five weeks, and measured pollinator effectiveness as the number of seeds produced after a single visit to a flower. The average effectiveness of pollinators and the expected rates of pollination success were lower for plants of both species flowering earlier than for plants flowering at historical times, suggesting there could be reproductive costs to earlier flowering. Whereas for A. incarnata, differences in average seed set among weeks were due primarily to changes in the composition of the pollinator assemblage, the differences for T. ohiensis were driven by the combined effects of compositional changes and increases over time in the effectiveness of some pollinator taxa. Both species face the possibility of temporal mismatch between the availability of the most effective pollinators and the onset of flowering, and changes in the effectiveness of individual pollinator taxa through time may add an unexpected element to the reproductive consequences of such mismatches.

  13. A Novel Time-Varying Friction Compensation Method for Servomechanism

    Directory of Open Access Journals (Sweden)

    Bin Feng

    2015-01-01

    Full Text Available Friction is an inevitable nonlinear phenomenon existing in servomechanisms. Friction errors often affect their motion and contour accuracies during the reverse motion. To reduce friction errors, a novel time-varying friction compensation method is proposed to solve the problem that the traditional friction compensation methods hardly deal with. This problem leads to an unsatisfactory friction compensation performance and the motion and contour accuracies cannot be maintained effectively. In this method, a trapezoidal compensation pulse is adopted to compensate for the friction errors. A generalized regression neural network algorithm is used to generate the optimal pulse amplitude function. The optimal pulse duration function and the pulse amplitude function can be established by the pulse characteristic parameter learning and then the optimal friction compensation pulse can be generated. The feasibility of friction compensation method was verified on a high-precision X-Y worktable. The experimental results indicated that the motion and contour accuracies were improved greatly with reduction of the friction errors, in different working conditions. Moreover, the overall friction compensation performance indicators were decreased by more than 54% and this friction compensation method can be implemented easily on most of servomechanisms in industry.

  14. On the Anonymity Risk of Time-Varying User Profiles

    Directory of Open Access Journals (Sweden)

    Silvia Puglisi

    2017-04-01

    Full Text Available Websites and applications use personalisation services to profile their users, collect their patterns and activities and eventually use this data to provide tailored suggestions. User preferences and social interactions are therefore aggregated and analysed. Every time a user publishes a new post or creates a link with another entity, either another user, or some online resource, new information is added to the user profile. Exposing private data does not only reveal information about single users’ preferences, increasing their privacy risk, but can expose more about their network that single actors intended. This mechanism is self-evident in social networks where users receive suggestions based on their friends’ activities. We propose an information-theoretic approach to measure the differential update of the anonymity risk of time-varying user profiles. This expresses how privacy is affected when new content is posted and how much third-party services get to know about the users when a new activity is shared. We use actual Facebook data to show how our model can be applied to a real-world scenario.

  15. Innovation diffusion on time-varying activity driven networks

    Science.gov (United States)

    Rizzo, Alessandro; Porfiri, Maurizio

    2016-01-01

    Since its introduction in the 1960s, the theory of innovation diffusion has contributed to the advancement of several research fields, such as marketing management and consumer behavior. The 1969 seminal paper by Bass [F.M. Bass, Manag. Sci. 15, 215 (1969)] introduced a model of product growth for consumer durables, which has been extensively used to predict innovation diffusion across a range of applications. Here, we propose a novel approach to study innovation diffusion, where interactions among individuals are mediated by the dynamics of a time-varying network. Our approach is based on the Bass' model, and overcomes key limitations of previous studies, which assumed timescale separation between the individual dynamics and the evolution of the connectivity patterns. Thus, we do not hypothesize homogeneous mixing among individuals or the existence of a fixed interaction network. We formulate our approach in the framework of activity driven networks to enable the analysis of the concurrent evolution of the interaction and individual dynamics. Numerical simulations offer a systematic analysis of the model behavior and highlight the role of individual activity on market penetration when targeted advertisement campaigns are designed, or a competition between two different products takes place.

  16. Crop yield response to climate change varies with cropping intensity.

    Science.gov (United States)

    Challinor, Andrew J; Parkes, Ben; Ramirez-Villegas, Julian

    2015-04-01

    Projections of the response of crop yield to climate change at different spatial scales are known to vary. However, understanding of the causes of systematic differences across scale is limited. Here, we hypothesize that heterogeneous cropping intensity is one source of scale dependency. Analysis of observed global data and regional crop modelling demonstrate that areas of high vs. low cropping intensity can have systematically different yields, in both observations and simulations. Analysis of global crop data suggests that heterogeneity in cropping intensity is a likely source of scale dependency for a number of crops across the globe. Further crop modelling and a meta-analysis of projected tropical maize yields are used to assess the implications for climate change assessments. The results show that scale dependency is a potential source of systematic bias. We conclude that spatially comprehensive assessments of climate impacts based on yield alone, without accounting for cropping intensity, are prone to systematic overestimation of climate impacts. The findings therefore suggest a need for greater attention to crop suitability and land use change when assessing the impacts of climate change. © 2015 John Wiley & Sons Ltd.

  17. Complexity Variability Assessment of Nonlinear Time-Varying Cardiovascular Control

    Science.gov (United States)

    Valenza, Gaetano; Citi, Luca; Garcia, Ronald G.; Taylor, Jessica Noggle; Toschi, Nicola; Barbieri, Riccardo

    2017-02-01

    The application of complex systems theory to physiology and medicine has provided meaningful information about the nonlinear aspects underlying the dynamics of a wide range of biological processes and their disease-related aberrations. However, no studies have investigated whether meaningful information can be extracted by quantifying second-order moments of time-varying cardiovascular complexity. To this extent, we introduce a novel mathematical framework termed complexity variability, in which the variance of instantaneous Lyapunov spectra estimated over time serves as a reference quantifier. We apply the proposed methodology to four exemplary studies involving disorders which stem from cardiology, neurology and psychiatry: Congestive Heart Failure (CHF), Major Depression Disorder (MDD), Parkinson’s Disease (PD), and Post-Traumatic Stress Disorder (PTSD) patients with insomnia under a yoga training regime. We show that complexity assessments derived from simple time-averaging are not able to discern pathology-related changes in autonomic control, and we demonstrate that between-group differences in measures of complexity variability are consistent across pathologies. Pathological states such as CHF, MDD, and PD are associated with an increased complexity variability when compared to healthy controls, whereas wellbeing derived from yoga in PTSD is associated with lower time-variance of complexity.

  18. Flow in curved ducts of varying cross-section

    Science.gov (United States)

    Sotiropoulos, F.; Patel, V. C.

    1992-07-01

    Two numerical methods for solving the incompressible Navier-Stokes equations are compared with each other by applying them to calculate laminar and turbulent flows through curved ducts of regular cross-section. Detailed comparisons, between the computed solutions and experimental data, are carried out in order to validate the two methods and to identify their relative merits and disadvantages. Based on the conclusions of this comparative study a numerical method is developed for simulating viscous flows through curved ducts of varying cross-sections. The proposed method is capable of simulating the near-wall turbulence using fine computational meshes across the sublayer in conjunction with a two-layer k-epsilon model. Numerical solutions are obtained for: (1) a straight transition duct geometry, and (2) a hydroturbine draft-tube configuration at model scale Reynolds number for various inlet swirl intensities. The report also provides a detailed literature survey that summarizes all the experimental and computational work in the area of duct flows.

  19. Linear parameter-varying control for engineering applications

    CERN Document Server

    White, Andrew P; Choi, Jongeun

    2013-01-01

    The objective of this brief is to carefully illustrate a procedure of applying linear parameter-varying (LPV) control to a class of dynamic systems via a systematic synthesis of gain-scheduling controllers with guaranteed stability and performance. The existing LPV control theories rely on the use of either H-infinity or H2 norm to specify the performance of the LPV system.  The challenge that arises with LPV control for engineers is twofold. First, there is no systematic procedure for applying existing LPV control system theory to solve practical engineering problems from modeling to control design. Second, there exists no LPV control synthesis theory to design LPV controllers with hard constraints. For example, physical systems usually have hard constraints on their required performance outputs along with their sensors and actuators. Furthermore, the H-infinity and H2 performance criteria cannot provide hard constraints on system outputs. As a result, engineers in industry could find it difficult to utiliz...

  20. Neutron fluctuations in a multiplying medium randomly varying in time

    Energy Technology Data Exchange (ETDEWEB)

    Pal, L. [KFKI Atomic Energy Research Inst., Budapest (Hungary); Pazsit, I. [Chalmers Univ. of Technology, Goeteborg (Sweden). Dept. of Nuclear Engineering

    2006-07-15

    The master equation approach, which has traditionally been used for the calculation of neutron fluctuations in multiplying systems with constant parameters, is extended to a case when the parameters of the system change randomly in time. A forward type master equation is considered for the case of a multiplying system whose properties jump randomly between two discrete states, both with and without a stationary external source. The first two factorial moments are calculated, including the covariance. This model can be considered as the unification of stochastic methods that were used either in a constant multiplying medium via the master equation technique, or in a fluctuating medium via the Langevin technique. The results obtained show a much richer characteristic of the zero power noise than that in constant systems. The results are relevant in medium power subcritical nuclear systems where the zero power noise is still significant, but they also have a bearing on all types of branching processes, such as evolution of biological systems, spreading of epidemics etc, which are set in a time-varying environment.

  1. Neutron fluctuations in a multiplying medium randomly varying in time

    International Nuclear Information System (INIS)

    Pal, L.; Pazsit, I.

    2006-01-01

    The master equation approach, which has traditionally been used for the calculation of neutron fluctuations in multiplying systems with constant parameters, is extended to a case when the parameters of the system change randomly in time. A forward type master equation is considered for the case of a multiplying system whose properties jump randomly between two discrete states, both with and without a stationary external source. The first two factorial moments are calculated, including the covariance. This model can be considered as the unification of stochastic methods that were used either in a constant multiplying medium via the master equation technique, or in a fluctuating medium via the Langevin technique. The results obtained show a much richer characteristic of the zero power noise than that in constant systems. The results are relevant in medium power subcritical nuclear systems where the zero power noise is still significant, but they also have a bearing on all types of branching processes, such as evolution of biological systems, spreading of epidemics etc, which are set in a time-varying environment

  2. Hydrophobicity studies of polymer thin films with varied CNT concentration

    Science.gov (United States)

    M. Rodzi, N. H.; M. Shahimin, M.; Poopalan, P.; Man, B.; M. Nor, M. N.

    2013-12-01

    Surface functionalization studies for re-creating a `Lotus Leaf' effect (superhydrophobic) have been carried out for the past decade; looking for the material which can provide high transparency, low energy surface and high surface roughness. Fabrication of polydimethylsiloxane (PDMS) and multiwalled carbon nanotubes (MWCNT) hybrid thin film variations on glass to produce near-superhydrophobic surfaces is presented in this paper. There are three important parameters studied in producing hydrophobic surfaces based on the hybrid thin films; concentration of PDMS, concentration of MWCNT and droplet sizes. The study is carried out by using PDMS of varied cross linker ratio (10:1, 30:1 and 50:1) with MWCNT concentration of 1mg, 10mg and 15mg for 0.5 μl, 2.0 μl, 5.0 μl and 10 μl droplet sizes. The resulting hybrid thin films show that hydrophobicity increased with increasing cross linker ratio and MWCNT percentage in the PDMS solution. A near superhydrophobic surface can be created when using 15 mg of MWCNT with 50:1 cross linker ratio PDMS thin films, measured on 10 μl droplet size. The hybrid thin films produced can be potentially tailored to the application of biosensors, MEMS and even commercial devices.

  3. Monopoly models with time-varying demand function

    Science.gov (United States)

    Cavalli, Fausto; Naimzada, Ahmad

    2018-05-01

    We study a family of monopoly models for markets characterized by time-varying demand functions, in which a boundedly rational agent chooses output levels on the basis of a gradient adjustment mechanism. After presenting the model for a generic framework, we analytically study the case of cyclically alternating demand functions. We show that both the perturbation size and the agent's reactivity to profitability variation signals can have counterintuitive roles on the resulting period-2 cycles and on their stability. In particular, increasing the perturbation size can have both a destabilizing and a stabilizing effect on the resulting dynamics. Moreover, in contrast with the case of time-constant demand functions, the agent's reactivity is not just destabilizing, but can improve stability, too. This means that a less cautious behavior can provide better performance, both with respect to stability and to achieved profits. We show that, even if the decision mechanism is very simple and is not able to always provide the optimal production decisions, achieved profits are very close to those optimal. Finally, we show that in agreement with the existing empirical literature, the price series obtained simulating the proposed model exhibit a significant deviation from normality and large volatility, in particular when underlying deterministic dynamics become unstable and complex.

  4. Time-varying multiplex network: Intralayer and interlayer synchronization

    Science.gov (United States)

    Rakshit, Sarbendu; Majhi, Soumen; Bera, Bidesh K.; Sinha, Sudeshna; Ghosh, Dibakar

    2017-12-01

    A large class of engineered and natural systems, ranging from transportation networks to neuronal networks, are best represented by multiplex network architectures, namely a network composed of two or more different layers where the mutual interaction in each layer may differ from other layers. Here we consider a multiplex network where the intralayer coupling interactions are switched stochastically with a characteristic frequency. We explore the intralayer and interlayer synchronization of such a time-varying multiplex network. We find that the analytically derived necessary condition for intralayer and interlayer synchronization, obtained by the master stability function approach, is in excellent agreement with our numerical results. Interestingly, we clearly find that the higher frequency of switching links in the layers enhances both intralayer and interlayer synchrony, yielding larger windows of synchronization. Further, we quantify the resilience of synchronous states against random perturbations, using a global stability measure based on the concept of basin stability, and this reveals that intralayer coupling strength is most crucial for determining both intralayer and interlayer synchrony. Lastly, we investigate the robustness of interlayer synchronization against a progressive demultiplexing of the multiplex structure, and we find that for rapid switching of intralayer links, the interlayer synchronization persists even when a large number of interlayer nodes are disconnected.

  5. Do plasma proteins distinguish between liposomes of varying charge density?

    KAUST Repository

    Capriotti, Anna Laura

    2012-03-01

    Cationic liposomes (CLs) are one of the most employed nonviral nanovector systems in gene therapy. However, their transfection efficiency is strongly affected by interactions with plasma components, that lead to the formation of a "protein corona" onto CL surface. The interactions between nanoparticles entering the body and biomolecules have an essential role for their biodistribution. Because the knowledge of proteins adsorbed onto vector surface could be useful in the screening of new, more efficient and more biocompatible liposomal formulations, the behavior of three CLs with different membrane charge densities was investigated. The proteins of the three coronas were identified by nano-liquid chromatography-tandem mass spectrometry, and quantified with label-free spectral counting strategy. Fibrinogen displayed higher association with CLs with high membrane charge density, while apolipoproteins and C4b-binding protein with CLs with low membrane charge density. These results are discussed in terms of the different lipid compositions of CLs and may have a deep biological impact for in vivo applications. Surface charge of nanoparticles is emerging as a relevant factor determining the corona composition after interaction with plasma proteins. Remarkably, it is also shown that the charge of the protein corona formed around CLs is strongly related to their membrane charge density. © 2012 Elsevier B.V.

  6. Evolution of trappin genes in mammals

    Directory of Open Access Journals (Sweden)

    Furutani Yutaka

    2010-01-01

    Full Text Available Abstract Background Trappin is a multifunctional host-defense peptide that has antiproteolytic, antiinflammatory, and antimicrobial activities. The numbers and compositions of trappin paralogs vary among mammalian species: human and sheep have a single trappin-2 gene; mouse and rat have no trappin gene; pig and cow have multiple trappin genes; and guinea pig has a trappin gene and two other derivativegenes. Independent duplications of trappin genes in pig and cow were observed recently after the species were separated. To determine whether these trappin gene duplications are restricted only to certain mammalian lineages, we analyzed recently-developed genome databases for the presence of duplicate trappin genes. Results The database analyses revealed that: 1 duplicated trappin multigenes were found recently in the nine-banded armadillo; 2 duplicated two trappin genes had been found in the Afrotherian species (elephant, tenrec, and hyrax since ancient days; 3 a single trappin-2 gene was found in various eutherians species; and 4 no typical trappin gene has been found in chicken, zebra finch, and opossum. Bayesian analysis estimated the date of the duplication of trappin genes in the Afrotheria, guinea pig, armadillo, cow, and pig to be 244, 35, 11, 13, and 3 million-years ago, respectively. The coding regions of trappin multigenes of almadillo, bovine, and pig evolved much faster than the noncoding exons, introns, and the flanking regions, showing that these genes have undergone accelerated evolution, and positive Darwinian selection was observed in pig-specific trappin paralogs. Conclusion These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes.

  7. GFP expression by intracellular gene delivery of GFP-coding fragments using nanocrystal quantum dots

    International Nuclear Information System (INIS)

    Hoshino, Akiyoshi; Manabe, Noriyoshi; Fujioka, Kouki; Hanada, Sanshiro; Yamamoto, Kenji; Yasuhara, Masato; Kondo, Akihiko

    2008-01-01

    Gene therapy is an attractive approach to supplement a deficient gene function. Although there has been some success with specific gene delivery using various methods including viral vectors and liposomes, most of these methods have a limited efficiency or also carry a risk for oncogenesis. We herein report that quantum dots (QDs) conjugated with nuclear localizing signal peptides (NLSP) successfully introduced gene-fragments with promoter elements, which promoted the expression of the enhanced green fluorescent protein (eGFP) gene in mammalian cells. The expression of eGFP protein was observed when the QD/gene-construct was added to the culture media. The gene-expression efficiency varied depending on multiple factors around QDs, such as (1) the reading direction of the gene-fragments, (2) the quantity of gene-fragments attached on the surface of the QD-constructs, (3) the surface electronic charges varied according to the structure of the QD/gene-constructs, and (4) the particle size of QD/gene complex varied according to the structure and amounts of gene-fragments. Using this QD/gene-construct system, eGFP protein could be detected 28 days after the gene-introduction whereas the fluorescence of QDs had disappeared. This system therefore provides another method for the intracellular delivery of gene-fragments without using either viral vectors or specific liposomes.

  8. Extreme events as foundation of Levy walks with varying velocity

    International Nuclear Information System (INIS)

    Kutner, Ryszard

    2002-01-01

    In this work we study the role of extreme events [E.W. Montroll, B.J. West, in: J.L. Lebowitz, E.W. Montrell (Eds.), Fluctuation Phenomena, SSM, vol. VII, North-Holland, Amsterdam, 1979, p. 63; J.-P. Bouchaud, M. Potters, Theory of Financial Risks from Statistical Physics to Risk Management, Cambridge University Press, Cambridge, 2001; D. Sornette, Critical Phenomena in Natural Sciences. Chaos, Fractals, Selforganization and Disorder: Concepts and Tools, Springer, Berlin, 2000] in determining the scaling properties of Levy walks with varying velocity. This model is an extension of the well-known Levy walks one [J. Klafter, G. Zumofen, M.F. Shlesinger, in M.F. Shlesinger, G.M. Zaslavsky, U. Frisch (Eds.), Levy Flights and Related Topics ion Physics, Lecture Notes in Physics, vol. 450, Springer, Berlin, 1995, p. 196; G. Zumofen, J. Klafter, M.F. Shlesinger, in: R. Kutner, A. Pekalski, K. Sznajd-Weron (Eds.), Anomalous Diffusion. From Basics to Applications, Lecture Note in Physics, vol. 519, Springer, Berlin, 1999, p. 15] introduced in the context of chaotic dynamics where a fixed value of the walker velocity is assumed for simplicity. Such an extension seems to be necessary when the open and/or complex system is studied. The model of Levy walks with varying velocity is spanned on two coupled velocity-temporal hierarchies: the first one consisting of velocities and the second of corresponding time intervals which the walker spends between the successive turning points. Both these hierarchical structures are characterized by their own self-similar dimensions. The extreme event, which can appear within a given time interval, is defined as a single random step of the walker having largest length. By finding power-laws which describe the time-dependence of this displacement and its statistics we obtained two independent diffusion exponents, which are related to the above-mentioned dimensions and which characterize the extreme event kinetics. In this work we show the

  9. Atmospheric particle formation in spatially and temporally varying conditions

    Energy Technology Data Exchange (ETDEWEB)

    Lauros, J.

    2011-07-01

    Atmospheric particles affect the radiation balance of the Earth and thus the climate. New particle formation from nucleation has been observed in diverse atmospheric conditions but the actual formation path is still unknown. The prevailing conditions can be exploited to evaluate proposed formation mechanisms. This study aims to improve our understanding of new particle formation from the view of atmospheric conditions. The role of atmospheric conditions on particle formation was studied by atmospheric measurements, theoretical model simulations and simulations based on observations. Two separate column models were further developed for aerosol and chemical simulations. Model simulations allowed us to expand the study from local conditions to varying conditions in the atmospheric boundary layer, while the long-term measurements described especially characteristic mean conditions associated with new particle formation. The observations show statistically significant difference in meteorological and back-ground aerosol conditions between observed event and non-event days. New particle formation above boreal forest is associated with strong convective activity, low humidity and low condensation sink. The probability of a particle formation event is predicted by an equation formulated for upper boundary layer conditions. The model simulations call into question if kinetic sulphuric acid induced nucleation is the primary particle formation mechanism in the presence of organic vapours. Simultaneously the simulations show that ignoring spatial and temporal variation in new particle formation studies may lead to faulty conclusions. On the other hand, the theoretical simulations indicate that short-scale variations in temperature and humidity unlikely have a significant effect on mean binary water sulphuric acid nucleation rate. The study emphasizes the significance of mixing and fluxes in particle formation studies, especially in the atmospheric boundary layer. The further

  10. Respiratory clearance of aerosolized radioactive solutes of varying molecular weight

    International Nuclear Information System (INIS)

    Huchon, G.J.; Montgomery, A.B.; Lipavsky, A.; Hoeffel, J.M.; Murray, J.F.

    1987-01-01

    To determine the influence of varying molecular weight (mol wt) on respiratory clearance of aerosolized solutes, we studied eight radiopharmaceuticals, each administered to four dogs: sodium /sup 99m/Tc pertechnetate (TcO4), /sup 99m/Tc glucoheptonate ([/sup 99m/Tc]GH), 51Cr-ethylenedinitrotetraacetate ([51Cr]EDTA), /sup 99m/Tc diethylenetriaminepentaacetate ([99mTc] DTPA), 111 In diethylenetriaminepentaacetate ([ 111 In]DTPA), 67 Ga desferoxaminemesylate ([ 67 Ga]DFOM), /sup 99m/Tc dextran ([/sup 99m/Tc]DX) and 111 In transferrin ([ 111 In]TF). After aerosolization (0.8 m MMD, 2.4 GSD), clearance was determined for 30 min and then corrected by intravenous injection for nonairspace radioactivity. In-TF clearance (0.11 +/- 0.10%/min) was lower than TcO4 (6.32 +/- 0.62%/min), [/sup 99m/Tc]GH (1.50 +/- 0.37%/min), [ 51 Cr]EDTA (2.38 +/- 1.02%/min), [/sup 99m/Tc]DTPA (3.51 +/- 0.40%/min), [ 111 In]DTPA (2.35 +/- 0.42%/min), [ 67 Ga] DFOM (1.99 +/- 0.49%/min) and [/sup 99m/Tc]DX (1.81 +/- 0.75%/min) clearances (p less than 0.001). TcO4 clearance was higher than others (p less than 0.001). Technetium binding to DX was unsatisfactory; aerosolization caused unbinding from DTPA. We conclude that respiratory clearance of large mol wt solutes within 30 min is negligible and, that clearance of molecules between 347-5099 daltons differs greatly, suggesting that binding and/or intrapulmonary retention affect transfer

  11. Atmospheric Energy Deposition Modeling and Inference for Varied Meteoroid Structures

    Science.gov (United States)

    Wheeler, Lorien; Mathias, Donovan; Stokan, Edward; Brown, Peter

    2018-01-01

    Asteroids populations are highly diverse, ranging from coherent monoliths to loosely-bound rubble piles with a broad range of material and compositional properties. These different structures and properties could significantly affect how an asteroid breaks up and deposits energy in the atmosphere, and how much ground damage may occur from resulting blast waves. We have previously developed a fragment-cloud model (FCM) for assessing the atmospheric breakup and energy deposition of asteroids striking Earth. The approach represents ranges of breakup characteristics by combining progressive fragmentation with releases of variable fractions of debris and larger discrete fragments. In this work, we have extended the FCM to also represent asteroids with varied initial structures, such as rubble piles or fractured bodies. We have used the extended FCM to model the Chelyabinsk, Benesov, Kosice, and Tagish Lake meteors, and have obtained excellent matches to energy deposition profiles derived from their light curves. These matches provide validation for the FCM approach, help guide further model refinements, and enable inferences about pre-entry structure and breakup behavior. Results highlight differences in the amount of small debris vs. discrete fragments in matching the various flare characteristics of each meteor. The Chelyabinsk flares were best represented using relatively high debris fractions, while Kosice and Benesov cases were more notably driven by their discrete fragmentation characteristics, perhaps indicating more cohesive initial structures. Tagish Lake exhibited a combination of these characteristics, with lower-debris fragmentation at high altitudes followed by sudden disintegration into small debris in the lower flares. Results from all cases also suggest that lower ablation coefficients and debris spread rates may be more appropriate for the way in which debris clouds are represented in FCM, offering an avenue for future model refinement.

  12. Latitudinal gradients in ecosystem engineering by oysters vary across habitats.

    Science.gov (United States)

    McAfee, Dominic; Cole, Victoria J; Bishop, Melanie J

    2016-04-01

    Ecological theory predicts that positive interactions among organisms will increase across gradients of increasing abiotic stress or consumer pressure. This theory has been supported by empirical studies examining the magnitude of ecosystem engineering across environmental gradients and between habitat settings at local scale. Predictions that habitat setting, by modifying both biotic and abiotic factors, will determine large-scale gradients in ecosystem engineering have not been tested, however. A combination of manipulative experiments and field surveys assessed whether along the east Australian coastline: (1) facilitation of invertebrates by the oyster Saccostrea glomerata increased across a latitudinal gradient in temperature; and (2) the magnitude of this effect varied between intertidal rocky shores and mangrove forests. It was expected that on rocky shores, where oysters are the primary ecosystem engineer, they would play a greater role in ameliorating latitudinal gradients in temperature than in mangroves, where they are a secondary ecosystem engineer living under the mangrove canopy. On rocky shores, the enhancement of invertebrate abundance in oysters as compared to bare microhabitat decreased with latitude, as the maximum temperatures experienced by intertidal organisms diminished. By contrast, in mangrove forests, where the mangrove canopy resulted in maximum temperatures that were cooler and of greater humidity than on rocky shores, we found no evidence of latitudinal gradients of oyster effects on invertebrate abundance. Contrary to predictions, the magnitude by which oysters enhanced biodiversity was in many instances similar between mangroves and rocky shores. Whether habitat-context modifies patterns of spatial variation in the effects of ecosystem engineers on community structure will depend, in part, on the extent to which the environmental amelioration provided by an ecosystem engineer replicates that of other co-occurring ecosystem engineers.

  13. Does the availability of snack foods in supermarkets vary internationally?

    Science.gov (United States)

    Thornton, Lukar E; Cameron, Adrian J; McNaughton, Sarah A; Waterlander, Wilma E; Sodergren, Marita; Svastisalee, Chalida; Blanchard, Laurence; Liese, Angela D; Battersby, Sarah; Carter, Mary-Ann; Sheeshka, Judy; Kirkpatrick, Sharon I; Sherman, Sandy; Cowburn, Gill; Foster, Charlie; Crawford, David A

    2013-05-14

    Cross-country differences in dietary behaviours and obesity rates have been previously reported. Consumption of energy-dense snack foods and soft drinks are implicated as contributing to weight gain, however little is known about how the availability of these items within supermarkets varies internationally. This study assessed variations in the display of snack foods and soft drinks within a sample of supermarkets across eight countries. Within-store audits were used to evaluate and compare the availability of potato chips (crisps), chocolate, confectionery and soft drinks. Displays measured included shelf length and the proportion of checkouts and end-of-aisle displays containing these products. Audits were conducted in a convenience sample of 170 supermarkets across eight developed nations (Australia, Canada, Denmark, Netherlands, New Zealand, Sweden, United Kingdom (UK), and United States of America (US)). The mean total aisle length of snack foods (adjusted for store size) was greatest in supermarkets from the UK (56.4 m) and lowest in New Zealand (21.7 m). When assessed by individual item, the greatest aisle length devoted to chips, chocolate and confectionery was found in UK supermarkets while the greatest aisle length dedicated to soft drinks was in Australian supermarkets. Only stores from the Netherlands (41%) had less than 70% of checkouts featuring displays of snack foods or soft drinks. Whilst between-country variations were observed, overall results indicate high levels of snack food and soft drinks displays within supermarkets across the eight countries. Exposure to snack foods is largely unavoidable within supermarkets, increasing the likelihood of purchases and particularly those made impulsively.

  14. Sensation seeking related to varied definition of risk

    International Nuclear Information System (INIS)

    Dastol, O.U.; Drottz-Sjoberg, B.M.

    1998-01-01

    This pilot study is based on the assumption that the normal use of the word risk varies across subjects. It has been shown in previous risk perception studies that some people report their definition or normal use of the concept of risk as e.g. mainly probability, a combination of probability and consequences, mainly consequences, or due to the nature of the event (Drottz-Sjoeberg, 1991). Another field of research has developed measures for personality traits, i.e. facets of Sensation Seeking; Disinhibition, Thrill and Adventure Seeking, Experience Seeking, and Boredom Susceptibility (Zuckerman, 1994). The design of the present study involved three independent groups of first year psychology students (N=93). They were presented with one of three response formats regarding their normal use of the word risk, i.e. an open-ended format, separate ratings of four items suggesting a definition of risk on five-point scales, and one single five-point scale with the extremes labelled probability and consequences, and with their combination as the scale mid-point. The results showed, e.g. that the typical open-ended response to the personal definition of risk was 'danger', but among the responses were also 'chance', and 'outcome'. Another finding was that people who defined risk as 'outcome' and 'chance', using the open-ended format tended to score higher on the total Sensation Seeking Scale than those who defined risk as 'danger'. In addition, subjects who defined risk as the 'combination' of probability and consequences, using other response formats, also tended to score higher on the total Sensation Seeking Scale (SSS), especially as compared to those defining risk as the 'probability' of an event. (authors)

  15. Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes.

    Science.gov (United States)

    Fortunato, Sofia A V; Adamski, Marcin; Ramos, Olivia Mendivil; Leininger, Sven; Liu, Jing; Ferrier, David E K; Adamska, Maja

    2014-10-30

    Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.

  16. Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue

    Directory of Open Access Journals (Sweden)

    Dunner Susana

    2008-09-01

    Full Text Available Abstract Background Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RTqPCR is a technique used to measure mRNA species copy number as a way to determine key genes involved in different biological processes. However, the expression level of these key genes may vary among tissues or cells not only as a consequence of differential expression but also due to different factors, including choice of reference genes to normalize the expression levels of the target genes; thus the selection of reference genes is critical for expression studies. For this purpose, ten candidate reference genes were investigated in bovine muscular tissue. Results The value of stability of ten candidate reference genes included in three groups was estimated: the so called 'classical housekeeping' genes (18S, GAPDH and ACTB, a second set of genes used in expression studies conducted on other tissues (B2M, RPII, UBC and HMBS and a third set of novel genes (SF3A1, EEF1A2 and CASC3. Three different statistical algorithms were used to rank the genes by their stability measures as produced by geNorm, NormFinder and Bestkeeper. The three methods tend to agree on the most stably expressed genes and the least in muscular tissue. EEF1A2 and HMBS followed by SF3A1, ACTB, and CASC3 can be considered as stable reference genes, and B2M, RPII, UBC and GAPDH would not be appropriate. Although the rRNA-18S stability measure seems to be within the range of acceptance, its use is not recommended because its synthesis regulation is not representative of mRNA levels. Conclusion Based on geNorm algorithm, we propose the use of three genes SF3A1, EEF1A2 and HMBS as references for normalization of real-time RTqPCR in muscle expression studies.

  17. Imaging gene expression in gene therapy

    International Nuclear Information System (INIS)

    Wiebe, Leonard I.

    1997-01-01

    Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

  18. Imaging gene expression in gene therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

    1997-12-31

    Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

  19. Three extracellular dipeptidyl peptidases found in Aspergillus oryzae show varying substrate specificities.

    Science.gov (United States)

    Maeda, Hiroshi; Sakai, Daisuke; Kobayashi, Takuji; Morita, Hiroto; Okamoto, Ayako; Takeuchi, Michio; Kusumoto, Ken-Ichi; Amano, Hitoshi; Ishida, Hiroki; Yamagata, Youhei

    2016-06-01

    Three extracellular dipeptidyl peptidase genes, dppB, dppE, and dppF, were unveiled by sequence analysis of the Aspergillus oryzae genome. We investigated their differential enzymatic profiles, in order to gain an understanding of the diversity of these genes. The three dipeptidyl peptidases were expressed using Aspergillus nidulans as the host. Each recombinant enzyme was purified and subsequently characterized. The enzymes displayed similar optimum pH values, but optimum temperatures, pH stabilities, and substrate specificities varied. DppB was identified as a Xaa-Prolyl dipeptidyl peptidase, while DppE scissile substrates were similar to the substrates for Aspergillus fumigatus DPPV (AfDPPV). DppF was found to be a novel enzyme that could digest both substrates for A. fumigatus DPPIV and AfDPPV. Semi-quantitative PCR revealed that the transcription of dppB in A. oryzae was induced by protein substrates and repressed by the addition of an inorganic nitrogen source, despite the presence of protein substrates. The transcription of dppE depended on its growth time, while the transcription of dppF was not affected by the type of the nitrogen source in the medium, and it started during the early stage of the fungal growth. Based on these results, we conclude that these enzymes may represent the nutrition acquisition enzymes. Additionally, DppF may be one of the sensor peptidases responsible for the detection of the protein substrates in A. oryzae environment. DppB may be involved in nitrogen assimilation control, since the transcription of dppB was repressed by NaNO3, despite the presence of protein substrates.

  20. Estimation of thermal sensation during varied air temperature conditions.

    Science.gov (United States)

    Katsuura, T; Tabuchi, R; Iwanaga, K; Harada, H; Kikuchi, Y

    1998-03-01

    Seven male students were exposed to four varied air temperature environments: hot (37 degrees C) to neutral (27 degrees C) (HN), neutral to hot (NH), cool (17 degrees C) to neutral (CN), and neutral to cool (NC). The air temperature was maintained at the first condition for 20 min, then was changed to the second condition after 15 min and was held there for 20 min. Each subject wore a T-shirt, briefs, trunks, and socks. Each sat on a chair and was continuously evaluated for thermal sensation, thermal comfort, and air velocity sensation. Some physiological and thermal parameters were also measured every 5 s during the experiment. The correlation between thermal sensation and skin temperature at 15 sites was found to be poor. The subjects felt much warmer during the rising phase of the air temperature (CN, NH) than during the descending phase (HN, NC) at a given mean skin temperature. However, thermal sensation at the same heat flux or at the same value of the difference between skin and air temperature (delta(Tsk - Ta)) was not so different among the four experimental conditions, and the correlation between thermal sensation and heat flux or delta(Tsk - Ta) was fairly good. The multiple regression equation of the thermal sensation (TS) on 15 sites of skin temperature (Tsk; degrees C) was calculated and the coefficient of determination (R*2) was found to be 0.656. Higher coefficients of determination were found in the equations of thermal sensation for the heat flux (H; kcal.m-2.h-1) at the right and left thighs of the subjects and on delta(Tsk - Ta) (degrees C) at 4 sites. They were as follows: TS = 2.04 - 0.016 Hright - 0.036 Hleft; R*2 = 0.717, TS = 1.649 + 0.013 delta(Tsk - Ta)UpperArm - 0.036 delta(Tsk - Ta)Chest - 0.223 delta(Tsk - Ta)Thigh-0.083 delta(Tsk - Ta)LowerLeg; R*2 = 0.752, respectively.

  1. Linear parameter varying representations for nonlinear control design

    Science.gov (United States)

    Carter, Lance Huntington

    Linear parameter varying (LPV) systems are investigated as a framework for gain-scheduled control design and optimal hybrid control. An LPV system is defined as a linear system whose dynamics depend upon an a priori unknown but measurable exogenous parameter. A gain-scheduled autopilot design is presented for a bank-to-turn (BTT) missile. The method is novel in that the gain-scheduled design does not involve linearizations about operating points. Instead, the missile dynamics are brought to LPV form via a state transformation. This idea is applied to the design of a coupled longitudinal/lateral BTT missile autopilot. The pitch and yaw/roll dynamics are separately transformed to LPV form, where the cross axis states are treated as "exogenous" parameters. These are actually endogenous variables, so such a plant is called "quasi-LPV." Once in quasi-LPV form, a family of robust controllers using mu synthesis is designed for both the pitch and yaw/roll channels, using angle-of-attack and roll rate as the scheduling variables. The closed-loop time response is simulated using the original nonlinear model and also using perturbed aerodynamic coefficients. Modeling and control of engine idle speed is investigated using LPV methods. It is shown how generalized discrete nonlinear systems may be transformed into quasi-LPV form. A discrete nonlinear engine model is developed and expressed in quasi-LPV form with engine speed as the scheduling variable. An example control design is presented using linear quadratic methods. Simulations are shown comparing the LPV based controller performance to that using PID control. LPV representations are also shown to provide a setting for hybrid systems. A hybrid system is characterized by control inputs consisting of both analog signals and discrete actions. A solution is derived for the optimal control of hybrid systems with generalized cost functions. This is shown to be computationally intensive, so a suboptimal strategy is proposed that

  2. Gene doping: gene delivery for olympic victory.

    Science.gov (United States)

    Gould, David

    2013-08-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

  3. The propagation of varied timescale perturbations in landscapes

    Science.gov (United States)

    Bingham, N.; Johnson, K. N.; Bookhagen, B.; Chadwick, O.

    2016-12-01

    The classic assumption of steady-state landscapes greatly simplifies models of earth-surface processes. Theoretically, steady-state denotes time independence, but in real landscapes steady-state requires a timescale over which to assume (or document) no change. In the past, poor spatiotemporal resolution of eroding landscapes necessitated that shorter timescale perturbations be ignored in favor of regional formulations of rock uplift = erosion, 105, 6 years. Now, novel techniques and technologies provide an opportunity to define local landscape response to various timescales of perturbations; thus, allowing us to consider multiple steady-states on adjacent watersheds or even along a single watershed. This study seeks to identify the physical propagation of varied timescale perturbations in landscapes in order to provide an updated geomorphic context for interpreting critical zone processes. At our study site - Santa Cruz Island (SCI), CA - perturbations include sea level and climate fluctuations over 105 years coupled with pulses of overgrazing and extreme storm events during the last 200 years. Comprehensive knickpoint location maps and dated marine and fill terraces tighten the spatiotemporal constraints on erosion for SCI. In addition, the island hosts a wide range of lithologies, allowing us to compare lithologic effects on landscape response to perturbations. Our study uses lidar point clouds and high resolution (0.25 and 1 m) digital elevation model analysis to segment landscapes by the degree of their response to perturbations. Landscape response is measured by increases in topographic roughness. We ascertain roughness by analyzing the changes in different terrain attributes on multiple spatial scales: catchment, sub-catchments and individual hillslopes. Terrain attributes utilized include slope, curvature, local relief, flowpath length and contributing catchment area. Statistical analysis of these properties indicates narrower ranges in values for regions

  4. University of Texas Southwestern Medical Center (UTSW): Functional Signature Ontology Tool: Triplicate Measurements of Reporter Gene Expression in Response to Individual Genetic and Chemical Perturbations in HCT116 Cells | Office of Cancer Genomics

    Science.gov (United States)

    The goal of this project is to use an eight-gene expression profile to define functional signatures for small molecules and natural products with heretofore undefined mechanism of action. Two genes in the eight gene set are used as internal controls and do not vary across gene expression array data collected from the public domain. The remaining six genes are found to vary independently across a large collection of publically available gene expression array datasets.  Read the abstract

  5. University of Texas Southwestern Medical Center: Functional Signature Ontology Tool: Triplicate Measurements of Reporter Gene Expression in Response to Individual Genetic and Chemical Perturbations in HCT116 Cells | Office of Cancer Genomics

    Science.gov (United States)

    The goal of this project is to use an eight-gene expression profile to define functional signatures for small molecules and natural products with heretofore undefined mechanism of action. Two genes in the eight gene set are used as internal controls and do not vary across gene expression array data collected from the public domain. The remaining six genes are found to vary independently across a large collection of publically available gene expression array datasets.  Read the abstract

  6. Evolution of homeobox genes.

    Science.gov (United States)

    Holland, Peter W H

    2013-01-01

    Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

  7. Gene cluster statistics with gene families.

    Science.gov (United States)

    Raghupathy, Narayanan; Durand, Dannie

    2009-05-01

    Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

  8. Nutritional composition of honey bee food stores vary with floral composition.

    Science.gov (United States)

    Donkersley, Philip; Rhodes, Glenn; Pickup, Roger W; Jones, Kevin C; Power, Eileen F; Wright, Geraldine A; Wilson, Kenneth

    2017-12-01

    Sufficiently diverse and abundant resources are essential for generalist consumers, and form an important part of a suite of conservation strategies for pollinators. Honey bees are generalist foragers and are dependent on diverse forage to adequately meet their nutritional needs. Through analysis of stored pollen (bee bread) samples obtained from 26 honey bee (Apis mellifera L.) hives across NW-England, we quantified bee bread nutritional content and the plant species that produced these stores from pollen. Protein was the most abundant nutrient by mass (63%), followed by carbohydrates (26%). Protein and lipid content (but not carbohydrate) contributed significantly to ordinations of floral diversity, linking dietary quality with forage composition. DNA sequencing of the ITS2 region of the nuclear ribosomal DNA gene identified pollen from 89 distinct plant genera, with each bee bread sample containing between 6 and 35 pollen types. Dominant genera included dandelion (Taraxacum), which was positively correlated with bee bread protein content, and cherry (Prunus), which was negatively correlated with the amount of protein. In addition, proportions of amino acids (e.g. histidine and valine) varied as a function of floral species composition. These results also quantify the effects of individual plant genera on the nutrition of honey bees. We conclude that pollens of different plants act synergistically to influence host nutrition; the pollen diversity of bee bread is linked to its nutrient content. Diverse environments compensate for the loss of individual forage plants, and diversity loss may, therefore, destabilize consumer communities due to restricted access to alternative resources.

  9. Carboxylesterase 1 genes

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Madsen, Majbritt Busk

    2018-01-01

    The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

  10. How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota.

    Science.gov (United States)

    Bost, Alyssa; Franzenburg, Soeren; Adair, Karen L; Martinson, Vincent G; Loeb, Greg; Douglas, Angela E

    2018-04-01

    Despite evidence from laboratory experiments that perturbation of the gut microbiota affects many traits of the animal host, our understanding of the effect of variation in microbiota composition on animals in natural populations is very limited. The core purpose of this study on the fruit fly Drosophila melanogaster was to identify the impact of natural variation in the taxonomic composition of gut bacterial communities on host traits, with the gut transcriptome as a molecular index of microbiota-responsive host traits. Use of the gut transcriptome was validated by demonstrating significant transcriptional differences between the guts of laboratory flies colonized with bacteria and maintained under axenic conditions. Wild Drosophila from six field collections made over two years had gut bacterial communities of diverse composition, dominated to varying extents by Acetobacteraceae and Enterobacteriaceae. The gut transcriptomes also varied among collections and differed markedly from those of laboratory flies. However, no overall relationship between variation in the wild fly transcriptome and taxonomic composition of the gut microbiota was evident at all taxonomic scales of bacteria tested for both individual fly genes and functional categories in Gene Ontology. We conclude that the interaction between microbiota composition and host functional traits may be confounded by uncontrolled variation in both ecological circumstance and host traits (e.g., genotype, age physiological condition) under natural conditions, and that microbiota effects on host traits identified in the laboratory should, therefore, be extrapolated to field population with great caution. © 2017 John Wiley & Sons Ltd.

  11. Thermal shock behaviour of different tungsten grades under varying conditions

    Energy Technology Data Exchange (ETDEWEB)

    Wirtz, Oliver Marius

    2012-07-19

    Thermonuclear fusion power plants are a promising option to ensure the energy supply for future generations, but in many fields of research enormous challenges have to be faced. A major step on the way to the prototype fusion reactor DEMO will be ITER which is build in Cadarache, southern France. One of the most critical issues is the field of in-vessel materials and components, in particular the plasma facing materials (PFM). PFMs that will be used in a device like ITER have to withstand severe environmental conditions in terms of steady state and transient thermal loads as well as high particle fluxes such as hydrogen, helium and neutrons. Candidate wall materials are beryllium, tungsten and carbon based materials like CFC (carbon fibre composite). Tungsten is the most promising material for an application in the divertor region with very severe loading conditions and it will most probably also be used as PFM for DEMO. Hence, this work focuses on the investigation of the thermal shock response of different tungsten grades in order to understand the damage mechanisms and to identify material parameters which influence this behaviour under ITER and DEMO relevant operation conditions. Therefore the microstructure and the mechanical and thermal properties of five industrially manufactured tungsten grades were characterised. All five tungsten grades were exposed to transient thermal events with very high power densities of up to 1.27 GWm{sup -2} at varying base temperatures between RT and 600 C in the electron beam device JUDITH 1. The pulse numbers were limited to a maximum of 1000 in order to avoid immoderate workload on the test facility and to have enough time to cover a wide range of loading conditions. The results of this damage mapping enable to define different damage and cracking thresholds for the investigated tungsten grades and to identify certain material parameters which influence the location of these thresholds and the distinction of the induced

  12. Thermal shock behaviour of different tungsten grades under varying conditions

    International Nuclear Information System (INIS)

    Wirtz, Oliver Marius

    2012-01-01

    Thermonuclear fusion power plants are a promising option to ensure the energy supply for future generations, but in many fields of research enormous challenges have to be faced. A major step on the way to the prototype fusion reactor DEMO will be ITER which is build in Cadarache, southern France. One of the most critical issues is the field of in-vessel materials and components, in particular the plasma facing materials (PFM). PFMs that will be used in a device like ITER have to withstand severe environmental conditions in terms of steady state and transient thermal loads as well as high particle fluxes such as hydrogen, helium and neutrons. Candidate wall materials are beryllium, tungsten and carbon based materials like CFC (carbon fibre composite). Tungsten is the most promising material for an application in the divertor region with very severe loading conditions and it will most probably also be used as PFM for DEMO. Hence, this work focuses on the investigation of the thermal shock response of different tungsten grades in order to understand the damage mechanisms and to identify material parameters which influence this behaviour under ITER and DEMO relevant operation conditions. Therefore the microstructure and the mechanical and thermal properties of five industrially manufactured tungsten grades were characterised. All five tungsten grades were exposed to transient thermal events with very high power densities of up to 1.27 GWm -2 at varying base temperatures between RT and 600 C in the electron beam device JUDITH 1. The pulse numbers were limited to a maximum of 1000 in order to avoid immoderate workload on the test facility and to have enough time to cover a wide range of loading conditions. The results of this damage mapping enable to define different damage and cracking thresholds for the investigated tungsten grades and to identify certain material parameters which influence the location of these thresholds and the distinction of the induced damages

  13. Gene Expression and Polymorphism of Myostatin Gene and its Association with Growth Traits in Chicken.

    Science.gov (United States)

    Dushyanth, K; Bhattacharya, T K; Shukla, R; Chatterjee, R N; Sitaramamma, T; Paswan, C; Guru Vishnu, P

    2016-10-01

    Myostatin is a member of TGF-β super family and is directly involved in regulation of body growth through limiting muscular growth. A study was carried out in three chicken lines to identify the polymorphism in the coding region of the myostatin gene through SSCP and DNA sequencing. A total of 12 haplotypes were observed in myostatin coding region of chicken. Significant associations between haplogroups with body weight at day 1, 14, 28, and 42 days, and carcass traits at 42 days were observed across the lines. It is concluded that the coding region of myostatin gene was polymorphic, with varied levels of expression among lines and had significant effects on growth traits. The expression of MSTN gene varied during embryonic and post hatch development stage.

  14. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  15. Introduction: Cancer Gene Networks.

    Science.gov (United States)

    Clarke, Robert

    2017-01-01

    Constructing, evaluating, and interpreting gene networks generally sits within the broader field of systems biology, which continues to emerge rapidly, particular with respect to its application to understanding the complexity of signaling in the context of cancer biology. For the purposes of this volume, we take a broad definition of systems biology. Considering an organism or disease within an organism as a system, systems biology is the study of the integrated and coordinated interactions of the network(s) of genes, their variants both natural and mutated (e.g., polymorphisms, rearrangements, alternate splicing, mutations), their proteins and isoforms, and the organic and inorganic molecules with which they interact, to execute the biochemical reactions (e.g., as enzymes, substrates, products) that reflect the function of that system. Central to systems biology, and perhaps the only approach that can effectively manage the complexity of such systems, is the building of quantitative multiscale predictive models. The predictions of the models can vary substantially depending on the nature of the model and its inputoutput relationships. For example, a model may predict the outcome of a specific molecular reaction(s), a cellular phenotype (e.g., alive, dead, growth arrest, proliferation, and motility), a change in the respective prevalence of cell or subpopulations, a patient or patient subgroup outcome(s). Such models necessarily require computers. Computational modeling can be thought of as using machine learning and related tools to integrate the very high dimensional data generated from modern, high throughput omics technologies including genomics (next generation sequencing), transcriptomics (gene expression microarrays; RNAseq), metabolomics and proteomics (ultra high performance liquid chromatography, mass spectrometry), and "subomic" technologies to study the kinome, methylome, and others. Mathematical modeling can be thought of as the use of ordinary

  16. Clinicopathologic and gene expression parameters predict liver cancer prognosis

    International Nuclear Information System (INIS)

    Hao, Ke; Zhong, Hua; Greenawalt, Danielle; Ferguson, Mark D; Ng, Irene O; Sham, Pak C; Poon, Ronnie T; Molony, Cliona; Schadt, Eric E; Dai, Hongyue; Luk, John M; Lamb, John; Zhang, Chunsheng; Xie, Tao; Wang, Kai; Zhang, Bin; Chudin, Eugene; Lee, Nikki P; Mao, Mao

    2011-01-01

    The prognosis of hepatocellular carcinoma (HCC) varies following surgical resection and the large variation remains largely unexplained. Studies have revealed the ability of clinicopathologic parameters and gene expression to predict HCC prognosis. However, there has been little systematic effort to compare the performance of these two types of predictors or combine them in a comprehensive model. Tumor and adjacent non-tumor liver tissues were collected from 272 ethnic Chinese HCC patients who received curative surgery. We combined clinicopathologic parameters and gene expression data (from both tissue types) in predicting HCC prognosis. Cross-validation and independent studies were employed to assess prediction. HCC prognosis was significantly associated with six clinicopathologic parameters, which can partition the patients into good- and poor-prognosis groups. Within each group, gene expression data further divide patients into distinct prognostic subgroups. Our predictive genes significantly overlap with previously published gene sets predictive of prognosis. Moreover, the predictive genes were enriched for genes that underwent normal-to-tumor gene network transformation. Previously documented liver eSNPs underlying the HCC predictive gene signatures were enriched for SNPs that associated with HCC prognosis, providing support that these genes are involved in key processes of tumorigenesis. When applied individually, clinicopathologic parameters and gene expression offered similar predictive power for HCC prognosis. In contrast, a combination of the two types of data dramatically improved the power to predict HCC prognosis. Our results also provided a framework for understanding the impact of gene expression on the processes of tumorigenesis and clinical outcome

  17. Gene doping in sports.

    Science.gov (United States)

    Unal, Mehmet; Ozer Unal, Durisehvar

    2004-01-01

    Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement. Copyright 2004 Adis Data Information BV

  18. A Nonlinear Model for Gene-Based Gene-Environment Interaction

    Directory of Open Access Journals (Sweden)

    Jian Sa

    2016-06-01

    Full Text Available A vast amount of literature has confirmed the role of gene-environment (G×E interaction in the etiology of complex human diseases. Traditional methods are predominantly focused on the analysis of interaction between a single nucleotide polymorphism (SNP and an environmental variable. Given that genes are the functional units, it is crucial to understand how gene effects (rather than single SNP effects are influenced by an environmental variable to affect disease risk. Motivated by the increasing awareness of the power of gene-based association analysis over single variant based approach, in this work, we proposed a sparse principle component regression (sPCR model to understand the gene-based G×E interaction effect on complex disease. We first extracted the sparse principal components for SNPs in a gene, then the effect of each principal component was modeled by a varying-coefficient (VC model. The model can jointly model variants in a gene in which their effects are nonlinearly influenced by an environmental variable. In addition, the varying-coefficient sPCR (VC-sPCR model has nice interpretation property since the sparsity on the principal component loadings can tell the relative importance of the corresponding SNPs in each component. We applied our method to a human birth weight dataset in Thai population. We analyzed 12,005 genes across 22 chromosomes and found one significant interaction effect using the Bonferroni correction method and one suggestive interaction. The model performance was further evaluated through simulation studies. Our model provides a system approach to evaluate gene-based G×E interaction.

  19. Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

    Directory of Open Access Journals (Sweden)

    Benjamin Mayne

    2016-10-01

    Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

  20. Human Gene Therapy: Genes without Frontiers?

    Science.gov (United States)

    Simon, Eric J.

    2002-01-01

    Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

  1. Zhang neural network for online solution of time-varying convex quadratic program subject to time-varying linear-equality constraints

    International Nuclear Information System (INIS)

    Zhang Yunong; Li Zhan

    2009-01-01

    In this Letter, by following Zhang et al.'s method, a recurrent neural network (termed as Zhang neural network, ZNN) is developed and analyzed for solving online the time-varying convex quadratic-programming problem subject to time-varying linear-equality constraints. Different from conventional gradient-based neural networks (GNN), such a ZNN model makes full use of the time-derivative information of time-varying coefficient. The resultant ZNN model is theoretically proved to have global exponential convergence to the time-varying theoretical optimal solution of the investigated time-varying convex quadratic program. Computer-simulation results further substantiate the effectiveness, efficiency and novelty of such ZNN model and method.

  2. Anti-EGFR immunonanoparticles containing IL12 and salmosin genes for targeted cancer gene therapy.

    Science.gov (United States)

    Kim, Jung Seok; Kang, Seong Jae; Jeong, Hwa Yeon; Kim, Min Woo; Park, Sang Il; Lee, Yeon Kyung; Kim, Hong Sung; Kim, Keun Sik; Park, Yong Serk

    2016-09-01

    Tumor-directed gene delivery is of major interest in the field of cancer gene therapy. Varied functionalizations of non-viral vectors have been suggested to enhance tumor targetability. In the present study, we prepared two different types of anti-EGF receptor (EGFR) immunonanoparticles containing pDNA, neutrally charged liposomes and cationic lipoplexes, for tumor-directed transfection of cancer therapeutic genes. Even though both anti-EGFR immunonanoparticles had a high binding affinity to the EGFR-positive cancer cells, the anti-EGFR immunolipoplex formulation exhibited approximately 100-fold higher transfection to the target cells than anti-EGFR immunoliposomes. The lipoplex formulation also showed a higher transfection to SK-OV-3 tumor xenografts in mice. Thus, IL12 and/or salmosin genes were loaded in the anti-EGFR immunolipoplexes and intravenously administered to mice carrying SK-OV-3 tumors. Co-transfection of IL12 and salmosin genes using anti-EGFR immunolipoplexes significantly reduced tumor growth and pulmonary metastasis. Furthermore, combinatorial treatment with doxorubicin synergistically inhibited tumor growth. These results suggest that anti-EGFR immunolipoplexes containing pDNA encoding therapeutic genes could be utilized as a gene-transfer modality for cancer gene therapy.

  3. Evaluation of candidate reference genes for gene expression normalization in Brassica juncea using real time quantitative RT-PCR.

    Directory of Open Access Journals (Sweden)

    Ruby Chandna

    Full Text Available The real time quantitative reverse transcription PCR (qRT-PCR is becoming increasingly important to gain insight into function of genes. Given the increased sensitivity, ease and reproducibility of qRT-PCR, the requirement of suitable reference genes for normalization has become important and stringent. It is now known that the expression of internal control genes in living organism vary considerably during developmental stages and under different experimental conditions. For economically important Brassica crops, only a couple of reference genes are reported till date. In this study, expression stability of 12 candidate reference genes including ACT2, ELFA, GAPDH, TUA, UBQ9 (traditional housekeeping genes, ACP, CAC, SNF, TIPS-41, TMD, TSB and ZNF (new candidate reference genes, in a diverse set of 49 tissue samples representing different developmental stages, stress and hormone treated conditions and cultivars of Brassica juncea has been validated. For the normalization of vegetative stages the ELFA, ACT2, CAC and TIPS-41 combination would be appropriate whereas TIPS-41 along with CAC would be suitable for normalization of reproductive stages. A combination of GAPDH, TUA, TIPS-41 and CAC were identified as the most suitable reference genes for total developmental stages. In various stress and hormone treated samples, UBQ9 and TIPS-41 had the most stable expression. Across five cultivars of B. juncea, the expression of CAC and TIPS-41 did not vary significantly and were identified as the most stably expressed reference genes. This study provides comprehensive information that the new reference genes selected herein performed better than the traditional housekeeping genes. The selection of most suitable reference genes depends on the experimental conditions, and is tissue and cultivar-specific. Further, to attain accuracy in the results more than one reference genes are necessary for normalization.

  4. Tumor targeted gene therapy

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2006-01-01

    Knowledge of molecular mechanisms governing malignant transformation brings new opportunities for therapeutic intervention against cancer using novel approaches. One of them is gene therapy based on the transfer of genetic material to an organism with the aim of correcting a disease. The application of gene therapy to the cancer treatment had led to the development of new experimental approaches such as suicidal gene therapy, inhibition of oncogenes and restoration of tumor-suppressor genes. Suicidal gene therapy is based on the expression in tumor cells of a gene encoding an enzyme that converts a prodrug into a toxic product. Representative suicidal genes are Herpes simplex virus type 1 thymidine kinase (HSV1-tk) and cytosine deaminase (CD). Especially, physicians and scientists of nuclear medicine field take an interest in suicidal gene therapy because they can monitor the location and magnitude, and duration of expression of HSV1-tk and CD by PET scanner

  5. Essential Bacillus subtilis genes

    DEFF Research Database (Denmark)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

  6. Spatially and temporally fluctuating selection at non-MHC immune genes: evidence from TAP polymorphism in populations of brown trout ( Salmo trutta , L.)

    DEFF Research Database (Denmark)

    Jensen, L.F.; Hansen, Michael Møller; Mensberg, Karen-Lise Dons

    2008-01-01

    Temporal samples of Danish brown trout (Salmo trutta) from populations representing varying geographical scales were analysed using eight putatively neutral microsatellite loci and two microsatellite loci embedded in TAP genes (Transporter associated with Antigen Processing). These genes encode m...

  7. Responses to high-fat challenges varying in fat type in subjects with different metabolic risk phenotypes: a randomized trial.

    Directory of Open Access Journals (Sweden)

    Susan J van Dijk

    Full Text Available The ability of subjects to respond to nutritional challenges can reflect the flexibility of their biological system. Nutritional challenge tests could be used as an indicator of health status but more knowledge on metabolic and immune responses of different subjects to nutritional challenges is needed. The aim of this study was to compare the responses to high-fat challenges varying in fat type in subjects with different metabolic risk phenotypes.In a cross-over design 42 men (age 50-70 y consumed three high-fat shakes containing saturated fat (SFA, monounsaturated fat (MUFA or n-3 polyunsaturated (PUFA. Men were selected on BMI and health status (lean, obese or obese diabetic and phenotyped with MRI for adipose tissue distribution. Before and 2 and 4 h after shake consumption blood was drawn for measurement of expression of metabolic and inflammation-related genes in peripheral blood mononuclear cells (PBMCs, plasma triglycerides (TAG, glucose, insulin, cytokines and ex vivo PBMC immune response capacity. The MUFA and n-3 PUFA challenge, compared to the SFA challenge, induced higher changes in expression of inflammation genes MCP1 and IL1β in PBMCs. Obese and obese diabetic subjects had different PBMC gene expression and metabolic responses to high-fat challenges compared to lean subjects. The MUFA challenge induced the most pronounced TAG response, mainly in obese and obese diabetic subjects.The PBMC gene expression response and metabolic response to high-fat challenges were affected by fat type and metabolic risk phenotype. Based on our results we suggest using a MUFA challenge to reveal differences in response capacity of subjects.ClinicalTrials.gov NCT00977262.

  8. Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

    Science.gov (United States)

    Chen, Hua; Chen, Kun

    2013-07-01

    The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by Tm the mth coalescent time, when m + 1 lineages coalesce into m lineages, and An(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, An(t), and the coalescence times, Tm, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n - An(t) follows a Poisson distribution, and as m → n, $$n\\left(n-1\\right){T}_{m}/2N\\left(0\\right)$$ follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.

  9. Molecular mechanisms of drug resistance in natural Leishmania populations vary with genetic background.

    Directory of Open Access Journals (Sweden)

    Saskia Decuypere

    Full Text Available The evolution of drug-resistance in pathogens is a major global health threat. Elucidating the molecular basis of pathogen drug-resistance has been the focus of many studies but rarely is it known whether a drug-resistance mechanism identified is universal for the studied pathogen; it has seldom been clarified whether drug-resistance mechanisms vary with the pathogen's genotype. Nevertheless this is of critical importance in gaining an understanding of the complexity of this global threat and in underpinning epidemiological surveillance of pathogen drug resistance in the field. This study aimed to assess the molecular and phenotypic heterogeneity that emerges in natural parasite populations under drug treatment pressure. We studied lines of the protozoan parasite Leishmania (L. donovani with differential susceptibility to antimonial drugs; the lines being derived from clinical isolates belonging to two distinct genetic populations that circulate in the leishmaniasis endemic region of Nepal. Parasite pathways known to be affected by antimonial drugs were characterised on five experimental levels in the lines of the two populations. Characterisation of DNA sequence, gene expression, protein expression and thiol levels revealed a number of molecular features that mark antimonial-resistant parasites in only one of the two populations studied. A final series of in vitro stress phenotyping experiments confirmed this heterogeneity amongst drug-resistant parasites from the two populations. These data provide evidence that the molecular changes associated with antimonial-resistance in natural Leishmania populations depend on the genetic background of the Leishmania population, which has resulted in a divergent set of resistance markers in the Leishmania populations. This heterogeneity of parasite adaptations provides severe challenges for the control of drug resistance in the field and the design of molecular surveillance tools for widespread

  10. Actin gene identification from selected medicinal plants for their use as internal controls for gene expression studies

    International Nuclear Information System (INIS)

    Mufti, F.U.D.; Banaras, S.

    2015-01-01

    Internal control genes are the constitutive genes which maintain the basic cellular functions and regularly express in both normal and stressed conditions in living organisms. They are used in normalization of gene expression studies in comparative analysis of target genes, as their expression remains comparatively unchanged in all varied conditions. Among internal control genes, actin is considered as a candidate gene for expression studies due to its vital role in shaping cytoskeleton and plant physiology. Unfortunately most of such knowledge is limited to only model plants or crops, not much is known about important medicinal plants. Therefore, we selected seven important medicinal wild plants for molecular identification of actin gene. We used gene specific primers designed from the conserved regions of several known orthologues or homologues of actin genes from other plants. The amplified products of 370-380 bp were sequenced and submitted to GeneBank after their confirmation using different bioinformatics tools. All the novel partial sequences of putative actin genes were submitted to GeneBank (Parthenium hysterophorus (KJ774023), Fagonia indica (KJ774024), Rhazya stricta (KJ774025), Whithania coagulans (KJ774026), Capparis decidua (KJ774027), Verbena officinalis (KJ774028) and Aerva javanica (KJ774029)). The comparisons of these partial sequences by Basic Local Alignment Search Tool (BLAST) and phylogenetic trees demonstrated high similarity with known actin genes of other plants. Our findings illustrated highly conserved nature of actin gene among these selected plants. These novel partial fragments of actin genes from these wild medicinal plants can be used as internal controls for future gene expression studies of these important plants after precise validations of their stable expression in such plants. (author)

  11. Radiotechnologies and gene therapy

    International Nuclear Information System (INIS)

    Xia Jinsong

    2001-01-01

    Gene therapy is an exciting frontier in medicine today. Radiologist will make an uniquely contribution to these exciting new technologies at every level by choosing sites for targeting therapy, perfecting and establishing routes of delivery, developing imaging strategies to monitor therapy and assess gene expression, developing radiotherapeutic used of gene therapy

  12. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  13. Stochastic gene expression in Arabidopsis thaliana.

    Science.gov (United States)

    Araújo, Ilka Schultheiß; Pietsch, Jessica Magdalena; Keizer, Emma Mathilde; Greese, Bettina; Balkunde, Rachappa; Fleck, Christian; Hülskamp, Martin

    2017-12-14

    Although plant development is highly reproducible, some stochasticity exists. This developmental stochasticity may be caused by noisy gene expression. Here we analyze the fluctuation of protein expression in Arabidopsis thaliana. Using the photoconvertible KikGR marker, we show that the protein expressions of individual cells fluctuate over time. A dual reporter system was used to study extrinsic and intrinsic noise of marker gene expression. We report that extrinsic noise is higher than intrinsic noise and that extrinsic noise in stomata is clearly lower in comparison to several other tissues/cell types. Finally, we show that cells are coupled with respect to stochastic protein expression in young leaves, hypocotyls and roots but not in mature leaves. Our data indicate that stochasticity of gene expression can vary between tissues/cell types and that it can be coupled in a non-cell-autonomous manner.

  14. Experimental evidence for amplitude death induced by a time-varying interaction

    Energy Technology Data Exchange (ETDEWEB)

    Suresh, K. [Centre for Nonlinear Dynamics, School of Physics, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu (India); Shrimali, M.D. [Department of Physics, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer 305 801 (India); Prasad, Awadhesh [Department of Physics and Astrophysics, University of Delhi, Delhi 110 007 (India); Thamilmaran, K., E-mail: maran.cnld@gmail.com [Centre for Nonlinear Dynamics, School of Physics, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu (India)

    2014-08-01

    In this paper, we study the time-varying interaction in coupled oscillatory systems. For this purpose, we have designed a novel time-varying resistive network using an analog switch and inverter circuits. We have applied this time-varying resistive network to mutually coupled identical Chua's oscillators. When the resistances are varied in time, we find that amplitude death arises in coupled identical oscillators. This has been observed numerically as well as verified through hardware experiments. - Highlights: • We have implemented the time-varying interaction in coupled oscillatory systems. • We have designed a novel time-varying resistive network using an analog switch and inverter circuits. • When the resistances are varied in time, we find that amplitude death arises in coupled identical oscillators.

  15. Gene therapy: An overview

    Directory of Open Access Journals (Sweden)

    Sudip Indu

    2013-01-01

    Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

  16. Gene therapy in periodontics.

    Science.gov (United States)

    Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

    2013-03-01

    GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

  17. Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

    Science.gov (United States)

    Kaznadzey, Anna; Shelyakin, Pavel; Gelfand, Mikhail S

    2017-11-25

    Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on a large-scale analysis of bacterial genomic loci related to the carbohydrate metabolism. We demonstrate that only 53% of 148,000 studied genes from over six hundred bacterial genomes are co-localized in bacterial genomes with other carbohydrate metabolism genes, which points to a significant role of singleton genes. Co-localized genes form cassettes, ranging in size from two to fifteen genes. Two major factors influencing the cassette-forming tendency are gene function and bacterial phylogeny. We have obtained a comprehensive picture of co-localization preferences of genes for nineteen major carbohydrate metabolism functional classes, over two hundred gene orthologous clusters, and thirty bacterial classes, and characterized the cassette variety in size and content among different species, highlighting a significant role of short cassettes. The preference towards co-localization of carbohydrate metabolism genes varies between 40 and 76% for bacterial taxa. Analysis of frequently co-localized genes yielded forty-five significant pairwise links between genes belonging to different functional classes. The number of such links per class range from zero to eight, demonstrating varying preferences of respective genes towards a specific chromosomal neighborhood. Genes from eleven functional classes tend to co-localize with genes from the same class, indicating an important role of clustering of genes with similar functions. At that, in most cases such co-localization does not originate from local duplication events. Overall, we describe a complex web formed by evolutionary relationships of bacterial

  18. Dichotomy of major genes and polygenes

    International Nuclear Information System (INIS)

    Jain, S.

    1989-01-01

    In order to facilitate domestication and breeding of new or underexploited crop species, the genetic basis of many traits must be critically investigated, and both naturally occurring and induced mutations should be utilized. Classically, most breeding procedures have invoked the dichotomy of major genes versus polygenes (or discrete versus continuously varying traits) which is briefly reviewed here from several viewpoints. Clearly, the evidence for two distinct classes of genes (or gene effects on phenotype) and traits is largely a product of different forms of genetic analyses and their primary objectives as well as of researchers' expectations. Superimposed on the simplest Mendelian ratios and genome maps are numerous sources of molecular variation and gene expression at many levels of phenotypic description. Many attempts to delineate developmental pathways and to identify genes controlling discrete vs. quantitative phenotypic variation have resulted in emphasis on multigenic models with specific gene effects at mappable loci but nonetheless modified by small effects. Thus, quantitative genetic variation may arise from multi-genic and multi-allelic systems of both structural and regulatory gene action and gene interactions which, from an empirical breeding perspective, might be adequately described by the biometrical and evolutionary models. Polygenic analyses were conceptually based on genetic parameters in these models (as caricatures of reality) but efforts to modify or reject them by identifying and mapping sources of phenotypic variation through newer genetic methods are likely to enrich and not displace biometrical methods. Domestication programmes, in particular, should employ the entire array of genetic discoveries and methodologies. (author). 71 refs, 1 fig., 1 tab

  19. Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

    Science.gov (United States)

    Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

    2016-01-01

    The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

  20. Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don

    Directory of Open Access Journals (Sweden)

    Zheng Xiao

    2016-10-01

    Full Text Available The quantitative real-time polymerase chain reaction (qRT-PCR approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder and BestKeeper. The results showed that EF1-α (elongation factor 1-alpha, 18S (18s ribosomal RNA and RPL3 (ribosomal protein L3 were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin (TUB was the least stable. ACT5 (actin, RPL3, 18S and EF1-α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle. Furthermore, the expression profiles of RmPSY (phytoene synthase and RmPDS (phytoene dehydrogenase were assessed using EF1-α, 18S, ACT5, and RPL3 and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle.

  1. Geographical patterns of adaptation within a species' range : Interactions between drift and gene flow

    NARCIS (Netherlands)

    Alleaume-Benharira, M; Pen, IR; Ronce, O

    We use individual-based stochastic simulations and analytical deterministic predictions to investigate the interaction between drift, natural selection and gene flow on the patterns of local adaptation across a fragmented species' range under clinally varying selection. Migration between populations

  2. Primetime for Learning Genes.

    Science.gov (United States)

    Keifer, Joyce

    2017-02-11

    Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene ( BDNF ), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

  3. CRDB: database of chemosensory receptor gene families in vertebrate.

    Directory of Open Access Journals (Sweden)

    Dong Dong

    Full Text Available Chemosensory receptors (CR are crucial for animals to sense the environmental changes and survive on earth. The emergence of whole-genome sequences provides us an opportunity to identify the entire CR gene repertoires. To completely gain more insight into the evolution of CR genes in vertebrates, we identified the nearly all CR genes in 25 vertebrates using homology-based approaches. Among these CR gene repertoires, nearly half of them were identified for the first time in those previously uncharacterized species, such as the guinea pig, giant panda and elephant, etc. Consistent with previous findings, we found that the numbers of CR genes vary extensively among different species, suggesting an extreme form of 'birth-and-death' evolution. For the purpose of facilitating CR gene analysis, we constructed a database with the goals to provide a resource for CR genes annotation and a web tool for exploring their evolutionary patterns. Besides a search engine for the gene extraction from a specific chromosome region, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of CR genes. Our work can provide a rigorous platform for further study on the evolution of CR genes in vertebrates.

  4. Ribosomal protein gene knockdown causes developmental defects in zebrafish.

    Directory of Open Access Journals (Sweden)

    Tamayo Uechi

    Full Text Available The ribosomal proteins (RPs form the majority of cellular proteins and are mandatory for cellular growth. RP genes have been linked, either directly or indirectly, to various diseases in humans. Mutations in RP genes are also associated with tissue-specific phenotypes, suggesting a possible role in organ development during early embryogenesis. However, it is not yet known how mutations in a particular RP gene result in specific cellular changes, or how RP genes might contribute to human diseases. The development of animal models with defects in RP genes will be essential for studying these questions. In this study, we knocked down 21 RP genes in zebrafish by using morpholino antisense oligos to inhibit their translation. Of these 21, knockdown of 19 RPs resulted in the development of morphants with obvious deformities. Although mutations in RP genes, like other housekeeping genes, would be expected to result in nonspecific developmental defects with widespread phenotypes, we found that knockdown of some RP genes resulted in phenotypes specific to each gene, with varying degrees of abnormality in the brain, body trunk, eyes, and ears at about 25 hours post fertilization. We focused further on the organogenesis of the brain. Each knocked-down gene that affected the morphogenesis of the brain produced a different pattern of abnormality. Among the 7 RP genes whose knockdown produced severe brain phenotypes, 3 human orthologs are located within chromosomal regions that have been linked to brain-associated diseases, suggesting a possible involvement of RP genes in brain or neurological diseases. The RP gene knockdown system developed in this study could be a powerful tool for studying the roles of ribosomes in human diseases.

  5. Characteristics of gene mutation in Chinese patients with hereditary hemochromatosis

    Directory of Open Access Journals (Sweden)

    LYU Tingxia

    2016-08-01

    Full Text Available ObjectiveTo investigate the characteristics of gene mutation in Chinese patients with hereditary hemochromatosis (HH. MethodsA total of 9 patients with HH who visited Beijing Friendship Hospital, Capital Medical University from January 2013 to December 2015 were enrolled. The genomic DNA was extracted, and PCR amplification and Sanger sequencing were performed for all the exons of four genotypes of HH, i.e., HFE (type Ⅰ, HJV (type ⅡA, HAMP (type ⅡB, TFR2 (type Ⅲ, and SLC40A1 (type Ⅳ to analyze gene mutations. A total of 50 healthy subjects were enrolled as control group to analyze the prevalence of identified gene mutations in a healthy population. ResultsOf all patients, 2 had H63D mutation of HFE gene in type Ⅰ HH, 1 had E3D mutation of HJV gene in type ⅡA HH, 2 had I238M mutation of TFR2 gene in type Ⅲ HH, and 1 had IVS 3+10 del GTT splice mutation of SLC40A1 gene in type Ⅳ HH. No patients had C282Y mutation of HFE gene in type Ⅰ HH which was commonly seen in European and American populations. Five patients had no missense mutation or splice mutation. In addition, it was found in a family that a HH patient had E3D mutation of HJV gene, H63D mutation of HFE gene, and I238M mutation of TFR2 gene, but the healthy brother and sister carrying two of these mutations did not had the phenotype of HH. ConclusionHH gene mutations vary significantly across patients of different races, and non-HFE-HH is dominant in the Chinese population. There may be HH genes which are different from known genes, and further investigation is needed.

  6. Observer-based linear parameter varying H∞ tracking control for hypersonic vehicles

    Directory of Open Access Journals (Sweden)

    Yiqing Huang

    2016-11-01

    Full Text Available This article aims to develop observer-based linear parameter varying output feedback H∞ tracking controller for hypersonic vehicles. Due to the complexity of an original nonlinear model of the hypersonic vehicle dynamics, a slow–fast loop linear parameter varying polytopic model is introduced for system stability analysis and controller design. Then, a state observer is developed by linear parameter varying technique in order to estimate the unmeasured attitude angular for slow loop system. Also, based on the designed linear parameter varying state observer, a kind of attitude tracking controller is presented to reduce tracking errors for all bounded reference attitude angular inputs. The closed-loop linear parameter varying system is proved to be quadratically stable by Lypapunov function technique. Finally, simulation results show that the developed linear parameter varying H∞ controller has good tracking capability for reference commands.

  7. A systematic study on drug-response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia

    Science.gov (United States)

    Liu, Xiaoming; Yang, Jiasheng; Zhang, Yi; Fang, Yun; Wang, Fayou; Wang, Jun; Zheng, Xiaoqi; Yang, Jialiang

    2016-03-01

    We have studied drug-response associated (DRA) gene expressions by applying a systems biology framework to the Cancer Cell Line Encyclopedia data. More than 4,000 genes are inferred to be DRA for at least one drug, while the number of DRA genes for each drug varies dramatically from almost 0 to 1,226. Functional enrichment analysis shows that the DRA genes are significantly enriched in genes associated with cell cycle and plasma membrane. Moreover, there might be two patterns of DRA genes between genders. There are significantly shared DRA genes between male and female for most drugs, while very little DRA genes tend to be shared between the two genders for a few drugs targeting sex-specific cancers (e.g., PD-0332991 for breast cancer and ovarian cancer). Our analyses also show substantial difference for DRA genes between young and old samples, suggesting the necessity of considering the age effects for personalized medicine in cancers. Lastly, differential module and key driver analyses confirm cell cycle related modules as top differential ones for drug sensitivity. The analyses also reveal the role of TSPO, TP53, and many other immune or cell cycle related genes as important key drivers for DRA network modules. These key drivers provide new drug targets to improve the sensitivity of cancer therapy.

  8. Identification of Time-Varying Pilot Control Behavior in Multi-Axis Control Tasks

    Science.gov (United States)

    Zaal, Peter M. T.; Sweet, Barbara T.

    2012-01-01

    Recent developments in fly-by-wire control architectures for rotorcraft have introduced new interest in the identification of time-varying pilot control behavior in multi-axis control tasks. In this paper a maximum likelihood estimation method is used to estimate the parameters of a pilot model with time-dependent sigmoid functions to characterize time-varying human control behavior. An experiment was performed by 9 general aviation pilots who had to perform a simultaneous roll and pitch control task with time-varying aircraft dynamics. In 8 different conditions, the axis containing the time-varying dynamics and the growth factor of the dynamics were varied, allowing for an analysis of the performance of the estimation method when estimating time-dependent parameter functions. In addition, a detailed analysis of pilots adaptation to the time-varying aircraft dynamics in both the roll and pitch axes could be performed. Pilot control behavior in both axes was significantly affected by the time-varying aircraft dynamics in roll and pitch, and by the growth factor. The main effect was found in the axis that contained the time-varying dynamics. However, pilot control behavior also changed over time in the axis not containing the time-varying aircraft dynamics. This indicates that some cross coupling exists in the perception and control processes between the roll and pitch axes.

  9. Genes and Social Behavior

    OpenAIRE

    Robinson, Gene E.; Fernald, Russell D.; Clayton, David F.

    2008-01-01

    What specific genes and regulatory sequences contribute to the organization and functioning of brain circuits that support social behavior? How does social experience interact with information in the genome to modulate these brain circuits? Here we address these questions by highlighting progress that has been made in identifying and understanding two key “vectors of influence” that link genes, brain, and social behavior: 1) social information alters gene readout in the brain to influence beh...

  10. An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity

    Directory of Open Access Journals (Sweden)

    Struchalin Maksim V

    2012-01-01

    Full Text Available Abstract Background Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties. We and Pare with colleagues (2010 developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants. Results In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests. Conclusions Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context.

  11. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.

    Science.gov (United States)

    Ben-Ari Fuchs, Shani; Lieder, Iris; Stelzer, Gil; Mazor, Yaron; Buzhor, Ella; Kaplan, Sergey; Bogoch, Yoel; Plaschkes, Inbar; Shitrit, Alina; Rappaport, Noa; Kohn, Asher; Edgar, Ron; Shenhav, Liraz; Safran, Marilyn; Lancet, Doron; Guan-Golan, Yaron; Warshawsky, David; Shtrichman, Ronit

    2016-03-01

    Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from "data-to-knowledge-to-innovation," a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ ( geneanalytics.genecards.org ), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®--the human gene database; the MalaCards-the human diseases database; and the PathCards--the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®--the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell "cards" in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics

  12. History of gene therapy.

    Science.gov (United States)

    Wirth, Thomas; Parker, Nigel; Ylä-Herttuala, Seppo

    2013-08-10

    Two decades after the initial gene therapy trials and more than 1700 approved clinical trials worldwide we not only have gained much new information and knowledge regarding gene therapy in general, but also learned to understand the concern that has persisted in society. Despite the setbacks gene therapy has faced, success stories have increasingly emerged. Examples for these are the positive recommendation for a gene therapy product (Glybera) by the EMA for approval in the European Union and the positive trials for the treatment of ADA deficiency, SCID-X1 and adrenoleukodystrophy. Nevertheless, our knowledge continues to grow and during the course of time more safety data has become available that helps us to develop better gene therapy approaches. Also, with the increased understanding of molecular medicine, we have been able to develop more specific and efficient gene transfer vectors which are now producing clinical results. In this review, we will take a historical view and highlight some of the milestones that had an important impact on the development of gene therapy. We will also discuss briefly the safety and ethical aspects of gene therapy and address some concerns that have been connected with gene therapy as an important therapeutic modality. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  14. Research progress of the bitter taste receptor genes in primates.

    Science.gov (United States)

    Feng, Ping; Luo, Rui-Jian

    2018-02-20

    Among the five basic tastes (umami, sweet, bitter, salty and sour), the perception of bitterness is believed to protect animals from digesting toxic and harmful substances, thus it is vital for animal survival. The taste of bitterness is triggered by the interaction between bitter substances and bitter taste receptors, which are encoded by Tas2rs. The gene numbers vary largely across species to meet different demands. So far, several ligands of bitter receptors have been identified in primates. They also discovered that the selective pressure of certain bitter taste receptor genes vary across taxa, genes or even different functional regions of the gene. In this review, we summarize the research progress of bitter taste receptor genes in primates by introducing the functional diversity of bitter receptors, the specific interaction between bitter taste receptors and ligands, the relationship between the evolutionary pattern of bitter taste receptors and diets, and the adaptive evolution of bitter taste receptor genes. We aim to provide a reference for further research on bitter receptor genes in primates.

  15. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi.

    Science.gov (United States)

    Huang, Xuena; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

    2016-01-15

    As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Dosage sensitivity shapes the evolution of copy-number varied regions.

    Directory of Open Access Journals (Sweden)

    Benjamin Schuster-Böckler

    2010-03-01

    Full Text Available Dosage sensitivity is an important evolutionary force which impacts on gene dispensability and duplicability. The newly available data on human copy-number variation (CNV allow an analysis of the most recent and ongoing evolution. Provided that heterozygous gene deletions and duplications actually change gene dosage, we expect to observe negative selection against CNVs encompassing dosage sensitive genes. In this study, we make use of several sources of population genetic data to identify selection on structural variations of dosage sensitive genes. We show that CNVs can directly affect expression levels of contained genes. We find that genes encoding members of protein complexes exhibit limited expression variation and overlap significantly with a manually derived set of dosage sensitive genes. We show that complexes and other dosage sensitive genes are underrepresented in CNV regions, with a particular bias against frequent variations and duplications. These results suggest that dosage sensitivity is a significant force of negative selection on regions of copy-number variation.

  17. Disruption of the neurexin 1 gene is associated with schizophrenia

    DEFF Research Database (Denmark)

    Rujescu, Dan; Ingason, Andres; Cichon, Sven

    2009-01-01

    may vary according to the level of functional impact on the gene, we next restricted the association analysis to CNVs that disrupt exons (0.24% of cases and 0.015% of controls). These were significantly associated with a high odds ratio (P = 0.0027; OR 8.97, 95% CI 1.8-51.9). We conclude that NRXN1...

  18. Association testing to detect gene-gene interactions on sex chromosomes in trio data

    Directory of Open Access Journals (Sweden)

    Yeonok eLee

    2013-11-01

    Full Text Available Autism Spectrum Disorder (ASD occurs more often among males than females in a 4:1 ratio. Among theories used to explain the causes of ASD, the X chromosome and the Y chromosome theories attribute ASD to X-linked mutation and the male-limited gene expressions on the Y chromosome, respectively. Despite the rationale of the theory, studies have failed to attribute the sex-biased ratio to the significant linkage or association on the regions of interest on X chromosome. We further study the gender biased ratio by examining the possible interaction effects between two genes in the sex chromosomes. We propose a logistic regression model with mixed effects to detect gene-gene interactions on sex chromosomes. We investigated the power and type I error rates of the approach for a range of minor allele frequencies and varying linkage disequilibrium between markers and QTLs. We also evaluated the robustness of the model to population stratification. We applied the model to a trio-family data set with an ASD affected male child to study gene-gene interactions on sex chromosomes.

  19. Gene Expression Commons: an open platform for absolute gene expression profiling.

    Directory of Open Access Journals (Sweden)

    Jun Seita

    Full Text Available Gene expression profiling using microarrays has been limited to comparisons of gene expression between small numbers of samples within individual experiments. However, the unknown and variable sensitivities of each probeset have rendered the absolute expression of any given gene nearly impossible to estimate. We have overcome this limitation by using a very large number (>10,000 of varied microarray data as a common reference, so that statistical attributes of each probeset, such as the dynamic range and threshold between low and high expression, can be reliably discovered through meta-analysis. This strategy is implemented in a web-based platform named "Gene Expression Commons" (https://gexc.stanford.edu/ which contains data of 39 distinct highly purified mouse hematopoietic stem/progenitor/differentiated cell populations covering almost the entire hematopoietic system. Since the Gene Expression Commons is designed as an open platform, investigators can explore the expression level of any gene, search by expression patterns of interest, submit their own microarray data, and design their own working models representing biological relationship among samples.

  20. Stabilization of the Wave Equation with Boundary Time-Varying Delay

    Directory of Open Access Journals (Sweden)

    Hao Li

    2014-01-01

    Full Text Available We study the stabilization of the wave equation with variable coefficients in a bounded domain and a time-varying delay term in the time-varying, weakly nonlinear boundary feedbacks. By the Riemannian geometry methods and a suitable assumption of nonlinearity, we obtain the uniform decay of the energy of the closed loop system.

  1. Eesti filmil läks hästi Karlovy Vary festivalil / Marianne Kõrver

    Index Scriptorium Estoniae

    Kõrver, Marianne, 1980-

    2006-01-01

    Lühimängufilm "Tühirand", režissöör Veiko Õunpuu, osales Karlovy Vary rahvusvahelise filmifestivali "Forum of Independents" programmis. 41. Karlovy Vary filmifestivali avas Korea režissööri Kim Ki-duki "Aeg". Lühidalt ka auhinnatutest ja huvitavamatest filmidest

  2. The Effects of Constant versus Varied Reinforcers on Preference and Resistance to Change

    Science.gov (United States)

    Milo, Jessie-Sue; Mace, F. Charles; Nevin, John A.

    2010-01-01

    Previous research has demonstrated that factors such as reinforcer frequency, amount, and delay have similar effects on resistance to change and preference. In the present study, 4 boys with autism made choices between a constant reinforcer (one that was the same food item every trial) and a varied food reinforcer (one that varied randomly between…

  3. Robust and Fault-Tolerant Linear Parameter-Varying Control of Wind Turbines

    DEFF Research Database (Denmark)

    Sloth, Christoffer; Esbensen, Thomas; Stoustrup, Jakob

    2011-01-01

    High performance and reliability are required for wind turbines to be competitive within the energy market. To capture their nonlinear behavior, wind turbines are often modeled using parameter-varying models. In this paper we design and compare multiple linear parameter-varying (LPV) controllers,...

  4. A Bacteriophage-Acquired O-Antigen Polymerase (Wzyβ) from P. aeruginosa Serotype O16 Performs a Varied Mechanism Compared to Its Cognate Wzyα

    DEFF Research Database (Denmark)

    Taylor, Veronique L.; Hoage, Jesse F. J.; Thrane, Sandra Wingaard

    2016-01-01

    Pseudomonas aeruginosa is a Gram-negative bacterium that produces highly varied lipopolysaccharide (LPS) structures. The O antigen (O-Ag) in the LPS is synthesized through the Wzx/Wzy-dependent pathway where lipid-linked O-Ag repeats are polymerized by Wzy. Horizontal-gene transfer has been assoc...

  5. Chromatin loops, gene positioning, and gene expression

    NARCIS (Netherlands)

    Holwerda, S.; de Laat, W.

    2012-01-01

    Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the alpha- and beta-globin

  6. Stably Expressed Genes Involved in Basic Cellular Functions.

    Directory of Open Access Journals (Sweden)

    Kejian Wang

    Full Text Available Stably Expressed Genes (SEGs whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age in both sexes of F344 rats (n = 4/group; 320 samples. Expression changes (calculated as the maximum expression / minimum expression for each gene of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination, RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics or exogenous agents (e.g., drugs, environmental factors may cause serious adverse effects.

  7. Your Genes, Your Choices

    Science.gov (United States)

    Table of Contents Your Genes, Your Choices describes the Human Genome Project, the science behind it, and the ethical, legal, and social issues that are ... Nothing could be further from the truth. Your Genes, Your Choices points out how the progress of ...

  8. DNA repair genes

    International Nuclear Information System (INIS)

    Morimyo, Mitsuoki

    1995-01-01

    Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

  9. Antisense gene silencing

    DEFF Research Database (Denmark)

    Nielsen, Troels T; Nielsen, Jørgen E

    2013-01-01

    Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied...

  10. Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes.

    Directory of Open Access Journals (Sweden)

    Quan Li

    Full Text Available The rapid progress of genomic technologies has been providing new opportunities to address the need of maturity-onset diabetes of the young (MODY molecular diagnosis. However, whether a new mutation causes MODY can be questionable. A number of in silico methods have been developed to predict functional effects of rare human mutations. The purpose of this study is to compare the performance of different bioinformatics methods in the functional prediction of nonsynonymous mutations in each MODY gene, and provides reference matrices to assist the molecular diagnosis of MODY. Our study showed that the prediction scores by different methods of the diabetes mutations were highly correlated, but were more complimentary than replacement to each other. The available in silico methods for the prediction of diabetes mutations had varied performances across different genes. Applying gene-specific thresholds defined by this study may be able to increase the performance of in silico prediction of disease-causing mutations.

  11. Cloning, sequencing and variability analysis of the gap gene from Mycoplasma hominis

    DEFF Research Database (Denmark)

    Mygind, Tina; Jacobsen, Iben Søgaard; Melkova, Renata

    2000-01-01

    The gap gene encodes the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The gene was cloned and sequenced from the Mycoplasma hominis type strain PG21(T). The intraspecies variability was investigated by inspection of restriction fragment length polymorphism (RFLP) patterns...... after polymerase chain reaction (PCR) amplification of the gap gene from 15 strains and furthermore by sequencing of part of the gene in eight strains. The M. hominis gap gene was found to vary more than the Escherichia coli counterpart, but the variation at nucleotide level gave rise to only a few...

  12. The emergence and fate of horizontally acquired genes in Escherichia coli

    NARCIS (Netherlands)

    Passel, van M.W.J.; Marri, P.R.; Ochman, H.

    2008-01-01

    Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the

  13. Fast space-varying convolution using matrix source coding with applications to camera stray light reduction.

    Science.gov (United States)

    Wei, Jianing; Bouman, Charles A; Allebach, Jan P

    2014-05-01

    Many imaging applications require the implementation of space-varying convolution for accurate restoration and reconstruction of images. Here, we use the term space-varying convolution to refer to linear operators whose impulse response has slow spatial variation. In addition, these space-varying convolution operators are often dense, so direct implementation of the convolution operator is typically computationally impractical. One such example is the problem of stray light reduction in digital cameras, which requires the implementation of a dense space-varying deconvolution operator. However, other inverse problems, such as iterative tomographic reconstruction, can also depend on the implementation of dense space-varying convolution. While space-invariant convolution can be efficiently implemented with the fast Fourier transform, this approach does not work for space-varying operators. So direct convolution is often the only option for implementing space-varying convolution. In this paper, we develop a general approach to the efficient implementation of space-varying convolution, and demonstrate its use in the application of stray light reduction. Our approach, which we call matrix source coding, is based on lossy source coding of the dense space-varying convolution matrix. Importantly, by coding the transformation matrix, we not only reduce the memory required to store it; we also dramatically reduce the computation required to implement matrix-vector products. Our algorithm is able to reduce computation by approximately factoring the dense space-varying convolution operator into a product of sparse transforms. Experimental results show that our method can dramatically reduce the computation required for stray light reduction while maintaining high accuracy.

  14. Radionuclide reporter gene imaging

    International Nuclear Information System (INIS)

    Min, Jung Joon

    2004-01-01

    Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studies published to date demonstrate that reporter gene imaging technologies will help to accelerate model validation as well as allow for clinical monitoring of human diseases

  15. Radionuclide reporter gene imaging

    Energy Technology Data Exchange (ETDEWEB)

    Min, Jung Joon [School of Medicine, Chonnam National Univ., Gwangju (Korea, Republic of)

    2004-04-01

    Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studies published to date demonstrate that reporter gene imaging technologies will help to accelerate model validation as well as allow for clinical monitoring of human diseases.

  16. Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets

    Directory of Open Access Journals (Sweden)

    Suegene Noh

    2016-02-01

    Full Text Available In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK and apolipoprotein A-1 binding protein (APBP. These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of

  17. A longitudinal study of gene expression in healthy individuals

    Directory of Open Access Journals (Sweden)

    Tessier Michel

    2009-06-01

    Full Text Available Abstract Background The use of gene expression in venous blood either as a pharmacodynamic marker in clinical trials of drugs or as a diagnostic test requires knowledge of the variability in expression over time in healthy volunteers. Here we defined a normal range of gene expression over 6 months in the blood of four cohorts of healthy men and women who were stratified by age (22–55 years and > 55 years and gender. Methods Eleven immunomodulatory genes likely to play important roles in inflammatory conditions such as rheumatoid arthritis and infection in addition to four genes typically used as reference genes were examined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR, as well as the full genome as represented by Affymetrix HG U133 Plus 2.0 microarrays. Results Gene expression levels as assessed by qRT-PCR and microarray were relatively stable over time with ~2% of genes as measured by microarray showing intra-subject differences over time periods longer than one month. Fifteen genes varied by gender. The eleven genes examined by qRT-PCR remained within a limited dynamic range for all individuals. Specifically, for the seven most stably expressed genes (CXCL1, HMOX1, IL1RN, IL1B, IL6R, PTGS2, and TNF, 95% of all samples profiled fell within 1.5–2.5 Ct, the equivalent of a 4- to 6-fold dynamic range. Two subjects who experienced severe adverse events of cancer and anemia, had microarray gene expression profiles that were distinct from normal while subjects who experienced an infection had only slightly elevated levels of inflammatory markers. Conclusion This study defines the range and variability of gene expression in healthy men and women over a six-month period. These parameters can be used to estimate the number of subjects needed to observe significant differences from normal gene expression in clinical studies. A set of genes that varied by gender was also identified as were a set of genes with elevated

  18. Increasing Power by Sharing Information from Genetic Background and Treatment in Clustering of Gene Expression Time Series

    OpenAIRE

    Sura Zaki Alrashid; Muhammad Arifur Rahman; Nabeel H Al-Aaraji; Neil D Lawrence; Paul R Heath

    2018-01-01

    Clustering of gene expression time series gives insight into which genes may be co-regulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with different conditions or genetic background. This paper develops
a new clustering method that allows each cluster to be parameterised according to whether the behaviour of the genes across conditions is correlated or anti-correlated. By specifying correlati...

  19. Clustering Gene Expression Time Series with Coregionalization: Speed propagation of ALS

    OpenAIRE

    Rahman, Muhammad Arifur; Heath, Paul R.; Lawrence, Neil D.

    2018-01-01

    Clustering of gene expression time series gives insight into which genes may be coregulated, allowing us to discern the activity of pathways in a given microarray experiment. Of particular interest is how a given group of genes varies with different model conditions or genetic background. Amyotrophic lateral sclerosis (ALS), an irreversible diverse neurodegenerative disorder showed consistent phenotypic differences and the disease progression is heterogeneous with significant variability. Thi...

  20. Genetic Localization of Foraging (For): A Major Gene for Larval Behavior in Drosophila Melanogaster

    OpenAIRE

    de-Belle, J. S.; Hilliker, A. J.; Sokolowski, M. B.

    1989-01-01

    Localizing genes for quantitative traits by conventional recombination mapping is a formidable challenge because environmental variation, minor genes, and genetic markers have modifying effects on continuously varying phenotypes. We describe ``lethal tagging,'' a method used in conjunction with deficiency mapping for localizing major genes associated with quantitative traits. Rover/sitter is a naturally occurring larval foraging polymorphism in Drosophila melanogaster which has a polygenic pa...

  1. An integrative time-varying frequency detection and channel sounding method for dynamic plasma sheath

    Science.gov (United States)

    Shi, Lei; Yao, Bo; Zhao, Lei; Liu, Xiaotong; Yang, Min; Liu, Yanming

    2018-01-01

    The plasma sheath-surrounded hypersonic vehicle is a dynamic and time-varying medium and it is almost impossible to calculate time-varying physical parameters directly. The in-fight detection of the time-varying degree is important to understand the dynamic nature of the physical parameters and their effect on re-entry communication. In this paper, a constant envelope zero autocorrelation (CAZAC) sequence based on time-varying frequency detection and channel sounding method is proposed to detect the plasma sheath electronic density time-varying property and wireless channel characteristic. The proposed method utilizes the CAZAC sequence, which has excellent autocorrelation and spread gain characteristics, to realize dynamic time-varying detection/channel sounding under low signal-to-noise ratio in the plasma sheath environment. Theoretical simulation under a typical time-varying radio channel shows that the proposed method is capable of detecting time-variation frequency up to 200 kHz and can trace the channel amplitude and phase in the time domain well under -10 dB. Experimental results conducted in the RF modulation discharge plasma device verified the time variation detection ability in practical dynamic plasma sheath. Meanwhile, nonlinear phenomenon of dynamic plasma sheath on communication signal is observed thorough channel sounding result.

  2. Regionally-varying and regionally-uniform electricity pricing policies compared across four usage categories

    International Nuclear Information System (INIS)

    Cho, Seong-Hoon; Kim, Taeyoung; Kim, Hyun Jae; Park, Kihyun; Roberts, Roland K.

    2015-01-01

    The objective of our research is to predict how electricity demand varies spatially between status quo regionally-uniform electricity pricing and hypothetical regionally-varying electricity pricing across usage categories. We summarize the empirical results of a case study of electricity demand in South Korea with three key findings and their related implications. First, the price elasticities of electricity demand differ across usage categories. Specifically, electricity demands for manufacturing and retail uses are price inelastic and close to unit elastic, respectively, while those for agricultural and residential uses are not statistically significant. This information is important in designing energy policy, because higher electricity prices could reduce electricity demands for manufacturing and retail uses, resulting in slower growth in those sectors. Second, spatial spillovers in electricity demand vary across uses. Understanding the spatial structure of electricity demand provides useful information to energy policy makers for anticipating changes in demand across regions via regionally-varying electricity pricing for different uses. Third, simulation results suggest that spatial variations among electricity demands by usage category under a regionally-varying electricity-pricing policy differ from those under a regionally-uniform electricity-pricing policy. Differences in spatial changes between the policies provide information for developing a realistic regionally-varying electricity-pricing policy according to usage category. - Highlights: • We compare regionally-varying and regionally-uniform electricity pricing policies. • We summarize empirical results of a case study of electricity demand in South Korea. • We confirm that spatial spillovers in electricity demands vary across different uses. • We find positive spatial spillovers in the manufacturing and residential sectors. • Our methods help policy makers evaluate regionally-varying pricing

  3. Gene amplification in carcinogenesis

    Directory of Open Access Journals (Sweden)

    Lucimari Bizari

    2006-01-01

    Full Text Available Gene amplification increases the number of genes in a genome and can give rise to karyotype abnormalities called double minutes (DM and homogeneously staining regions (HSR, both of which have been widely observed in human tumors but are also known to play a major role during embryonic development due to the fact that they are responsible for the programmed increase of gene expression. The etiology of gene amplification during carcinogenesis is not yet completely understood but can be considered a result of genetic instability. Gene amplification leads to an increase in protein expression and provides a selective advantage during cell growth. Oncogenes such as CCND1, c-MET, c-MYC, ERBB2, EGFR and MDM2 are amplified in human tumors and can be associated with increased expression of their respective proteins or not. In general, gene amplification is associated with more aggressive tumors, metastases, resistance to chemotherapy and a decrease in the period during which the patient stays free of the disease. This review discusses the major role of gene amplification in the progression of carcinomas, formation of genetic markers and as possible therapeutic targets for the development of drugs for the treatment of some types of tumors.

  4. Synchronization of uncertain time-varying network based on sliding mode control technique

    Science.gov (United States)

    Lü, Ling; Li, Chengren; Bai, Suyuan; Li, Gang; Rong, Tingting; Gao, Yan; Yan, Zhe

    2017-09-01

    We research synchronization of uncertain time-varying network based on sliding mode control technique. The sliding mode control technique is first modified so that it can be applied to network synchronization. Further, by choosing the appropriate sliding surface, the identification law of uncertain parameter, the adaptive law of the time-varying coupling matrix element and the control input of network are designed, it is sure that the uncertain time-varying network can synchronize effectively the synchronization target. At last, we perform some numerical simulations to demonstrate the effectiveness of the proposed results.

  5. Experimental study on the critical heat flux in a varying acceleration field, (1)

    International Nuclear Information System (INIS)

    Kusunoki, Tsuyoshi; Yokomura, Takeyoshi; Otsuji, Tomoo; Ikawa, Masahiro; Kurosawa, Akira.

    1988-12-01

    It is very important for the thermohydraulic design and for the safety assesement of marine reactors, to understand the effect of varying acceleration induced by ship motion on critical heart flux. The purpose of this joint study is to examine quantitatively the influence of varying acceleration on the behavior of bubbles. In the experiment, FREON-113 was used as working fluid. This report describes some experimental results; measurements of void fraction and bubble velocity near the heat transfer surface, measurement of bubble size under stationary acceleration field and observation of bubble behavior under varying acceleration field. (author)

  6. Exponential stability of fuzzy cellular neural networks with constant and time-varying delays

    International Nuclear Information System (INIS)

    Liu Yanqing; Tang Wansheng

    2004-01-01

    In this Letter, the global stability of delayed fuzzy cellular neural networks (FCNN) with either constant delays or time varying delays is proposed. Firstly, we give the existence and uniqueness of the equilibrium point by using the theory of topological degree and the properties of nonsingular M-matrix and the sufficient conditions for ascertaining the global exponential stability by constructing a suitable Lyapunov functional. Secondly, the criteria for guaranteeing the global exponential stability of FCNN with time varying delays are given and the estimation of exponential convergence rate with regard to speed of vary of delays is presented by constructing a suitable Lyapunov functional

  7. Globally Asymptotic Stability of Stochastic Nonlinear Systems with Time-Varying Delays via Output Feedback Control

    Directory of Open Access Journals (Sweden)

    Mingzhu Song

    2016-01-01

    Full Text Available We address the problem of globally asymptotic stability for a class of stochastic nonlinear systems with time-varying delays. By the backstepping method and Lyapunov theory, we design a linear output feedback controller recursively based on the observable linearization for a class of stochastic nonlinear systems with time-varying delays to guarantee that the closed-loop system is globally asymptotically stable in probability. In particular, we extend the deterministic nonlinear system to stochastic nonlinear systems with time-varying delays. Finally, an example and its simulations are given to illustrate the theoretical results.

  8. Robustness Analysis of Hybrid Stochastic Neural Networks with Neutral Terms and Time-Varying Delays

    Directory of Open Access Journals (Sweden)

    Chunmei Wu

    2015-01-01

    Full Text Available We analyze the robustness of global exponential stability of hybrid stochastic neural networks subject to neutral terms and time-varying delays simultaneously. Given globally exponentially stable hybrid stochastic neural networks, we characterize the upper bounds of contraction coefficients of neutral terms and time-varying delays by using the transcendental equation. Moreover, we prove theoretically that, for any globally exponentially stable hybrid stochastic neural networks, if additive neutral terms and time-varying delays are smaller than the upper bounds arrived, then the perturbed neural networks are guaranteed to also be globally exponentially stable. Finally, a numerical simulation example is given to illustrate the presented criteria.

  9. On the synchronization of neural networks containing time-varying delays and sector nonlinearity

    International Nuclear Information System (INIS)

    Yan, J.-J.; Lin, J.-S.; Hung, M.-L.; Liao, T.-L.

    2007-01-01

    We present a systematic design procedure for synchronization of neural networks subject to time-varying delays and sector nonlinearity in the control input. Based on the drive-response concept and the Lyapunov stability theorem, a memoryless decentralized control law is proposed which guarantees exponential synchronization even when input nonlinearity is present. The supplementary requirement that the time-derivative of time-varying delays must be smaller than one is released for the proposed control scheme. A four-dimensional Hopfield neural network with time-varying delays is presented as the illustrative example to demonstrate the effectiveness of the proposed synchronization scheme

  10. Dynamic evolution of bitter taste receptor genes in vertebrates

    Directory of Open Access Journals (Sweden)

    Jones Gareth

    2009-01-01

    Full Text Available Abstract Background Sensing bitter tastes is crucial for many animals because it can prevent them from ingesting harmful foods. This process is mainly mediated by the bitter taste receptors (T2R, which are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires, and marked variation in repertoire size has been noted among species. However, the mechanisms underlying the evolution of vertebrate T2R genes remain poorly understood. Results To better understand the evolutionary pattern of these genes, we identified 16 T2R gene repertoires based on the high coverage genome sequences of vertebrates and studied the evolutionary changes in the number of T2R genes during birth-and-death evolution using the reconciled-tree method. We found that the number of T2R genes and the fraction of pseudogenes vary extensively among species. Based on the results of phylogenetic analysis, we showed that T2R gene families in teleost fishes are more diverse than those in tetrapods. In addition to the independent gene expansions in teleost fishes, frogs and mammals, lineage-specific gene duplications were also detected in lizards. Furthermore, extensive gains and losses of T2R genes were detected in each lineage during their evolution, resulting in widely differing T2R gene repertoires. Conclusion These results further support the hypotheses that T2R gene repertoires are closely related to the dietary habits of different species and that birth-and-death evolution is associated with adaptations to dietary changes.

  11. Gene Overexpression: Uses, Mechanisms, and Interpretation

    Science.gov (United States)

    2012-01-01

    The classical genetic approach for exploring biological pathways typically begins by identifying mutations that cause a phenotype of interest. Overexpression or misexpression of a wild-type gene product, however, can also cause mutant phenotypes, providing geneticists with an alternative yet powerful tool to identify pathway components that might remain undetected using traditional loss-of-function analysis. This review describes the history of overexpression, the mechanisms that are responsible for overexpression phenotypes, tests that begin to distinguish between those mechanisms, the varied ways in which overexpression is used, the methods and reagents available in several organisms, and the relevance of overexpression to human disease. PMID:22419077

  12. Discharge characteristics of He-Ne-Xe gas mixture with varying Xe contents and at varying sustain electrode gap lengths in the plasma display panel

    International Nuclear Information System (INIS)

    Kwon, Ohyung; Whang, Ki-Woong; Bae, Hyun Sook

    2009-01-01

    The discharge characteristics of He-Ne-Xe gas mixture in the plasma display panel were investigated using a two-dimensional numerical simulation to understand the effects of adding He and varying the Xe contents in the gas mixture, and also varying sustain electrode gap. With 5% Xe content and 60 μm sustain electrode gap, decreased ionization led to the improvement of the vacuum ultraviolet (vuv) efficacy at increasing He mixing ratios. However, at 20% Xe content and 60 μm sustain electrode gap, increased electron heating improved the vuv efficacy until the He mixing ratio reached 0.7, but the efficacy decreased beyond the ratio of 0.7 due to the increased ionization of Xe atoms. At 5% Xe content and 200 μm sustain electrode gap, the vuv efficacy increased as a result of increased electron heating at the gap space at increasing He mixing ratios.

  13. Methanogenesis and methane genes

    International Nuclear Information System (INIS)

    Reeve, J.N.; Shref, B.A.

    1991-01-01

    An overview of the pathways leading to methane biosynthesis is presented. The steps investigated to date by gene cloning and DNA sequencing procedures are identified and discussed. The primary structures of component C of methyl coenzyme M reductase encoded by mcr operons in different methanogens are compared. Experiments to detect the primary structure of the genes encoding F420 reducing hydrogenase (frhABG) and methyl hydrogen reducing hydrogenase (mvhDGA) in methanobacterium thermoautotrophicum strain H are compared with each other and with eubacterial hydrogenase encoding genes. A biotechnological use for hydrogenases from hypermorphillic archaebacteria is suggested. (author)

  14. Quality assurance of Vari-source high dose rate (HDR) brachytherapy- remote after loader and cost effectiveness of Vari-source HDR- brachytherapy: NORI, Islamabad experience

    International Nuclear Information System (INIS)

    Ahmad, N.; Mahmood, H.; Jafri, S.R.A.

    2004-01-01

    A quality control of Vari-Source high dose rate (HDR) remote after loading brachytherapy machine was carried out and the cost effectiveness of HDR brachytherapy machine was also evaluated considering the cost of ten Iridium-192 wire sources at Nuclear Medicine, Oncology and Radiotherapy Institute (NORI), Islamabad, Pakistan. A total number of 253 intracavitary insertions were done in 98 patients from October 1996 to May 2001. The results of the quality control tests performed during 1996 to 2001 were within the acceptable limits. The cost effectiveness of Vari-Source HDR brachytherapy machine was also evaluated. The average cost per patient was calculated as US$ 491. Small number of patients was treated as the machine was used for gynecologic malignancies only. The objective was to assess the quality control status of HDR brachytherapy machine on patient treatment day, source exchange day and periodic day (monthly basis). It was found that the cost per patient can be minimized if other type of cancer patients are also treated on Vari-Source HDR machine. (author)

  15. Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes.

    Science.gov (United States)

    Choi, Kyuha; Reinhard, Carsten; Serra, Heïdi; Ziolkowski, Piotr A; Underwood, Charles J; Zhao, Xiaohui; Hardcastle, Thomas J; Yelina, Nataliya E; Griffin, Catherine; Jackson, Matthew; Mézard, Christine; McVean, Gil; Copenhaver, Gregory P; Henderson, Ian R

    2016-07-01

    Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.

  16. Sex Differences in Drosophila Somatic Gene Expression: Variation and Regulation by doublesex

    Directory of Open Access Journals (Sweden)

    Michelle N. Arbeitman

    2016-07-01

    Full Text Available Sex differences in gene expression have been widely studied in Drosophila melanogaster. Sex differences vary across strains, but many molecular studies focus on only a single strain, or on genes that show sexually dimorphic expression in many strains. How extensive variability is and whether this variability occurs among genes regulated by sex determination hierarchy terminal transcription factors is unknown. To address these questions, we examine differences in sexually dimorphic gene expression between two strains in Drosophila adult head tissues. We also examine gene expression in doublesex (dsx mutant strains to determine which sex-differentially expressed genes are regulated by DSX, and the mode by which DSX regulates expression. We find substantial variation in sex-differential expression. The sets of genes with sexually dimorphic expression in each strain show little overlap. The prevalence of different DSX regulatory modes also varies between the two strains. Neither the patterns of DSX DNA occupancy, nor mode of DSX regulation explain why some genes show consistent sex-differential expression across strains. We find that the genes identified as regulated by DSX in this study are enriched with known sites of DSX DNA occupancy. Finally, we find that sex-differentially expressed genes and genes regulated by DSX are highly enriched on the fourth chromosome. These results provide insights into a more complete pool of potential DSX targets, as well as revealing the molecular flexibility of DSX regulation.

  17. Porcine E. coli: virulence-associated genes, resistance genes and adhesion and probiotic activity tested by a new screening method.

    Science.gov (United States)

    Schierack, Peter; Rödiger, Stefan; Kuhl, Christoph; Hiemann, Rico; Roggenbuck, Dirk; Li, Ganwu; Weinreich, Jörg; Berger, Enrico; Nolan, Lisa K; Nicholson, Bryon; Römer, Antje; Frömmel, Ulrike; Wieler, Lothar H; Schröder, Christian

    2013-01-01

    We established an automated screening method to characterize adhesion of Escherichia coli to intestinal porcine epithelial cells (IPEC-J2) and their probiotic activity against infection by enteropathogenic E. coli (EPEC). 104 intestinal E. coli isolates from domestic pigs were tested by PCR for the occurrence of virulence-associated genes, genes coding for resistances to antimicrobial agents and metals, and for phylogenetic origin by PCR. Adhesion rates and probiotic activity were examined for correlation with the presence of these genes. Finally, data were compared with those from 93 E. coli isolates from wild boars. Isolates from domestic pigs carried a broad variety of all tested genes and showed great diversity in gene patterns. Adhesions varied with a maximum of 18.3 or 24.2 mean bacteria adherence per epithelial cell after 2 or 6 hours respectively. Most isolates from domestic pigs and wild boars showed low adherence, with no correlation between adhesion/probiotic activity and E. coli genes or gene clusters. The gene sfa/foc, encoding for a subunit of F1C fimbriae did show a positive correlative association with adherence and probiotic activity; however E. coli isolates from wild boars with the sfa/foc gene showed less adhesion and probiotic activity than E. coli with the sfa/foc gene isolated from domestic pigs after 6 hour incubation. In conclusion, screening porcine E. coli for virulence associated genes genes, adhesion to intestinal epithelial cells, and probiotic activity revealed a single important adhesion factor, several probiotic candidates, and showed important differences between E. coli of domestic pigs and wild boars.

  18. Porcine E. coli: virulence-associated genes, resistance genes and adhesion and probiotic activity tested by a new screening method.

    Directory of Open Access Journals (Sweden)

    Peter Schierack

    Full Text Available We established an automated screening method to characterize adhesion of Escherichia coli to intestinal porcine epithelial cells (IPEC-J2 and their probiotic activity against infection by enteropathogenic E. coli (EPEC. 104 intestinal E. coli isolates from domestic pigs were tested by PCR for the occurrence of virulence-associated genes, genes coding for resistances to antimicrobial agents and metals, and for phylogenetic origin by PCR. Adhesion rates and probiotic activity were examined for correlation with the presence of these genes. Finally, data were compared with those from 93 E. coli isolates from wild boars. Isolates from domestic pigs carried a broad variety of all tested genes and showed great diversity in gene patterns. Adhesions varied with a maximum of 18.3 or 24.2 mean bacteria adherence per epithelial cell after 2 or 6 hours respectively. Most isolates from domestic pigs and wild boars showed low adherence, with no correlation between adhesion/probiotic activity and E. coli genes or gene clusters. The gene sfa/foc, encoding for a subunit of F1C fimbriae did show a positive correlative association with adherence and probiotic activity; however E. coli isolates from wild boars with the sfa/foc gene showed less adhesion and probiotic activity than E. coli with the sfa/foc gene isolated from domestic pigs after 6 hour incubation. In conclusion, screening porcine E. coli for virulence associated genes genes, adhesion to intestinal epithelial cells, and probiotic activity revealed a single important adhesion factor, several probiotic candidates, and showed important differences between E. coli of domestic pigs and wild boars.

  19. Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies.

    Directory of Open Access Journals (Sweden)

    Lucie Kosinová

    Full Text Available The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3 in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information

  20. A 3D domain decomposition approach for the identification of spatially varying elastic material parameters

    KAUST Repository

    Moussawi, Ali; Lubineau, Gilles; Xu, Jiangping; Pan, Bing

    2015-01-01

    Summary: The post-treatment of (3D) displacement fields for the identification of spatially varying elastic material parameters is a large inverse problem that remains out of reach for massive 3D structures. We explore here the potential

  1. Analysing how plants in coastal wetlands respond to varying tidal regimes throughout their life cycles.

    Science.gov (United States)

    Xie, Tian; Cui, Baoshan; Li, Shanze

    2017-10-15

    Important to conserve plant species in coastal wetlands throughout their life cycle. All life stages in these habitats are exposed to varying tidal cycles. It is necessary to investigate all life stages as to how they respond to varying tidal regimes. We examine three wetlands containing populations of an endangered halophyte species, each subjected to different tidal regimes: (1). wetlands completely closed to tidal cycles; (2). wetlands directly exposed to tidal cycles (3). wetlands exposed to a partially closed tidal regime. Our results showed that the most threatened stage varied between wetlands subjected to these varying tidal regimes. We hypothesis that populations of this species have adapted to these different tidal regimes. Such information is useful in developing management options for coastal wetlands and modifying future barriers restricting tidal flushing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Chaetognath community and their responses to varying environmental factors in the northern Indian ocean.

    Digital Repository Service at National Institute of Oceanography (India)

    Kusum, K.K.; Vineetha, G.; Raveendran, T.V.; Nair, V.R.; Muraleedharan, K.R.; Achuthankutty, C.T.; Joseph, T.

    The ecology of the chaetognath community and its relation to varying environmental factors were studied in the eastern half of the northern Indian Ocean. Analysis of data from two major oceanographic programmes performed over four decades apart...

  3. Modeling of Electricity Demand for Azerbaijan: Time-Varying Coefficient Cointegration Approach

    Directory of Open Access Journals (Sweden)

    Jeyhun I. Mikayilov

    2017-11-01

    Full Text Available Recent literature has shown that electricity demand elasticities may not be constant over time and this has investigated using time-varying estimation methods. As accurate modeling of electricity demand is very important in Azerbaijan, which is a transitional country facing significant change in its economic outlook, we analyze whether the response of electricity demand to income and price is varying over time in this economy. We employed the Time-Varying Coefficient cointegration approach, a cutting-edge time-varying estimation method. We find evidence that income elasticity demonstrates sizeable variation for the period of investigation ranging from 0.48% to 0.56%. The study has some useful policy implications related to the income and price aspects of the electricity consumption in Azerbaijan.

  4. Positive Almost Periodic Solutions for a Time-Varying Fishing Model with Delay

    Directory of Open Access Journals (Sweden)

    Xia Li

    2011-01-01

    Full Text Available This paper is concerned with a time-varying fishing model with delay. By means of the continuation theorem of coincidence degree theory, we prove that it has at least one positive almost periodic solution.

  5. Long memory of financial time series and hidden Markov models with time-varying parameters

    DEFF Research Database (Denmark)

    Nystrup, Peter; Madsen, Henrik; Lindström, Erik

    Hidden Markov models are often used to capture stylized facts of daily returns and to infer the hidden state of financial markets. Previous studies have found that the estimated models change over time, but the implications of the time-varying behavior for the ability to reproduce the stylized...... facts have not been thoroughly examined. This paper presents an adaptive estimation approach that allows for the parameters of the estimated models to be time-varying. It is shown that a two-state Gaussian hidden Markov model with time-varying parameters is able to reproduce the long memory of squared...... daily returns that was previously believed to be the most difficult fact to reproduce with a hidden Markov model. Capturing the time-varying behavior of the parameters also leads to improved one-step predictions....

  6. Identification of time-varying nonlinear systems using differential evolution algorithm

    DEFF Research Database (Denmark)

    Perisic, Nevena; Green, Peter L; Worden, Keith

    2013-01-01

    (DE) algorithm for the identification of time-varying systems. DE is an evolutionary optimisation method developed to perform direct search in a continuous space without requiring any derivative estimation. DE is modified so that the objective function changes with time to account for the continuing......, thus identification of time-varying systems with nonlinearities can be a very challenging task. In order to avoid conventional least squares and gradient identification methods which require uni-modal and double differentiable objective functions, this work proposes a modified differential evolution...... inclusion of new data within an error metric. This paper presents results of identification of a time-varying SDOF system with Coulomb friction using simulated noise-free and noisy data for the case of time-varying friction coefficient, stiffness and damping. The obtained results are promising and the focus...

  7. Forecast Accuracy and Economic Gains from Bayesian Model Averaging using Time Varying Weights

    NARCIS (Netherlands)

    L.F. Hoogerheide (Lennart); R.H. Kleijn (Richard); H.K. van Dijk (Herman); M.J.C.M. Verbeek (Marno)

    2009-01-01

    textabstractSeveral Bayesian model combination schemes, including some novel approaches that simultaneously allow for parameter uncertainty, model uncertainty and robust time varying model weights, are compared in terms of forecast accuracy and economic gains using financial and macroeconomic time

  8. An Explicit MOT-TD-VIE Solver for Time Varying Media

    KAUST Repository

    Sayed, Sadeed Bin; Ulku, Huseyin Arda; Bagci, Hakan

    2016-01-01

    An explicit marching on-in-time (MOT) scheme for solving the time domain electric field integral equation enforced on volumes with time varying dielectric permittivity is proposed. Unknowns of the integral equation and the constitutive relation, i

  9. Gene Expression Omnibus (GEO)

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided...

  10. Holographic dark energy with varying gravitational constant in Hořava-Lifshitz cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Setare, M.R. [Department of Physics, University of Kurdistan, Pasdaran Ave., Sanandaj (Iran, Islamic Republic of); Jamil, Mubasher, E-mail: rezakord@ipm.ir, E-mail: mjamil@camp.nust.edu.pk [Center for Advanced Mathematics and Physics, National University of Sciences and Technology, Rawalpindi, 46000 (Pakistan)

    2010-02-01

    We investigate the holographic dark energy scenario with a varying gravitational constant in a flat background in the context of Hořava-Lifshitz gravity. We extract the exact differential equation determining the evolution of the dark energy density parameter, which includes G variation term. Also we discuss a cosmological implication of our work by evaluating the dark energy equation of state for low redshifts containing varying G corrections.

  11. Forced solitary Rossby waves under the influence of slowly varying topography with time

    International Nuclear Information System (INIS)

    Yang Hong-Wei; Yin Bao-Shu; Yang De-Zhou; Xu Zhen-Hua

    2011-01-01

    By using a weakly nonlinear and perturbation method, the generalized inhomogeneous Korteweg—de Vries (KdV)—Burgers equation is derived, which governs the evolution of the amplitude of Rossby waves under the influence of dissipation and slowly varying topography with time. The analysis indicates that dissipation and slowly varying topography with time are important factors in causing variation in the mass and energy of solitary waves. (general)

  12. Diversité variétale de manioc sur la base des nominations ...

    African Journals Online (AJOL)

    SARAH

    31 août 2016 ... très inégale, entrainant de fortes différences de portefeuilles variétaux entre villages et entre agriculteurs au sein de chaque site. Compte tenu des différences de portefeuilles variétaux observés, la mise en place d'une stratégie de conservation ..... Caillon S. et Lanouguère –Bruneau V. 2005 Gestion de.

  13. Should Unemployment Insurance Vary with the Unemployment Rate? Theory and Evidence

    OpenAIRE

    Kroft, Kory; Notowidigdo, Matthew J.

    2012-01-01

    We study how optimal unemployment insurance (UI) benefits vary over the business cycle by estimating how the moral hazard cost and the consumption smoothing benefit of UI vary with the unemployment rate. We find that the moral hazard cost is procyclical, greater when the unemployment rate is relatively low. By contrast, our evidence suggests that the consumption smoothing benefit of UI is acyclical. Using these estimates to calibrate our job search model, we find that a one standard deviation...

  14. Wavelet ridge diagnosis of time-varying elliptical signals with application to an oceanic eddy

    OpenAIRE

    Lilly , J. M.; Gascard , Jean-Claude

    2006-01-01

    International audience; A method for diagnosing the physical properties of a time-varying ellipse is presented. This essentially involves extending the notion of instantaneous frequency to the bivariate case. New complications, and possibilities, arise from the fact that there are several meaningful forms in which a time-varying ellipse may be represented. A perturbation analysis valid for the near-circular case clarifies these issues. Diagnosis of the ellipse properties may then be performed...

  15. Global stabilization of linear continuous time-varying systems with bounded controls

    International Nuclear Information System (INIS)

    Phat, V.N.

    2004-08-01

    This paper deals with the problem of global stabilization of a class of linear continuous time-varying systems with bounded controls. Based on the controllability of the nominal system, a sufficient condition for the global stabilizability is proposed without solving any Riccati differential equation. Moreover, we give sufficient conditions for the robust stabilizability of perturbation/uncertain linear time-varying systems with bounded controls. (author)

  16. Global exponential stability of uncertain fuzzy BAM neural networks with time-varying delays

    International Nuclear Information System (INIS)

    Syed Ali, M.; Balasubramaniam, P.

    2009-01-01

    In this paper, the Takagi-Sugeno (TS) fuzzy model representation is extended to the stability analysis for uncertain Bidirectional Associative Memory (BAM) neural networks with time-varying delays using linear matrix inequality (LMI) theory. A novel LMI-based stability criterion is obtained by LMI optimization algorithms to guarantee the exponential stability of uncertain BAM neural networks with time-varying delays which are represented by TS fuzzy models. Finally, the proposed stability conditions are demonstrated with numerical examples.

  17. Overexpression of antibiotic resistance genes in hospital effluents over time.

    Science.gov (United States)

    Rowe, Will P M; Baker-Austin, Craig; Verner-Jeffreys, David W; Ryan, Jim J; Micallef, Christianne; Maskell, Duncan J; Pearce, Gareth P

    2017-06-01

    Effluents contain a diverse abundance of antibiotic resistance genes that augment the resistome of receiving aquatic environments. However, uncertainty remains regarding their temporal persistence, transcription and response to anthropogenic factors, such as antibiotic usage. We present a spatiotemporal study within a river catchment (River Cam, UK) that aims to determine the contribution of antibiotic resistance gene-containing effluents originating from sites of varying antibiotic usage to the receiving environment. Gene abundance in effluents (municipal hospital and dairy farm) was compared against background samples of the receiving aquatic environment (i.e. the catchment source) to determine the resistome contribution of effluents. We used metagenomics and metatranscriptomics to correlate DNA and RNA abundance and identified differentially regulated gene transcripts. We found that mean antibiotic resistance gene and transcript abundances were correlated for both hospital ( ρ  = 0.9, two-tailed P  hospital effluent samples. High β-lactam resistance gene transcript abundance was related to hospital antibiotic usage over time and hospital effluents contained antibiotic residues. We conclude that effluents contribute high levels of antibiotic resistance genes to the aquatic environment; these genes are expressed at significant levels and are possibly related to the level of antibiotic usage at the effluent source. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

  18. Finding Genes for Schizophrenia

    OpenAIRE

    Åberg, Karolina

    2005-01-01

    Schizophrenia is one of our most common psychiatric diseases. It severely affects all aspects of psychological functions and results in loss of contact with reality. No cure exists and the treatments available today produce only partial relief for disease symptoms. The aim of this work is to better understand the etiology of schizophrenia by identification of candidate genes and gene pathways involved in the development of the disease. In a preliminarily study, the effects of medication and g...

  19. Epigenetics: beyond genes

    CSIR Research Space (South Africa)

    Fossey, A

    2009-06-01

    Full Text Available in forestry breeding. Keywords Gene regulation; chromatin; histone code hyporthesis; RNA silencing; post transcriptional gene silencing; forestry. Introduction to epigenetic phenomena Most living organisms share a vast amount of genetic information... (Rapp and Wendel, 2005). Epigenetic phenomena pervade all aspects of cell proliferation and plant development and are often in conflict with Mendelian models of genetics (Grant-Downton and Dickinson, 2005). A key element in many epigenetic effects...

  20. Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis

    Directory of Open Access Journals (Sweden)

    Nilsson Anders

    2010-03-01

    Full Text Available Abstract Background The histone-like protein Hc2 binds DNA in Chlamydia trachomatis and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the hctB gene, which encodes Hc2, were compared. Results This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in Bordetella but was now also found in other genera, including Burkholderia, Herminiimonas, Minibacterium and Ralstonia. Sequence determination resulted in 41 hctB variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements. Conclusions The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the Chlamydiacae. The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis.

  1. Time-varying output performances of piezoelectric vibration energy harvesting under nonstationary random vibrations

    Science.gov (United States)

    Yoon, Heonjun; Kim, Miso; Park, Choon-Su; Youn, Byeng D.

    2018-01-01

    Piezoelectric vibration energy harvesting (PVEH) has received much attention as a potential solution that could ultimately realize self-powered wireless sensor networks. Since most ambient vibrations in nature are inherently random and nonstationary, the output performances of PVEH devices also randomly change with time. However, little attention has been paid to investigating the randomly time-varying electroelastic behaviors of PVEH systems both analytically and experimentally. The objective of this study is thus to make a step forward towards a deep understanding of the time-varying performances of PVEH devices under nonstationary random vibrations. Two typical cases of nonstationary random vibration signals are considered: (1) randomly-varying amplitude (amplitude modulation; AM) and (2) randomly-varying amplitude with randomly-varying instantaneous frequency (amplitude and frequency modulation; AM-FM). In both cases, this study pursues well-balanced correlations of analytical predictions and experimental observations to deduce the relationships between the time-varying output performances of the PVEH device and two primary input parameters, such as a central frequency and an external electrical resistance. We introduce three correlation metrics to quantitatively compare analytical prediction and experimental observation, including the normalized root mean square error, the correlation coefficient, and the weighted integrated factor. Analytical predictions are in an excellent agreement with experimental observations both mechanically and electrically. This study provides insightful guidelines for designing PVEH devices to reliably generate electric power under nonstationary random vibrations.

  2. Adaptive Neural Network Control for Nonlinear Hydraulic Servo-System with Time-Varying State Constraints

    Directory of Open Access Journals (Sweden)

    Shu-Min Lu

    2017-01-01

    Full Text Available An adaptive neural network control problem is addressed for a class of nonlinear hydraulic servo-systems with time-varying state constraints. In view of the low precision problem of the traditional hydraulic servo-system which is caused by the tracking errors surpassing appropriate bound, the previous works have shown that the constraint for the system is a good way to solve the low precision problem. Meanwhile, compared with constant constraints, the time-varying state constraints are more general in the actual systems. Therefore, when the states of the system are forced to obey bounded time-varying constraint conditions, the high precision tracking performance of the system can be easily realized. In order to achieve this goal, the time-varying barrier Lyapunov function (TVBLF is used to prevent the states from violating time-varying constraints. By the backstepping design, the adaptive controller will be obtained. A radial basis function neural network (RBFNN is used to estimate the uncertainties. Based on analyzing the stability of the hydraulic servo-system, we show that the error signals are bounded in the compacts sets; the time-varying state constrains are never violated and all singles of the hydraulic servo-system are bounded. The simulation and experimental results show that the tracking accuracy of system is improved and the controller has fast tracking ability and strong robustness.

  3. Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

    National Research Council Canada - National Science Library

    Adegoke, Olufemi

    2003-01-01

    The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

  4. Radiosensitivity and genes

    Energy Technology Data Exchange (ETDEWEB)

    Qiyue, Hu; Mingyue, Lun [Suzhou Medical Coll., JS (China)

    1995-07-01

    Reported effects of some oncogenes, tumour suppressor genes and DNA repair genes on sensitivity of cells to ionizing radiation are reviewed. The role of oncogenes in cellular response to irradiation is discussed, especially the extensively studied oncogenes such as the ras gene family. For tumour suppressor genes, mainly the p53, which is increasingly implicated as a gene affecting radiosensitivity, is reviewed. It is considered that there is a cell cycle checkpoint determinant which is postulated to be able to arrest the irradiated cells in G{sub 1} phase to allow them to repair damage before they undergo DNA synthesis. So far there are six DNA repair genes which have been cloned in mammalian cells, but only one, XRCC1, appears to be involved in repair of human X-ray damage. XRCC1 can correct high sisterchromatid exchange levels when transferred into EM{sub 9} cells, but its expression seems to have no correlation with radiosensitivity of human neck and head tumour cells. Radiosensitivity is an intricate issue which may involve many factors. A scheme of cellular reactions after exposure to irradiation is proposed to indicate a possible sequence of events initiated by ionizing radiation.

  5. Radiosensitivity and genes

    International Nuclear Information System (INIS)

    Hu Qiyue; Lun Mingyue

    1995-07-01

    Reported effects of some oncogenes, tumour suppressor genes and DNA repair genes on sensitivity of cells to ionizing radiation are reviewed. The role of oncogenes in cellular response to irradiation is discussed, especially the extensively studied oncogenes such as the ras gene family. For tumour suppressor genes, mainly the p53, which is increasingly implicated as a gene affecting radiosensitivity, is reviewed. It is considered that there is a cell cycle checkpoint determinant which is postulated to be able to arrest the irradiated cells in G 1 phase to allow them to repair damage before they undergo DNA synthesis. So far there are six DNA repair genes which have been cloned in mammalian cells, but only one, XRCC1, appears to be involved in repair of human X-ray damage. XRCC1 can correct high sisterchromatid exchange levels when transferred into EM 9 cells, but its expression seems to have no correlation with radiosensitivity of human neck and head tumour cells. Radiosensitivity is an intricate issue which may involve many factors. A scheme of cellular reactions after exposure to irradiation is proposed to indicate a possible sequence of events initiated by ionizing radiation

  6. Evidence for homosexuality gene

    Energy Technology Data Exchange (ETDEWEB)

    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  7. Unicellular cyanobacteria synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties

    Digital Repository Service at National Institute of Oceanography (India)

    Anas, A.; Sageer, S.; Jasmin, C.; Vijayan, V.; Pavanan, P.; Athiyanathil, S.; Nair, S.

    unicellular cyanobacterium Synechocystis sp. that came from a heavy metal contaminated region of Cochin estuary, southwest coast of India. Based on 16S rRNA gene sequence similarities, the heterotrophic bacteria were grouped into three phyla: namely...

  8. The Mycoplasma hominis vaa gene displays a mosaic gene structure

    DEFF Research Database (Denmark)

    Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.

    1998-01-01

    Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular...

  9. Host transcriptional responses following ex vivo re-challenge with Mycobacterium tuberculosis vary with disease status.

    Directory of Open Access Journals (Sweden)

    Elaine A Yu

    Full Text Available The identification of immune correlates that are predictive of disease outcome for tuberculosis remains an ongoing challenge. To address this issue, we evaluated gene expression profiles from peripheral blood mononuclear cells following ex vivo challenge with Mycobacterium tuberculosis, among participants with active TB disease (ATBD, n = 10, latent TB infection (LTBI, n = 10, and previous active TB disease (after successful treatment; PTBD, n = 10, relative to controls (n = 10. Differential gene expression profiles were assessed by suppression-subtractive hybridization, dot blot, real-time polymerase chain reaction, and the comparative cycle threshold methods. Comparing ATBD to control samples, greater fold-increases of gene expression were observed for a number of chemotactic factors (CXCL1, CXCL3, IL8, MCP1, MIP1α. ATBD was also associated with higher IL1B gene expression, relative to controls. Among LTBI samples, gene expression of several chemotactic factors (CXCL2, CXCL3, IL8 was similarly elevated, compared to individuals with PTBD. Our results demonstrated that samples from participants with ATBD and LTBI have distinct gene expression profiles in response to ex vivo M. tuberculosis infection. These findings indicate the value in further characterizing the peripheral responses to M. tuberculosis challenge as a route to defining immune correlates of disease status or outcome.

  10. Host transcriptional responses following ex vivo re-challenge with Mycobacterium tuberculosis vary with disease status.

    Science.gov (United States)

    Yu, Elaine A; John, Serene H; Tablante, Elizabeth C; King, Christine A; Kenneth, John; Russell, David G; Mehta, Saurabh

    2017-01-01

    The identification of immune correlates that are predictive of disease outcome for tuberculosis remains an ongoing challenge. To address this issue, we evaluated gene expression profiles from peripheral blood mononuclear cells following ex vivo challenge with Mycobacterium tuberculosis, among participants with active TB disease (ATBD, n = 10), latent TB infection (LTBI, n = 10), and previous active TB disease (after successful treatment; PTBD, n = 10), relative to controls (n = 10). Differential gene expression profiles were assessed by suppression-subtractive hybridization, dot blot, real-time polymerase chain reaction, and the comparative cycle threshold methods. Comparing ATBD to control samples, greater fold-increases of gene expression were observed for a number of chemotactic factors (CXCL1, CXCL3, IL8, MCP1, MIP1α). ATBD was also associated with higher IL1B gene expression, relative to controls. Among LTBI samples, gene expression of several chemotactic factors (CXCL2, CXCL3, IL8) was similarly elevated, compared to individuals with PTBD. Our results demonstrated that samples from participants with ATBD and LTBI have distinct gene expression profiles in response to ex vivo M. tuberculosis infection. These findings indicate the value in further characterizing the peripheral responses to M. tuberculosis challenge as a route to defining immune correlates of disease status or outcome.

  11. Heterologous gene expression driven by carbonic anhydrase gene promoter in Dunaliella salina

    Science.gov (United States)

    Yurong, Chai; Yumin, Lu; Tianyun, Wang; Weihong, Hou; Lexun, Xue

    2006-12-01

    Dunaliella salina, a halotolerant unicellular green alga without a rigid cell wall, can live in salinities ranging from 0.05 to 5 mol/L NaCl. These features of D. salina make it an ideal host for the production of antibodies, oral vaccine, and commercially valuable polypeptides. To produce high level of heterologous proteins from D. salina, highly efficient promoters are required to drive expression of target genes under controlled condition. In the present study, we cloned a 5' franking region of 1.4 kb from the carbonic anhydrase ( CAH) gene of D. salina by genomic walking and PCR. The fragment was ligated to the pMD18-T vector and characterized. Sequence analysis indicated that this region contained conserved motifs, including a TATA- like box and CAAT-box. Tandem (GT)n repeats that had a potential role of transcriptional control, were also found in this region. The transcription start site (TSS) of the CAH gene was determined by 5' RACE and nested PCR method. Transformation assays showed that the 1.4 kb fragment was able to drive expression of the selectable bar (bialaphos resistance) gene when the fusion was transformed into D. salina by biolistics. Northern blotting hybridizations showed that the bar transcript was most abundant in cells grown in 2 mol/L NaCl, and less abundant in 0.5 mol/L NaCl, indicating that expression of the bar gene was induced at high salinity. These results suggest the potential use of the CAH gene promoter to induce the expression of heterologous genes in D. salina under varied salt condition.

  12. Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa

    Directory of Open Access Journals (Sweden)

    Jin-Sung Hong

    2013-09-01

    Full Text Available Polygalacturonase (PG gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

  13. Investigation of a thiolated polymer in gene delivery

    Science.gov (United States)

    Bacalocostantis, Irene

    Thiol-containing bioreducible polymers show significant potential as delivery vectors in gene therapy, a rapidly growing field which seeks to treat genetic-based disorders by delivering functional synthetic genes to diseased cells. Studies have shown that thiolated polymers exhibit improved biodegradability and prolonged in vivo circulation times over non-thiolated polymers. However, the extent to which thiol concentrations impact the carrier's delivery potential has not been well explored. The aim of this dissertation is to investigate how relative concentrations of free thiols and disulfide crosslinks impact a polymeric carriers delivery performance with respect to DNA packaging, complex stability, cargo protection, gene release, internalization efficiency and cytotoxicity. To accomplish this goal, several fluorescent polymers containing varying concentrations of thiol groups were synthesized by conjugating thiol-pendant chains onto the primary amines of cationic poly(allylamine). In vitro delivery assays and characterization techniques were employed to assess the effect of thiols in gene delivery.

  14. The evolution of gene expression levels in mammalian organs

    DEFF Research Database (Denmark)

    Brawand, David; Soumillon, Magali; Necsulea, Anamaria

    2011-01-01

    and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped......Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across...... ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages...

  15. The ALMT Gene Family Performs Multiple Functions in Plants

    Directory of Open Access Journals (Sweden)

    Jie Liu

    2018-02-01

    Full Text Available The aluminium activated malate transporter (ALMT gene family is named after the first member of the family identified in wheat (Triticum aestivum L.. The product of this gene controls resistance to aluminium (Al toxicity. ALMT genes encode transmembrane proteins that function as anion channels and perform multiple functions involving the transport of organic anions (e.g., carboxylates and inorganic anions in cells. They share a PF11744 domain and are classified in the Fusaric acid resistance protein-like superfamily, CL0307. The proteins typically have five to seven transmembrane regions in the N-terminal half and a long hydrophillic C-terminal tail but predictions of secondary structure vary. Although widely spread in plants, relatively little information is available on the roles performed by other members of this family. In this review, we summarized functions of ALMT gene families, including Al resistance, stomatal function, mineral nutrition, microbe interactions, fruit acidity, light response and seed development.

  16. Vector-field statistics for the analysis of time varying clinical gait data.

    Science.gov (United States)

    Donnelly, C J; Alexander, C; Pataky, T C; Stannage, K; Reid, S; Robinson, M A

    2017-01-01

    In clinical settings, the time varying analysis of gait data relies heavily on the experience of the individual(s) assessing these biological signals. Though three dimensional kinematics are recognised as time varying waveforms (1D), exploratory statistical analysis of these data are commonly carried out with multiple discrete or 0D dependent variables. In the absence of an a priori 0D hypothesis, clinicians are at risk of making type I and II errors in their analyis of time varying gait signatures in the event statistics are used in concert with prefered subjective clinical assesment methods. The aim of this communication was to determine if vector field waveform statistics were capable of providing quantitative corroboration to practically significant differences in time varying gait signatures as determined by two clinically trained gait experts. The case study was a left hemiplegic Cerebral Palsy (GMFCS I) gait patient following a botulinum toxin (BoNT-A) injection to their left gastrocnemius muscle. When comparing subjective clinical gait assessments between two testers, they were in agreement with each other for 61% of the joint degrees of freedom and phases of motion analysed. For tester 1 and tester 2, they were in agreement with the vector-field analysis for 78% and 53% of the kinematic variables analysed. When the subjective analyses of tester 1 and tester 2 were pooled together and then compared to the vector-field analysis, they were in agreement for 83% of the time varying kinematic variables analysed. These outcomes demonstrate that in principle, vector-field statistics corroborates with what a team of clinical gait experts would classify as practically meaningful pre- versus post time varying kinematic differences. The potential for vector-field statistics to be used as a useful clinical tool for the objective analysis of time varying clinical gait data is established. Future research is recommended to assess the usefulness of vector-field analyses

  17. Variation in gene expression within clones of the earthworm Dendrobaena octaedra.

    Directory of Open Access Journals (Sweden)

    Marina Mustonen

    Full Text Available Gene expression is highly plastic, which can help organisms to both acclimate and adapt to changing environments. Possible variation in gene expression among individuals with the same genotype (among clones is not widely considered, even though it could impact the results of studies that focus on gene expression phenotypes, for example studies using clonal lines. We examined the extent of within and between clone variation in gene expression in the earthworm Dendrobaena octaedra, which reproduces through apomictic parthenogenesis. Five microsatellite markers were developed and used to confirm that offspring are genetic clones of their parent. After that, expression of 12 genes was measured from five individuals each from six clonal lines after exposure to copper contaminated soil. Variation in gene expression was higher over all genotypes than within genotypes, as initially assumed. A subset of the genes was also examined in the offspring of exposed individuals in two of the clonal lines. In this case, variation in gene expression within genotypes was as high as that observed over all genotypes. One gene in particular (chymotrypsin inhibitor also showed significant differences in the expression levels among genetically identical individuals. Gene expression can vary considerably, and the extent of variation may depend on the genotypes and genes studied. Ensuring a large sample, with many different genotypes, is critical in studies comparing gene expression phenotypes. Researchers should be especially cautious inferring gene expression phenotypes when using only a single clonal or inbred line, since the results might be specific to only certain genotypes.

  18. Inductive matrix completion for predicting gene-disease associations.

    Science.gov (United States)

    Natarajan, Nagarajan; Dhillon, Inderjit S

    2014-06-15

    Most existing methods for predicting causal disease genes rely on specific type of evidence, and are therefore limited in terms of applicability. More often than not, the type of evidence available for diseases varies-for example, we may know linked genes, keywords associated with the disease obtained by mining text, or co-occurrence of disease symptoms in patients. Similarly, the type of evidence available for genes varies-for example, specific microarray probes convey information only for certain sets of genes. In this article, we apply a novel matrix-completion method called Inductive Matrix Completion to the problem of predicting gene-disease associations; it combines multiple types of evidence (features) for diseases and genes to learn latent factors that explain the observed gene-disease associations. We construct features from different biological sources such as microarray expression data and disease-related textual data. A crucial advantage of the method is that it is inductive; it can be applied to diseases not seen at training time, unlike traditional matrix-completion approaches and network-based inference methods that are transductive. Comparison with state-of-the-art methods on diseases from the Online Mendelian Inheritance in Man (OMIM) database shows that the proposed approach is substantially better-it has close to one-in-four chance of recovering a true association in the top 100 predictions, compared to the recently proposed Catapult method (second best) that has bigdata.ices.utexas.edu/project/gene-disease. © The Author 2014. Published by Oxford University Press.

  19. Does the heritability of cognitive abilities vary as a function of parental education? Evidence from a German twin sample.

    Science.gov (United States)

    Spengler, Marion; Gottschling, Juliana; Hahn, Elisabeth; Tucker-Drob, Elliot M; Harzer, Claudia; Spinath, Frank M

    2018-01-01

    A well-known hypothesis in the behavioral genetic literature predicts that the heritability of cognitive abilities is higher in the presence of higher socioeconomic contexts. However, studies suggest that the effect of socioeconomic status (SES) on the heritability of cognitive ability may not be universal, as it has mostly been demonstrated in the United States, but not in other Western nations. In the present study we tested whether the importance of genetic and environmental effects on cognitive abilities varies as a function of parental education in a German twin sample. Cognitive ability scores (general, verbal, and nonverbal) were obtained on 531 German twin pairs (192 monozygotic, 339 dizygotic, ranging from 7 to 14 years of age; Mage = 10.25, SD = 1.83). Data on parental education were available from mothers and fathers. Results for general cognitive ability and nonverbal ability indicated no significant gene x parental education interaction effect. For verbal ability, a significant nonshared environment (E) x parental education interaction was found in the direction of greater nonshared environmental influences on verbal abilities among children raised by more educated parents.

  20. The cag PAI is intact and functional but HP0521 varies significantly in Helicobacter pylori isolates from Malaysia and Singapore.

    Science.gov (United States)

    Schmidt, H-M A; Andres, S; Nilsson, C; Kovach, Z; Kaakoush, N O; Engstrand, L; Goh, K-L; Fock, K M; Forman, D; Mitchell, H

    2010-04-01

    Helicobacter pylori-related disease is at least partially attributable to the genotype of the infecting strain, particularly the presence of specific virulence factors. We investigated the prevalence of a novel combination of H. pylori virulence factors, including the cag pathogenicity island (PAI), and their association with severe disease in isolates from the three major ethnicities in Malaysia and Singapore, and evaluated whether the cag PAI was intact and functional in vitro. Polymerase chain reaction (PCR) was used to detect dupA, cagA, cagE, cagT, cagL and babA, and to type vacA, the EPIYA motifs, HP0521 alleles and oipA ON status in 159 H. pylori clinical isolates. Twenty-two strains were investigated for IL-8 induction and CagA translocation in vitro. The prevalence of cagA, cagE, cagL, cagT, babA, oipA ON and vacA s1 and i1 was >85%, irrespective of the disease state or ethnicity. The prevalence of dupA and the predominant HP0521 allele and EPIYA motif varied significantly with ethnicity (p < 0.05). A high prevalence of an intact cag PAI was found in all ethnic groups; however, no association was observed between any virulence factor and disease state. The novel association between the HP0521 alleles, EPIYA motifs and host ethnicity indicates that further studies to determine the function of this gene are important.

  1. RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells.

    Directory of Open Access Journals (Sweden)

    Tara Macrae

    Full Text Available Accurate quantification of gene expression by qRT-PCR relies on normalization against a consistently expressed control gene. However, control genes in common use often vary greatly between samples, especially in cancer. The advent of Next Generation Sequencing technology offers the possibility to better select control genes with the least cell to cell variability in steady state transcript levels. Here we analyze the transcriptomes of 55 leukemia samples to identify the most consistent genes. This list is enriched for components of the proteasome (ex. PSMA1 and spliceosome (ex. SF3B2, and also includes the translation initiation factor EIF4H, and many heterogeneous nuclear ribonucleoprotein genes (ex. HNRNPL. We have validated the consistency of our new control genes in 1933 cancer and normal tissues using publically available RNA-seq data, and their usefulness in qRT-PCR analysis is clearly demonstrated.

  2. Genome-wide identification, phylogeny and expression analyses of SCARECROW-LIKE(SCL) genes in millet (Setaria italica).

    Science.gov (United States)

    Liu, Hongyun; Qin, Jiajia; Fan, Hui; Cheng, Jinjin; Li, Lin; Liu, Zheng

    2017-07-01

    As a member of the GRAS gene family, SCARECROW - LIKE ( SCL ) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis , maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis -elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C 4 photosynthesis and bioenergy studies.

  3. FunGene: the functional gene pipeline and repository.

    Science.gov (United States)

    Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

    2013-01-01

    Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  4. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  5. Gene therapy prospects--intranasal delivery of therapeutic genes.

    Science.gov (United States)

    Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

    2012-01-01

    Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

  6. Radionuclide reporter gene imaging for cardiac gene therapy

    International Nuclear Information System (INIS)

    Inubushi, Masayuki; Tamaki, Nagara

    2007-01-01

    In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

  7. GoGene: gene annotation in the fast lane.

    Science.gov (United States)

    Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

    2009-07-01

    High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

  8. Robustness analysis of the Zhang neural network for online time-varying quadratic optimization

    International Nuclear Information System (INIS)

    Zhang Yunong; Ruan Gongqin; Li Kene; Yang Yiwen

    2010-01-01

    A general type of recurrent neural network (termed as Zhang neural network, ZNN) has recently been proposed by Zhang et al for the online solution of time-varying quadratic-minimization (QM) and quadratic-programming (QP) problems. Global exponential convergence of the ZNN could be achieved theoretically in an ideal error-free situation. In this paper, with the normal differentiation and dynamics-implementation errors considered, the robustness properties of the ZNN model are investigated for solving these time-varying problems. In addition, linear activation functions and power-sigmoid activation functions could be applied to such a perturbed ZNN model. Both theoretical-analysis and computer-simulation results demonstrate the good ZNN robustness and superior performance for online time-varying QM and QP problem solving, especially when using power-sigmoid activation functions.

  9. Critical velocities in He II for independently varied superfluid and normal fluid velocities

    International Nuclear Information System (INIS)

    Baehr, M.L.

    1984-01-01

    Experiments were performed to measure the critical velocity in pure superflow and compare to the theoretical prediction; to measure the first critical velocity for independently varied superfluid and normal fluid velocities; and to investigate the propagation of the second critical velocity from the thermal counterflow line through the V/sub n/,-V/sub s/ quadrant. The experimental apparatus employed a thermal counterflow heater to adjust the normal fluid velocity, a fountain pump to vary the superfluid velocity, and a level sensing capacitor to measure the superfluid velocity. The results of the pure superfluid critical velocity measurements indicate that this velocity is temperature independent contrary to Schwarz's theory. It was found that the first critical velocity for independently varied V/sub n/ and V/sub s/ could be described by a linear function of V/sub n/ and was otherwise temperature independent. It was found that the second critical velocity could only be distinguished near the thermal counterflow line

  10. Frequency-scanning interferometry using a time-varying Kalman filter for dynamic tracking measurements.

    Science.gov (United States)

    Jia, Xingyu; Liu, Zhigang; Tao, Long; Deng, Zhongwen

    2017-10-16

    Frequency scanning interferometry (FSI) with a single external cavity diode laser (ECDL) and time-invariant Kalman filtering is an effective technique for measuring the distance of a dynamic target. However, due to the hysteresis of the piezoelectric ceramic transducer (PZT) actuator in the ECDL, the optical frequency sweeps of the ECDL exhibit different behaviors, depending on whether the frequency is increasing or decreasing. Consequently, the model parameters of Kalman filter appear time varying in each iteration, which produces state estimation errors with time-invariant filtering. To address this, in this paper, a time-varying Kalman filter is proposed to model the instantaneous movement of a target relative to the different optical frequency tuning durations of the ECDL. The combination of the FSI method with the time-varying Kalman filter was theoretically analyzed, and the simulation and experimental results show the proposed method greatly improves the performance of dynamic FSI measurements.

  11. Towards artificial intelligence based diesel engine performance control under varying operating conditions using support vector regression

    Directory of Open Access Journals (Sweden)

    Naradasu Kumar Ravi

    2013-01-01

    Full Text Available Diesel engine designers are constantly on the look-out for performance enhancement through efficient control of operating parameters. In this paper, the concept of an intelligent engine control system is proposed that seeks to ensure optimized performance under varying operating conditions. The concept is based on arriving at the optimum engine operating parameters to ensure the desired output in terms of efficiency. In addition, a Support Vector Machines based prediction model has been developed to predict the engine performance under varying operating conditions. Experiments were carried out at varying loads, compression ratios and amounts of exhaust gas recirculation using a variable compression ratio diesel engine for data acquisition. It was observed that the SVM model was able to predict the engine performance accurately.

  12. Finite-time stability of neutral-type neural networks with random time-varying delays

    Science.gov (United States)

    Ali, M. Syed; Saravanan, S.; Zhu, Quanxin

    2017-11-01

    This paper is devoted to the finite-time stability analysis of neutral-type neural networks with random time-varying delays. The randomly time-varying delays are characterised by Bernoulli stochastic variable. This result can be extended to analysis and design for neutral-type neural networks with random time-varying delays. On the basis of this paper, we constructed suitable Lyapunov-Krasovskii functional together and established a set of sufficient linear matrix inequalities approach to guarantee the finite-time stability of the system concerned. By employing the Jensen's inequality, free-weighting matrix method and Wirtinger's double integral inequality, the proposed conditions are derived and two numerical examples are addressed for the effectiveness of the developed techniques.

  13. Modelling and Control of Ionic Electroactive Polymer Actuators under Varying Humidity Conditions

    Directory of Open Access Journals (Sweden)

    S. Sunjai Nakshatharan

    2018-02-01

    Full Text Available In this work, we address the problem of position control of ionic electroactive polymer soft actuators under varying relative humidity conditions. The impact of humidity on the actuation performance of ionic actuators is studied through frequency response and impedance spectroscopy analysis. Considering the uncertain performance of the actuator under varying humidity conditions, an adaptable model using the neural network method is developed. The model uses relative humidity magnitude as one of the model parameters, making it robust to different environmental conditions. Utilizing the model, a closed-loop controller based on the model predictive controller is developed for position control of the actuator. The developed model and controller are experimentally verified and found to be capable of predicting and controlling the actuators with excellent tracking accuracy under relative humidity conditions varying in the range of 10–90%.

  14. Some properties of zero power neutron noise in a time-varying medium with delayed neutrons

    International Nuclear Information System (INIS)

    Kitamura, Y.; Pal, L.; Pazsit, I.; Yamamoto, A.; Yamane, Y.

    2008-01-01

    The temporal evolution of the distribution of the number of neutrons in a time-varying multiplying system, producing only prompt neutrons, was treated recently with the master equation technique by some of the present authors. Such a treatment gives account of both the so-called zero power reactor noise and the power reactor noise simultaneously. In particular, the first two moments of the neutron number, as well as the concept of criticality for time-varying systems, were investigated and discussed. The present paper extends these investigations to the case when delayed neutrons are also taken into account. Due to the complexity of the description, only the expectation of the neutron number is calculated. The concept of criticality of a time-varying system is also generalized to systems with delayed neutrons. The temporal behaviour of the expectation of the number of neutrons and its asymptotic properties are displayed and discussed

  15. New Inference Procedures for Semiparametric Varying-Coefficient Partially Linear Cox Models

    Directory of Open Access Journals (Sweden)

    Yunbei Ma

    2014-01-01

    Full Text Available In biomedical research, one major objective is to identify risk factors and study their risk impacts, as this identification can help clinicians to both properly make a decision and increase efficiency of treatments and resource allocation. A two-step penalized-based procedure is proposed to select linear regression coefficients for linear components and to identify significant nonparametric varying-coefficient functions for semiparametric varying-coefficient partially linear Cox models. It is shown that the penalized-based resulting estimators of the linear regression coefficients are asymptotically normal and have oracle properties, and the resulting estimators of the varying-coefficient functions have optimal convergence rates. A simulation study and an empirical example are presented for illustration.

  16. Robust stability analysis of uncertain stochastic neural networks with interval time-varying delay

    International Nuclear Information System (INIS)

    Feng Wei; Yang, Simon X.; Fu Wei; Wu Haixia

    2009-01-01

    This paper addresses the stability analysis problem for uncertain stochastic neural networks with interval time-varying delays. The parameter uncertainties are assumed to be norm bounded, and the delay factor is assumed to be time-varying and belong to a given interval, which means that the lower and upper bounds of interval time-varying delays are available. A sufficient condition is derived such that for all admissible uncertainties, the considered neural network is robustly, globally, asymptotically stable in the mean square. Some stability criteria are formulated by means of the feasibility of a linear matrix inequality (LMI), which can be effectively solved by some standard numerical packages. Finally, numerical examples are provided to demonstrate the usefulness of the proposed criteria.

  17. Administrative database code accuracy did not vary notably with changes in disease prevalence.

    Science.gov (United States)

    van Walraven, Carl; English, Shane; Austin, Peter C

    2016-11-01

    Previous mathematical analyses of diagnostic tests based on the categorization of a continuous measure have found that test sensitivity and specificity varies significantly by disease prevalence. This study determined if the accuracy of diagnostic codes varied by disease prevalence. We used data from two previous studies in which the true status of renal disease and primary subarachnoid hemorrhage, respectively, had been determined. In multiple stratified random samples from the two previous studies having varying disease prevalence, we measured the accuracy of diagnostic codes for each disease using sensitivity, specificity, and positive and negative predictive value. Diagnostic code sensitivity and specificity did not change notably within clinically sensible disease prevalence. In contrast, positive and negative predictive values changed significantly with disease prevalence. Disease prevalence had no important influence on the sensitivity and specificity of diagnostic codes in administrative databases. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Hierarchical classification of dynamically varying radar pulse repetition interval modulation patterns.

    Science.gov (United States)

    Kauppi, Jukka-Pekka; Martikainen, Kalle; Ruotsalainen, Ulla

    2010-12-01

    The central purpose of passive signal intercept receivers is to perform automatic categorization of unknown radar signals. Currently, there is an urgent need to develop intelligent classification algorithms for these devices due to emerging complexity of radar waveforms. Especially multifunction radars (MFRs) capable of performing several simultaneous tasks by utilizing complex, dynamically varying scheduled waveforms are a major challenge for automatic pattern classification systems. To assist recognition of complex radar emissions in modern intercept receivers, we have developed a novel method to recognize dynamically varying pulse repetition interval (PRI) modulation patterns emitted by MFRs. We use robust feature extraction and classifier design techniques to assist recognition in unpredictable real-world signal environments. We classify received pulse trains hierarchically which allows unambiguous detection of the subpatterns using a sliding window. Accuracy, robustness and reliability of the technique are demonstrated with extensive simulations using both static and dynamically varying PRI modulation patterns. Copyright © 2010 Elsevier Ltd. All rights reserved.

  19. New results on global exponential stability of recurrent neural networks with time-varying delays

    International Nuclear Information System (INIS)

    Xu Shengyuan; Chu Yuming; Lu Junwei

    2006-01-01

    This Letter provides new sufficient conditions for the existence, uniqueness and global exponential stability of the equilibrium point of recurrent neural networks with time-varying delays by employing Lyapunov functions and using the Halanay inequality. The time-varying delays are not necessarily differentiable. Both Lipschitz continuous activation functions and monotone nondecreasing activation functions are considered. The derived stability criteria are expressed in terms of linear matrix inequalities (LMIs), which can be checked easily by resorting to recently developed algorithms solving LMIs. Furthermore, the proposed stability results are less conservative than some previous ones in the literature, which is demonstrated via some numerical examples

  20. H ∞ synchronization of the coronary artery system with input time-varying delay

    International Nuclear Information System (INIS)

    Li Xiao-Meng; Zhao Zhan-Shan; Sun Lian-Kun; Zhang Jing

    2016-01-01

    This paper investigates the H ∞ synchronization of the coronary artery system with input delay and disturbance. We focus on reducing the conservatism of existing synchronization strategies. Base on the triple integral forms of the Lyapunov–Krasovskii functional (LKF), we utilize single and double integral forms of Wirtinger-based inequality to guarantee that the synchronization feedback controller has good performance against time-varying delay and external disturbance. The effectiveness of our strategy can be exhibited by simulations under the different time-varying delays and different disturbances. (paper)

  1. Generalized Projective Synchronization between Two Complex Networks with Time-Varying Coupling Delay

    International Nuclear Information System (INIS)

    Mei, Sun; Chang-Yan, Zeng; Li-Xin, Tian

    2009-01-01

    Generalized projective synchronization (GPS) between two complex networks with time-varying coupling delay is investigated. Based on the Lyapunov stability theory, a nonlinear controller and adaptive updated laws are designed. Feasibility of the proposed scheme is proven in theory. Moreover, two numerical examples are presented, using the energy resource system and Lü's system [Physica A 382 (2007) 672] as the nodes of the networks. GPS between two energy resource complex networks with time-varying coupling delay is achieved. This study can widen the application range of the generalized synchronization methods and will be instructive for the demand–supply of energy resource in some regions of China

  2. Time-varying long term memory in the European Union stock markets

    Science.gov (United States)

    Sensoy, Ahmet; Tabak, Benjamin M.

    2015-10-01

    This paper proposes a new efficiency index to model time-varying inefficiency in stock markets. We focus on European stock markets and show that they have different degrees of time-varying efficiency. We observe that the 2008 global financial crisis has an adverse effect on almost all EU stock markets. However, the Eurozone sovereign debt crisis has a significant adverse effect only on the markets in France, Spain and Greece. For the late members, joining EU does not have a uniform effect on stock market efficiency. Our results have important implications for policy makers, investors, risk managers and academics.

  3. Novel criteria for exponential synchronization of inner time-varying complex networks with coupling delay

    International Nuclear Information System (INIS)

    Zhang Qun-Jiao; Zhao Jun-Chan

    2012-01-01

    This paper mainly investigates the exponential synchronization of an inner time-varying complex network with coupling delay. Firstly, the synchronization of complex networks is decoupled into the stability of the corresponding dynamical systems. Based on the Lyapunov function theory, some sufficient conditions to guarantee its stability with any given convergence rate are derived, thus the synchronization of the networks is achieved. Finally, the results are illustrated by a simple time-varying network model with a coupling delay. All involved numerical simulations verify the correctness of the theoretical analysis. (general)

  4. New results on global exponential stability of recurrent neural networks with time-varying delays

    Energy Technology Data Exchange (ETDEWEB)

    Xu Shengyuan [Department of Automation, Nanjing University of Science and Technology, Nanjing 210094 (China)]. E-mail: syxu02@yahoo.com.cn; Chu Yuming [Department of Mathematics, Huzhou Teacher' s College, Huzhou, Zhejiang 313000 (China); Lu Junwei [School of Electrical and Automation Engineering, Nanjing Normal University, 78 Bancang Street, Nanjing, 210042 (China)

    2006-04-03

    This Letter provides new sufficient conditions for the existence, uniqueness and global exponential stability of the equilibrium point of recurrent neural networks with time-varying delays by employing Lyapunov functions and using the Halanay inequality. The time-varying delays are not necessarily differentiable. Both Lipschitz continuous activation functions and monotone nondecreasing activation functions are considered. The derived stability criteria are expressed in terms of linear matrix inequalities (LMIs), which can be checked easily by resorting to recently developed algorithms solving LMIs. Furthermore, the proposed stability results are less conservative than some previous ones in the literature, which is demonstrated via some numerical examples.

  5. Generalized Projective Synchronization between Two Complex Networks with Time-Varying Coupling Delay

    Science.gov (United States)

    Sun, Mei; Zeng, Chang-Yan; Tian, Li-Xin

    2009-01-01

    Generalized projective synchronization (GPS) between two complex networks with time-varying coupling delay is investigated. Based on the Lyapunov stability theory, a nonlinear controller and adaptive updated laws are designed. Feasibility of the proposed scheme is proven in theory. Moreover, two numerical examples are presented, using the energy resource system and Lü's system [Physica A 382 (2007) 672] as the nodes of the networks. GPS between two energy resource complex networks with time-varying coupling delay is achieved. This study can widen the application range of the generalized synchronization methods and will be instructive for the demand-supply of energy resource in some regions of China.

  6. Constructing Regional Groundwater Models from Geophysical Data of Varying Type, Age, and Quality

    DEFF Research Database (Denmark)

    Vest Christiansen, Anders; Auken, Esben; Marker, Pernille Aabye

    for parameterization of a 3D model of the subsurface, integrating lithological information from boreholes with resistivity models. The objective is to create a direct input to regional groundwater models for sedimentary areas, where the sand/clay distribution governs the groundwater flow. The resistivity input is all......-inclusive in the sense that we include data from a variety of instruments (DC and EM, ground-based and airborne), with a varying spatial density and varying ages and quality. The coupling between hydrological and geophysical parameters is managed using a translator function with spatially variable parameters, which...

  7. Modal Vibration Control in Periodic Time-Varying Structures with Focus on Rotor Blade Systems

    DEFF Research Database (Denmark)

    Christensen, Rene Hardam; Santos, Ilmar

    2004-01-01

    of active modal controllers. The main aim is to reduce vibrations in periodic time-varying structures. Special emphasis is given to vibration control of coupled bladed rotor systems. A state feedback modal control law is developed based on modal analysis in periodic time-varying structures. The first step...... in the procedure is a transformation of the model into a time-invariant modal form by applying the modal matrices, which are also periodic time-variant. Due to coupled rotor and blade motions complex vibration modes occur in the modal transformed state space model. This implies that the modal transformed model...

  8. Long Memory of Financial Time Series and Hidden Markov Models with Time-Varying Parameters

    DEFF Research Database (Denmark)

    Nystrup, Peter; Madsen, Henrik; Lindström, Erik

    2016-01-01

    Hidden Markov models are often used to model daily returns and to infer the hidden state of financial markets. Previous studies have found that the estimated models change over time, but the implications of the time-varying behavior have not been thoroughly examined. This paper presents an adaptive...... to reproduce with a hidden Markov model. Capturing the time-varying behavior of the parameters also leads to improved one-step density forecasts. Finally, it is shown that the forecasting performance of the estimated models can be further improved using local smoothing to forecast the parameter variations....

  9. A Method of Time-Varying Rayleigh Channel Tracking in MIMO Radio System

    Institute of Scientific and Technical Information of China (English)

    GONG Yan-fei; HE Zi-shu; HAN Chun-lin

    2005-01-01

    A method of MIMO channel tracking based on Kalman filter and MMSE-DFE is proposed. The Kalman filter tracks the time-varying channel by using the MMSE-DFE decision and the MMSE-DFE conducts the next decision by using the channel estimates produced by the Kalman filter. Polynomial fitting is used to bridge the gap between the channel estimates produced by the Kalman filter and those needed for the DFE decision. Computer simulation demonstrates that this method can track the MIMO time-varying channel effectively.

  10. Modeling polar cap F-region patches using time varying convection

    International Nuclear Information System (INIS)

    Sojka, J.J.; Bowline, M.D.; Schunk, R.W.; Decker, D.T.; Valladares, C.E.; Sheehan, R.; Anderson, D.N.; Heelis, R.A.

    1993-01-01

    Here the authors present the results of computerized simulations of the polar cap regions which were able to model the formation of polar cap patches. They used the Utah State University Time-Dependent Ionospheric Model (TDIM) and the Phillips Laboratory (PL) F-region models in this work. By allowing a time varying magnetospheric electric field in the models, they were able to generate the patches. This time varying field generates a convection in the ionosphere. This convection is similar to convective changes observed in the ionosphere at times of southward pointing interplanetary magnetic field, due to changes in the B y component of the IMF

  11. Phantom dark energy with varying-mass dark matter particles: Acceleration and cosmic coincidence problem

    International Nuclear Information System (INIS)

    Leon, Genly; Saridakis, Emmanuel N.

    2010-01-01

    We investigate several varying-mass dark matter particle models in the framework of phantom cosmology. We examine whether there exist late-time cosmological solutions, corresponding to an accelerating universe and possessing dark energy and dark matter densities of the same order. Imposing exponential or power-law potentials and exponential or power-law mass dependence, we conclude that the coincidence problem cannot be solved or even alleviated. Thus, if dark energy is attributed to the phantom paradigm, varying-mass dark matter models cannot fulfill the basic requirement that led to their construction.

  12. Mean Square Exponential Stability of Stochastic Switched System with Interval Time-Varying Delays

    Directory of Open Access Journals (Sweden)

    Manlika Rajchakit

    2012-01-01

    Full Text Available This paper is concerned with mean square exponential stability of switched stochastic system with interval time-varying delays. The time delay is any continuous function belonging to a given interval, but not necessary to be differentiable. By constructing a suitable augmented Lyapunov-Krasovskii functional combined with Leibniz-Newton’s formula, a switching rule for the mean square exponential stability of switched stochastic system with interval time-varying delays and new delay-dependent sufficient conditions for the mean square exponential stability of the switched stochastic system are first established in terms of LMIs. Numerical example is given to show the effectiveness of the obtained result.

  13. A modified Friedmann equation for a system with varying gravitational mass

    Science.gov (United States)

    Gorkavyi, Nick; Vasilkov, Alexander

    2018-05-01

    The Laser Interferometer Gravitational-Wave Observatory (LIGO) detection of gravitational waves that take away 5 per cent of the total mass of two merging black holes points out on the importance of considering varying gravitational mass of a system. Using an assumption that the energy-momentum pseudo-tensor of gravitational waves is not considered as a source of gravitational field, we analyse a perturbation of the Friedmann-Robertson-Walker metric caused by the varying gravitational mass of a system. This perturbation leads to a modified Friedmann equation that contains a term similar to the `cosmological constant'. Theoretical estimates of the effective cosmological constant quantitatively corresponds to observed cosmological acceleration.

  14. Varied Understanding and Application of Counter Transference in Active Music Therapy in Adult Psychiatry

    DEFF Research Database (Denmark)

    Pedersen, Inge Nygaard

    2006-01-01

    The article presents varied ways of understanding and applying the clinical concept of counter transference. The sources are drawn from the author's own clinical praxis, from psychoanalytic and music therapy literature and from a qualitative interview examination among experienced music therapist...... applying the concept in music therapy improvisational work in adult psychiatry.......The article presents varied ways of understanding and applying the clinical concept of counter transference. The sources are drawn from the author's own clinical praxis, from psychoanalytic and music therapy literature and from a qualitative interview examination among experienced music therapists...

  15. Time-Varying Biased Proportional Guidance with Seeker’s Field-of-View Limit

    OpenAIRE

    Yang, Zhe; Wang, Hui; Lin, Defu

    2016-01-01

    Traditional guidance laws with range-to-go information or time-to-go estimation may not be implemented in passive homing missiles since passive seekers cannot measure relative range directly. A time-varying biased proportional guidance law, which only uses line-of-sight (LOS) rate and look angle information, is proposed to satisfy both impact angle constraint and seeker’s field-of-view (FOV) limit. In the proposed guidance law, two time-varying bias terms are applied to divide the trajectory ...

  16. Robust stability for uncertain stochastic fuzzy BAM neural networks with time-varying delays

    Science.gov (United States)

    Syed Ali, M.; Balasubramaniam, P.

    2008-07-01

    In this Letter, by utilizing the Lyapunov functional and combining with the linear matrix inequality (LMI) approach, we analyze the global asymptotic stability of uncertain stochastic fuzzy Bidirectional Associative Memory (BAM) neural networks with time-varying delays which are represented by the Takagi-Sugeno (TS) fuzzy models. A new class of uncertain stochastic fuzzy BAM neural networks with time varying delays has been studied and sufficient conditions have been derived to obtain conservative result in stochastic settings. The developed results are more general than those reported in the earlier literatures. In addition, the numerical examples are provided to illustrate the applicability of the result using LMI toolbox in MATLAB.

  17. Robust stability for uncertain stochastic fuzzy BAM neural networks with time-varying delays

    International Nuclear Information System (INIS)

    Syed Ali, M.; Balasubramaniam, P.

    2008-01-01

    In this Letter, by utilizing the Lyapunov functional and combining with the linear matrix inequality (LMI) approach, we analyze the global asymptotic stability of uncertain stochastic fuzzy Bidirectional Associative Memory (BAM) neural networks with time-varying delays which are represented by the Takagi-Sugeno (TS) fuzzy models. A new class of uncertain stochastic fuzzy BAM neural networks with time varying delays has been studied and sufficient conditions have been derived to obtain conservative result in stochastic settings. The developed results are more general than those reported in the earlier literatures. In addition, the numerical examples are provided to illustrate the applicability of the result using LMI toolbox in MATLAB

  18. Block Empirical Likelihood for Longitudinal Single-Index Varying-Coefficient Model

    Directory of Open Access Journals (Sweden)

    Yunquan Song

    2013-01-01

    Full Text Available In this paper, we consider a single-index varying-coefficient model with application to longitudinal data. In order to accommodate the within-group correlation, we apply the block empirical likelihood procedure to longitudinal single-index varying-coefficient model, and prove a nonparametric version of Wilks’ theorem which can be used to construct the block empirical likelihood confidence region with asymptotically correct coverage probability for the parametric component. In comparison with normal approximations, the proposed method does not require a consistent estimator for the asymptotic covariance matrix, making it easier to conduct inference for the model's parametric component. Simulations demonstrate how the proposed method works.

  19. Optimal critic learning for robot control in time-varying environments.

    Science.gov (United States)

    Wang, Chen; Li, Yanan; Ge, Shuzhi Sam; Lee, Tong Heng

    2015-10-01

    In this paper, optimal critic learning is developed for robot control in a time-varying environment. The unknown environment is described as a linear system with time-varying parameters, and impedance control is employed for the interaction control. Desired impedance parameters are obtained in the sense of an optimal realization of the composite of trajectory tracking and force regulation. Q -function-based critic learning is developed to determine the optimal impedance parameters without the knowledge of the system dynamics. The simulation results are presented and compared with existing methods, and the efficacy of the proposed method is verified.

  20. Genes and inheritance.

    Science.gov (United States)

    Middelton, L A; Peters, K F

    2001-10-01

    The information gained from the Human Genome Project and related genetic research will undoubtedly create significant changes in healthcare practice. It is becoming increasingly clear that nurses in all areas of clinical practice will require a fundamental understanding of basic genetics. This article provides the oncology nurse with an overview of basic genetic concepts, including inheritance patterns of single gene conditions, pedigree construction, chromosome aberrations, and the multifactorial basis underlying the common diseases of adulthood. Normal gene structure and function are introduced and the biochemistry of genetic errors is described.